Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Proteins that bind to the 3' polyadenylated region of MRNA. When complexed with RNA the proteins serve an array of functions such as stabilizing the 3' end of RNA, promoting poly(A) synthesis and stimulating mRNA translation.
Transport proteins that carry specific substances in the blood or across cell membranes.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
Proteins found in any species of bacterium.
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
The process by which a DNA molecule is duplicated.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Established cell cultures that have the potential to propagate indefinitely.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Proteins found in any species of virus.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
A single-stranded DNA-binding protein that is found in EUKARYOTIC CELLS. It is required for DNA REPLICATION; DNA REPAIR; and GENETIC RECOMBINATION.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Deoxyribonucleic acid that makes up the genetic material of viruses.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Proteins prepared by recombinant DNA technology.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
A group of thymine nucleotides in which the phosphate residues of each thymine nucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A family of immunophilin proteins that bind to the immunosuppressive drugs TACROLIMUS (also known as FK506) and SIROLIMUS. EC 5.2.1.-
The rate dynamics in chemical or physical systems.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Proteins obtained from ESCHERICHIA COLI.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
A poly(A) binding protein that has a variety of functions such as mRNA stabilization and protection of RNA from nuclease activity. Although poly(A) binding protein I is considered a major cytoplasmic RNA-binding protein it is also found in the CELL NUCLEUS and may be involved in transport of mRNP particles.
A class of proteins that were originally identified by their ability to bind the DNA sequence CCAAT. The typical CCAAT-enhancer binding protein forms dimers and consists of an activation domain, a DNA-binding basic region, and a leucine-rich dimerization domain (LEUCINE ZIPPERS). CCAAT-BINDING FACTOR is structurally distinct type of CCAAT-enhancer binding protein consisting of a trimer of three different subunits.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Transcription factors that were originally identified as site-specific DNA-binding proteins essential for DNA REPLICATION by ADENOVIRUSES. They play important roles in MAMMARY GLAND function and development.
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
DNA-binding motifs formed from two alpha-helixes which intertwine for about eight turns into a coiled coil and then bifurcate to form Y shaped structures. Leucines occurring in heptad repeats end up on the same sides of the helixes and are adjacent to each other in the stem of the Y (the "zipper" region). The DNA-binding residues are located in the bifurcated region of the Y.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)
A family of soluble proteins that bind insulin-like growth factors and modulate their biological actions at the cellular level. (Int J Gynaecol Obstet 1992;39(1):3-9)
The sum of the weight of all the atoms in a molecule.
Nucleic acid sequences involved in regulating the expression of genes.
Y-box-binding protein 1 was originally identified as a DNA-binding protein that interacts with Y-box PROMOTER REGIONS of MHC CLASS II GENES. It is a highly conserved transcription factor that regulates expression of a wide variety of GENES.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Proteins found in any species of fungus.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A protein that has been shown to function as a calcium-regulated transcription factor as well as a substrate for depolarization-activated CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES. This protein functions to integrate both calcium and cAMP signals.
A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.
A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Intracellular proteins that reversibly bind hydrophobic ligands including: saturated and unsaturated FATTY ACIDS; EICOSANOIDS; and RETINOIDS. They are considered a highly conserved and ubiquitously expressed family of proteins that may play a role in the metabolism of LIPIDS.
A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. They are found in many sequence-specific DNA-BINDING PROTEINS and in CALCIUM-BINDING PROTEINS.
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.
Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Proteins that specifically bind to TELOMERES. Proteins in this class include those that perform functions such as telomere capping, telomere maintenance and telomere stabilization.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A family of transcription factors found primarily in PLANTS that bind to the G-box DNA sequence CACGTG or to a consensus sequence CANNTG.
A cellular transcriptional coactivator that was originally identified by its requirement for the stable assembly IMMEDIATE-EARLY PROTEINS of the HERPES SIMPLEX VIRUS. It is a nuclear protein that is a transcriptional coactivator for a number of transcription factors including VP16 PROTEIN; GA-BINDING PROTEIN; EARLY GROWTH RESPONSE PROTEIN 2; and E2F4 TRANSCRIPTION FACTOR. It also interacts with and stabilizes HERPES SIMPLEX VIRUS PROTEIN VMW65 and helps regulate GENETIC TRANSCRIPTION of IMMEDIATE-EARLY GENES in HERPES SIMPLEX VIRUS.
A genus of aerobic, chemolithotrophic, coccoid ARCHAEA whose organisms are thermoacidophilic. Its cells are highly irregular in shape, often lobed, but occasionally spherical. It has worldwide distribution with organisms isolated from hot acidic soils and water. Sulfur is used as an energy source.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
A ubiquitously expressed sequence-specific transcriptional repressor that is normally the target of signaling by NOTCH PROTEINS.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.
A poly(A) binding protein that is involved in promoting the extension of the poly A tails of MRNA. The protein requires a minimum of ten ADENOSINE nucleotides in order for binding to mRNA. Once bound it works in conjunction with CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR to stimulate the rate of poly A synthesis by POLY A POLYMERASE. Once poly-A tails reach around 250 nucleotides in length poly(A) binding protein II no longer stimulates POLYADENYLATION. Mutations within a GCG repeat region in the gene for poly(A) binding protein II have been shown to cause the disease MUSCULAR DYSTROPHY, OCULOPHARYNGEAL.
A family of low-molecular weight, non-histone proteins found in chromatin.
A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.
Preparations of cell constituents or subcellular materials, isolates, or substances.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
Species of the genus MASTADENOVIRUS, causing a wide range of diseases in humans. Infections are mostly asymptomatic, but can be associated with diseases of the respiratory, ocular, and gastrointestinal systems. Serotypes (named with Arabic numbers) have been grouped into species designated Human adenovirus A-F.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
A DNA-dependent DNA polymerase characterized in E. coli and other lower organisms but may be present in higher organisms. Use also for a more complex form of DNA polymerase III designated as DNA polymerase III* or pol III* which is 15 times more active biologically than DNA polymerase I in the synthesis of DNA. This polymerase has both 3'-5' and 5'-3' exonuclease activities, is inhibited by sulfhydryl reagents, and has the same template-primer dependence as pol II. EC
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.
Inhibitor of differentiation proteins are negative regulators of BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS. They inhibit CELL DIFFERENTIATION and induce CELL PROLIFERATION by modulating different CELL CYCLE regulators.
A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.
A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.
A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.
One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.
Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
Periplasmic proteins that scavenge or sense diverse nutrients. In the bacterial environment they usually couple to transporters or chemotaxis receptors on the inner bacterial membrane.
Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.
Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.
An individual having only one allele at a given locus because of the loss of the other allele through a mutation (e.g., CHROMOSOME DELETION).
A member of the p300-CBP transcription factor family that was initially identified as a binding partner for CAMP RESPONSE ELEMENT-BINDING PROTEIN. Mutations in CREB-binding protein are associated with RUBINSTEIN-TAYBI SYNDROME.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The type species of the genus MICROVIRUS. A prototype of the small virulent DNA coliphages, it is composed of a single strand of supercoiled circular DNA, which on infection, is converted to a double-stranded replicative form by a host enzyme.
Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.
A 12-KDa tacrolimus binding protein that is found associated with and may modulate the function of calcium release channels. It is a peptidyl-prolyl cis/trans isomerase which is inhibited by both tacrolimus (commonly called FK506) and SIROLIMUS.
Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.
Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
A family of secreted multidomain proteins that were originally identified by their association with the latent form of TRANSFORMING GROWTH FACTORS. They interact with a variety of EXTRACELLULAR MATRIX PROTEINS and may play a role in the regulation of TGB-beta bioavailability.
A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.
Biochemical identification of mutational changes in a nucleotide sequence.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.
Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.
Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.
Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.
A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.
Proteins found in any species of archaeon.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Bacterial proteins that are used by BACTERIOPHAGES to incorporate their DNA into the DNA of the "host" bacteria. They are DNA-binding proteins that function in genetic recombination as well as in transcriptional and translational regulation.
Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A genus of gram-positive aerobic cocci found in the soil, that is highly resistant to radiation, especially ionizing radiation (RADIATION, IONIZING). Deinococcus radiodurans is the type species.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
A family of non-enveloped viruses infecting mammals (MASTADENOVIRUS) and birds (AVIADENOVIRUS) or both (ATADENOVIRUS). Infections may be asymptomatic or result in a variety of diseases.
Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.
A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.
A family of enzymes that catalyze the exonucleolytic cleavage of DNA. It includes members of the class EC 3.1.11 that produce 5'-phosphomonoesters as cleavage products.
A highly abundant DNA binding protein whose expression is strongly correlated with the growth phase of bacteria. The protein plays a role in regulating DNA topology and activation of RIBOSOMAL RNA transcription. It was originally identified as a factor required for inversion stimulation by the Hin recombinase of SALMONELLA and Gin site-specific recombinase of BACTERIOPHAGE MU.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
A family of structurally related proteins that were originally discovered for their role in cell-cycle regulation in CAENORHABDITIS ELEGANS. They play important roles in regulation of the CELL CYCLE and as components of UBIQUITIN-PROTEIN LIGASES.
A complex of several closely related glycosidic antibiotics from Streptomyces griseus. The major component, CHROMOMYCIN A3, is used as a fluorescent stain of DNA where it attaches and inhibits RNA synthesis. It is also used as an antineoplastic agent, especially for solid tumors.
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.
One of the six homologous proteins that specifically bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions. The function of this protein is not completely defined. However, several studies demonstrate that it inhibits IGF binding to cell surface receptors and thereby inhibits IGF-mediated mitogenic and cell metabolic actions. (Proc Soc Exp Biol Med 1993;204(1):4-29)
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
The functional hereditary units of FUNGI.

The surface ectoderm is essential for nephric duct formation in intermediate mesoderm. (1/69904)

The nephric duct is the first epithelial tubule to differentiate from intermediate mesoderm that is essential for all further urogenital development. In this study we identify the domain of intermediate mesoderm that gives rise to the nephric duct and demonstrate that the surface ectoderm is required for its differentiation. Removal of the surface ectoderm resulted in decreased levels of Sim-1 and Pax-2 mRNA expression in mesenchymal nephric duct progenitors, and caused inhibition of nephric duct formation and subsequent kidney development. The surface ectoderm expresses BMP-4 and we show that it is required for the maintenance of high-level BMP-4 expression in lateral plate mesoderm. Addition of a BMP-4-coated bead to embryos lacking the surface ectoderm restored normal levels of Sim-1 and Pax-2 mRNA expression in nephric duct progenitors, nephric duct formation and the initiation of nephrogenesis. Thus, BMP-4 signaling can substitute for the surface ectoderm in supporting nephric duct morphogenesis. Collectively, these data suggest that inductive interactions between the surface ectoderm, lateral mesoderm and intermediate mesoderm are essential for nephric duct formation and the initiation of urogenital development.  (+info)

Separation of shoot and floral identity in Arabidopsis. (2/69904)

The overall morphology of an Arabidopsis plant depends on the behaviour of its meristems. Meristems derived from the shoot apex can develop into either shoots or flowers. The distinction between these alternative fates requires separation between the function of floral meristem identity genes and the function of an antagonistic group of genes, which includes TERMINAL FLOWER 1. We show that the activities of these genes are restricted to separate domains of the shoot apex by different mechanisms. Meristem identity genes, such as LEAFY, APETALA 1 and CAULIFLOWER, prevent TERMINAL FLOWER 1 transcription in floral meristems on the apex periphery. TERMINAL FLOWER 1, in turn, can inhibit the activity of meristem identity genes at the centre of the shoot apex in two ways; first by delaying their upregulation, and second, by preventing the meristem from responding to LEAFY or APETALA 1. We suggest that the wild-type pattern of TERMINAL FLOWER 1 and floral meristem identity gene expression depends on the relative timing of their upregulation.  (+info)

Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (3/69904)

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.  (+info)

Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation. (4/69904)

The product of the oskar gene directs posterior patterning in the Drosophila oocyte, where it must be deployed specifically at the posterior pole. Proper expression relies on the coordinated localization and translational control of the oskar mRNA. Translational repression prior to localization of the transcript is mediated, in part, by the Bruno protein, which binds to discrete sites in the 3' untranslated region of the oskar mRNA. To begin to understand how Bruno acts in translational repression, we performed a yeast two-hybrid screen to identify Bruno-interacting proteins. One interactor, described here, is the product of the apontic gene. Coimmunoprecipitation experiments lend biochemical support to the idea that Bruno and Apontic proteins physically interact in Drosophila. Genetic experiments using mutants defective in apontic and bruno reveal a functional interaction between these genes. Given this interaction, Apontic is likely to act together with Bruno in translational repression of oskar mRNA. Interestingly, Apontic, like Bruno, is an RNA-binding protein and specifically binds certain regions of the oskar mRNA 3' untranslated region.  (+info)

Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. (5/69904)

Early developmental patterning of the Drosophila embryo is driven by the activities of a diverse set of maternally and zygotically derived transcription factors, including repressors encoded by gap genes such as Kruppel, knirps, giant and the mesoderm-specific snail. The mechanism of repression by gap transcription factors is not well understood at a molecular level. Initial characterization of these transcription factors suggests that they act as short-range repressors, interfering with the activity of enhancer or promoter elements 50 to 100 bp away. To better understand the molecular mechanism of short-range repression, we have investigated the properties of the Giant gap protein. We tested the ability of endogenous Giant to repress when bound close to the transcriptional initiation site and found that Giant effectively represses a heterologous promoter when binding sites are located at -55 bp with respect to the start of transcription. Consistent with its role as a short-range repressor, as the binding sites are moved to more distal locations, repression is diminished. Rather than exhibiting a sharp 'step-function' drop-off in activity, however, repression is progressively restricted to areas of highest Giant concentration. Less than a two-fold difference in Giant protein concentration is sufficient to determine a change in transcriptional status of a target gene. This effect demonstrates that Giant protein gradients can be differentially interpreted by target promoters, depending on the exact location of the Giant binding sites within the gene. Thus, in addition to binding site affinity and number, cis element positioning within a promoter can affect the response of a gene to a repressor gradient. We also demonstrate that a chimeric Gal4-Giant protein lacking the basic/zipper domain can specifically repress reporter genes, suggesting that the Giant effector domain is an autonomous repression domain.  (+info)

A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (6/69904)

The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates.  (+info)

Requirement of a novel gene, Xin, in cardiac morphogenesis. (7/69904)

A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.  (+info)

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (8/69904)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

TY - JOUR. T1 - Crystallographic studies of a novel DNA-binding domain from the yeast transcriptional activator Ndt80. AU - Montano, Sherwin P.. AU - Pierce, Michael. AU - Coté, Marie L.. AU - Vershon, Andrew K.. AU - Georgiadis, Millie. PY - 2002/12/1. Y1 - 2002/12/1. N2 - The Ndt80 protein is a transcriptional activator that plays a key role in the progression of the meiotic divisions in the yeast Saccharomyces cerevisiae. Ndt80 is strongly induced during the middle stages of the sporulation pathway and binds specifically to a promoter element called the MSE to activate transcription of genes required for the meiotic divisions. Here, the preliminary structural and functional studies to characterize the DNA-binding activity of this protein are reported. Through deletion analysis and limited proteolysis studies of Ndt80, a novel 32 kDa DNA-binding domain that is sufficient for DNA-binding in vitro has been defined. Crystals of the DNA-binding domain of Ndt80 in two distinct lattices have been ...
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences (k-mers). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other ...
p53 is an allosterically regulated protein with a latent DNA-binding activity. Posttranslational modification of a carboxy-terminal regulatory site in vitro, by casein kinase II and protein kinase C, can activate the sequence-specific DNA-binding function of the wild-type protein. The latent form of...
DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of
Members of the ARID (AT-rich interaction domain) (see ,PDOC51011,) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. Bright/ARID3a and the other two members (Bdp/ARID3b and Bright-like/ARID3c) have been described as the extended or eARID subfamily, having additional conserved sequences at both the N and C termini of the core ARID domain. In addition to the conserved regions immediately adjacent to the core ARID, the eARID proteins also share a conserved motif C-terminal to the ARID, named the REKLES domain after a conserved amino acid motif. The REKLES domain has not been found in any non-ARID proteins. REKLES consists of two subdomains: a modestly conserved N-terminal REKLESα and a highly conserved C-terminal REKLESβ. REKLES is a multifunctional domain that as co-evolved with and regulates functional properties of the eARID DNA-binding domain. REKLESα and -β are required, respectively, for nuclear entry and export of Bright during its ...
The manipulation of DNA by proteins is central to the life of a cell. It is critical for processes ranging from replication and recombination to transcription and the repair of DNA damage. Introduction to Protein-DNA Interactions, written by Gary Stormo, provides an up-to-date and interdisciplinary perspective on protein-DNA interactions, with an emphasis on DNA-binding proteins…
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA-binding protein with a gcm-motif (glial cell missing motif). The encoded protein is a homolog of the Drosophila glial cells missing gene (gcm). This protein binds to the GCM-motif (A/G)CCCGCAT, a novel sequence among known targets of DNA-binding proteins. The N-terminal DNA-binding domain confers the unique DNA-binding activity of this protein. [provided by RefSeq, Jul 2008 ...
XRCC genes (X-ray cross-complementing group) were discovered mainly for their roles in protecting mammalian cells against damage caused by ionizing radiation. Studies determined that these genes are important in the genetic stability of DNA. Although the loss of some of these genes does not necessarily confer high levels of sensitivity to radiation, they have been found to represent ... more ...
IRF-4 binds with LANA through its DNA-binding domain in vitro.(A) IRF-4 binds to C-terminal domain of LANA in vitro. The 35S-radiolabeled in vitro-translated pr
iDNA-Prot,dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid ...
Lachke, Salil A.; OConnell, Daniel J.; Aboukhalil, Anton; Choe, Sung E.; Turbe-Doan, Annick; Robertson, Erin A.; Amendt, Brad A. et al. (PLoS ONE, 2012) Link to Published Version ...
DDB1 was originally identified as a large subunit of damaged DNA-binding protein (DDB), which plays a role in DNA repair. DDB1 also functions as an adaptor molecule of Cul4/DDB1 ubiquitin E3 ligase and participates in various cellular processes. ...
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
Fig 5: regulation of transcription : which evidence code should be used? kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a) kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b ...
The ssb gene, coding for single-stranded-DNA-binding protein (SSB), was cloned from four marine Shewanella strains that differed in their temperature and pressure optima and ranges of growth. All four Shewanella ssb genes complemented Escherichia coli ssb point and deletion mutants, with efficiencies that varied with temperature and ssb gene source. The Shewanella SSBs are the largest bacterial SSBs identified to date (24.9-26.3 kDa) and may be divided into conserved amino- and carboxy-terminal regions and a highly variable central region. Greater amino acid sequence homology was observed between the Shewanella SSBs as a group (72-87%) than with other bacterial SSBs (52-69%). Analysis of the amino acid composition of the Shewanella SSBs revealed several features that could correlate with pressure or temperature adaptation. SSBs from the three low-temperature-adapted Shewanella strains were an order of magnitude more hydrophilic than that from the mesophilic strain, and differences in the distribution of
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Looking for online definition of DNA-binding protein RFX8 in the Medical Dictionary? DNA-binding protein RFX8 explanation free. What is DNA-binding protein RFX8? Meaning of DNA-binding protein RFX8 medical term. What does DNA-binding protein RFX8 mean?
Summary Evidence is presented here which indicates that the adenovirus DNA-binding protein (DBP) is phosphorylated at a tyrosine residue early in infection. This was suggested by the discovery that a proportion of the label in 32P-labelled DBP was resistant to alkali, and was substantiated by acid hydrolysis of DBP immunoprecipitates and by immunoblotting with a monoclonal antibody against phosphotyrosine. Treatment of [35S] methionine-labelled DBPs with chymotrypsin produced fragments of apparent M r 45K and 39K whereas digestion of 32P-labelled DBP resulted in fragments of 45K and 26K. Consideration of the distribution of 32P label and its alkali stability in these fragments suggested that chymotrypsin cleaved populations of DBP at different sites depending on their phosphorylation states. The conservation, in all of the seven adenovirus serotypes sequenced, of a tyrosine residue (at amino acid 195 in adenovirus type 2) together with its surrounding residues, suggests that phosphorylation
The human transcription enhancer factor-1 (TEF-1) belongs to a family of evolutionarily conserved proteins that have a DNA binding TEA domain. TEF-1 shares a 98% homology with Drosophila scalloped (sd) in the DNA binding domain and a 50% similarity in the activation domain. We have expressed human TEF-1 in Drosophila under the hsp-70 promoter and find that it can substitute for Sd function. The transformants rescue the wingblade defects as well as the lethality of loss-of-function alleles. Observation of reporter activity in the imaginal wing discs of the enhancer-trap alleles suggests that TEF-1 is capable of promoting sd gene regulation. The functional capability of the TEF-1 product was assessed by comparing the extent of rescue by heat shock (hs)-TEF-1 with that of hs-sd. The finding that TEF-1 can function in vivo during wingblade development offers a potent genetic system for the analysis of its function and in the identification of the molecular partners of TEF-1.. ...
The molecular determinants necessary and sufficient for recognition of its specific DNA target are contained in the C-domain (H-NSctd) of nucleoid-associated protein H-NS. H-NSctd protects from DNaseI cleavage a few short DNA segments of the H-NS-sensitive hns promoter whose sequences closely match the recently identified H-NS consensus motif (tCGt/aTa/tAATT) and, ... read more alone or fused to the protein oligomerization domain of phage λ CI repressor, inhibits transcription from the hns promoter in vitro and in vivo. The importance of H-NS oligomerization is indicated by the fact that with an extended hns promoter construct (400 bp), which allows protein oligomerization, DNA binding and transcriptional repression are highly and almost equally efficient with native H-NS and H-NSctd::λCI and much less effective with the monomeric H-NSctd. With a shorter (110 bp) construct, which does not sustain extensive protein oligomerization, transcriptional repression is less effective, but native H-NS, ...
TY - JOUR. T1 - A proteolytic fragment from the central region of p53 has marked sequence-specific DNA-binding activity when generated from wild-type but not from oncogenic mutant p53 protein. AU - Bargonetti, Jill. AU - Manfredi, James J.. AU - Chen, Xinbin. AU - Marshak, Daniel R.. AU - Prives, Carol. PY - 1993. Y1 - 1993. N2 - p53 is a sequence-specific DNA-binding oligomeric protein that can activate transcription from promoters bearing p53-binding sites. Whereas the activation region of p53 has been identified within the amino terminus, the location of the specific DNA-binding domain has not been reported. Thermolysin treatment of p53 protein generates a stable protease-resistant fragment that binds with marked specificity to p53 DNA-binding sites. Amino-terminal sequencing of the fragment located the thennolysin cleavage site to residue 91. Because the fragment does not contain the cdc2 phosphorylation site at Ser-315, we conclude that the the site-specific DNA-binding domain of p53 spans ...
TY - JOUR. T1 - Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. AU - Senear, D. F.. AU - Brenowitz, M.. PY - 1991/9/9. Y1 - 1991/9/9. N2 - We have investigated the question of whether the gel mobility-shift assay can provide data that are useful to the demonstration of cooperativity in the site-specific binding of proteins to DNA. Three common patterns of protein-DNA interaction were considered: (i) the cooperative binding of a protein to two sites (illustrated by the Escherichia coli Gal repressor); (ii) the cooperative binding of a bidentate protein to two sites (illustrated by the E. coli Lac repressor); and (iii) the cooperative binding of a protein to three sites (illustrated by the λcI repressor). A simple, rigorous, and easily extendable statistical mechanical approach to the derivation of the binding equations for the different patterns is presented. Both stimulated and experimental data for each case are ...
Naturally elaborated membrane bleb fractions BI and BII of Neisseria gonorrhoeae contain both linear and circular DNAs. Because little is known about the interactions between DNA and blebs, studies were initiated to identify specific proteins that bind DNA in elaborated membrane blebs. Western immunoblots of whole-cell and bleb proteins from transformation-competent and DNA-uptake-deficient (dud) mutants were probed with single- or double-stranded gonococcal DNA, pBR322, or synthetic DNA oligomers containing intact or altered gonococcal transformation uptake sequences. The specificity and sensitivity of a nonradioactive DNA-binding protein assay was evaluated, and the assay was used to visualize DNA-protein complexes on the blots. The complexes were then characterized by molecular mass, DNA-binding specificity, and expression in bleb fractions. The assay effectively detected blotted DNA-binding proteins. At least 17 gonococcal DNA-binding proteins were identified; unique subsets occurred in BI ...
Purpose To evaluate the prognostic significance of DNA excision repair gene polymorphisms, excision repair cross-complementation group 1 ( ERCC1) and X-ray repair complementing defective repair in...
An inducible program of inflammatory gene expression is a hallmark of antimicrobial defenses. This response is controlled by a collaboration involving signal-dependent activation of transcription factors, transcriptional co-regulators, and chromatin-modifying factors. Here we have identified a highly conserved Zinc finger DNA binding protein CNBP (also called ZNF9) upregulated in myeloid cells exposed to lipopolysaccharide. CNBP resides primarily in the cytosol and upon TLR4 engagement, CNBP translocate to the nucleus. To investigate the functional consequences of these events, we generated mice lacking CNBP and characterized the role of CNBP in controlling the inducible transcriptional program using a combination of RNA-sequencing and multiplex gene expression analysis (Nanostring). In response to an array of signals such as LPS, CNBP-deficient macrophages were impaired in their ability to induce important immune genes including IL12p40 and IL6 amongst others. CNBP-deficient cells showed normal ...
Author Summary The main role of transcription factors is to modulate the expression levels of functionally related genes in response to environmental and cellular cues. For this process to be precise, the transcription factor needs to locate and bind specific DNA sequences in the genome and needs to bind these sites with a strength that appropriately adjusts the amount of gene expressed. Both specific protein-DNA interactions and transcription factor activity are intimately coupled, because they are both dependent upon the biochemical properties of the DNA-binding domain. Here we experimentally probe how variable these properties are using a novel in vivo selection assay. We observed that the specific binding preferences for the transcription factor MarA and its transcriptional activity can be altered over a large range with a few mutations and that selection on one function will impact the other. This work helps us to better understand the mechanism of transcriptional regulation and its evolution, and
Cervical cancer is a public health problem and the molecular mechanisms underlying radioresistance are still poorly understood. Here, we evaluated the modulation of key molecules involved in cell proliferation, cell cycle and DNA repair in cervical cancer cell lines (CASKI and C33A) and in malignant tissues biopsied from 10 patients before and after radiotherapy. The expression patterns of epidermal growth factor receptor (EGFR), excision repair cross-complementation group 1 (ERCC1) and p53 were evaluated in cancer cell lines by quantitative PCR and western blotting, and in human malignant tissues by immunohistochemistry. The mutation status of TP53 gene was evaluated by direct sequencing. Among cell lines, absent or weak modulations of EGFR, ERCC1 and p53 ...
Genome replication and maintenance occurs through the collective action of proteins that operate on single-stranded DNA (ssDNA). All cells express single-stranded DNA binding proteins (SSBs), which prevent errors by sequestering ssDNA with high-affinity, keeping it free from transient structures and protecting it from unwanted chemical modification. SSBs must be easily repositioned, or else risk stalling DNA replication and repair processes. How does a protein simulataneously bind DNA tightly yet diffuse rapidly?. Through a set of extensive all-atom molecular dynamics (MD) simulations, we have elucidated the molecular mechanism of SSB association with ssDNA. First, we showed that the same SSB-ssDNA complex can both spontaneously rearrange its structure and maintain its stable conformation depending on whether it is surrounded by physiological solution or a protein-crystal environment. Next, we probed the local interaction between ssDNA and SSB through simulations of mechanical unraveling of the ...
XPB antibody (excision repair cross-complementation group 3) for IHC-P, WB. Anti-XPB pAb (GTX55844) is tested in Human, Mouse, Rat samples. 100% Ab-Assurance.
TY - JOUR. T1 - Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. AU - Kalodimos, Charalampos G.. AU - Biris, Nikolaos. AU - Bonvin, Alexandre M.J.J.. AU - Levandoski, Marc M.. AU - Guennuegues, Marc. AU - Boelens, Rolf. AU - Kaptein, Robert. PY - 2004/7/16. Y1 - 2004/7/16. N2 - Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient ...
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Binding of transcriptional activators to a promoter is a prerequisite process in transcriptional activation. It is well established that the efficiency of activator binding to a promoter is determined by the affinity of direct interactions between the DNA-binding domain of an activator and its specific target sequences. However, I describe here that activator binding to a promoter is augmented in vivo by the effects of two other determinants that have not been generally appreciated: (i) the number of activator binding sites present in a promoter and (ii) the potency of activation domains of activators. Multiple sites within a promoter can cooperatively recruit cognate factors regardless of whether they contain an effective activation domain. This cooperativity can result in the synergistic activation of transcription. The second effect is the enhancement of activator binding to a promoter by the presence of activation domains. In this case, activation domains are not simply tethered to the ...
The hns gene is a member of the cold-shock regulon, indicating that the nucleoid-associated, DNA-binding protein H-NS plays an important role in the adaptation of Escherichia coli to low temperatures. We show here that the ability to cope efficiently with a cold environment (12 degrees C and 25 degr …
Genes expressed in erythroid cells contain binding sites for a cell-specific nuclear factor, GF-1 (NF-E1, Eryf 1), believed to be an important transcriptional regulator. Previously we characterized murine GF-1 as a 413-amino acid polypeptide containing two cysteine-cysteine regions reminiscent of zinc-finger DNA-binding domains. By cross-hybridization to the finger domain of murine GF-1 we have isolated cDNA encoding the human homolog. Peptide sequencing of purified human GF-1 confirmed the authenticity of the human cDNA. The predicted primary sequence of human GF-1 is highly similar to that of murine GF-1, particularly in the DNA-binding region. Although the DNA-binding domains of human, murine, and chicken proteins are remarkably conserved, the mammalian polypeptides are strikingly divergent from the avian counterpart in other regions, most likely those responsible for transcriptional activation. By hybridization to panels of human-rodent DNAs we have assigned the human GF-1 locus to Xp21-11. ...
The initiation of transcription is accomplished via interactions of many different proteins with common and gene-specific regulatory motifs. Clearly, sequence-specific transcription factors play a crucial role in the specificity of transcription initiation. A group of sequence-specific DNA-binding proteins, related to the transcription factor Sp1, has been implicated in the regulation of many different genes, since binding sites for these transcription factors (GC/GT boxes) are a recurrent motif in regulatory sequences such as promoters, enhancers and CpG islands of these genes. The simultaneous occurrence of several homologous GC/GT box-binding factors precludes a straightforward deduction of their role in transcriptional regulation. In this review, we focus on the connection between functional specificity and biochemical properties including glycosylation, phosphorylation and acetylation of Sp1-related factors.. ...
The human ERYF1 gene (summary) NF-E1 DNA-binding protein GATA1, locus Xp11.23 [§§; †] containing 2 finger motifs referred to as ERYF1 of an erythroid-specific gene. The cDNA for the human ERYF1 gene is almost identical to that of chicken and mouse GATA1 gene consisting of 2 zinc finger type motifs its activator domain contains the binding…
Tumor protein p53, encoded in humans by the TP53 gene, was originally identified based on its interaction with the large T antigen of simian virus 40 (SV40). p53 is expressed at low levels in most cell types but is upregulated in many transformed (cancer) cell lines. In response to cellular stress, p53 regulates over 100 target genes that control cell cycle arrest, apoptosis, senescence, DNA repair, and metabolic changes. p53 protein has multiple domains that include DNA-binding, transactivation, and oligomerization activities. Mutations in the TP53 gene cause loss of tumor suppression activity and are found in more than 50% of human tumors. Multiple isoforms of p53 are known, with distinct DNA-binding and transcriptional activation properties. p53 is also known as cellular tumor antigen p53, p53 tumor suppressor, transformation-related protein 53, BCC7, LFS1, TRP53, and antigen NY-CO-13.. ...
Single stranded binding protein (SSB) is a prokaryotic DNA protein that binds to single stranded DNA during times when the DNA is rendered from its double stranded form during times of genetic recombination or DNA damage in order to stabilize and protect it from further unnecessary harm. The protein exists as a tetramer with each monomer being made of an N-terminal and Cterminal domain. The C-terminal domain is made of two smaller sub-domains, both of which have yet to resolve properly in a crystal structure, named the intrinsically disordered linker and the acidic tip, with limited understanding on how they function and relate to other proteins and SSB itself. Due to the disordered nature of its C-terminal domain limiting the ability to yield a concise crystal structure, much of the function and nearly all of the structure of the C-terminal domain has yet to be identified. While some function has been determined for these disordered regions, its relationship with other binding partners, DNA, ...
DNA-binding proteins from starved cells (DPS) are proteins that belong to the ferritin superfamily and are characterized by strong similarities but also distinctive differences with respect to canonical ferritins. DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. DPS are highly symmetrical dodecameric proteins of 200 kDa characterized from a shell-like structure of 2:3 tetrahedral symmetry assembled from identical subunits with an external diameter of ~ 9 nm and a central cavity of ~ 4.5 nm in diameter. Dps proteins belong to the ferritin superfamily and the DNA protection is afforded by means of a double mechanism: The first was discovered in Escherichia coli Dps in 1992 and has given the name to the protein family; during stationary phase, Dps binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and ...
Zinc finger proteins contain DNA-binding domains and have a wide variety of functions, most of which encompass some form of transcriptional activation or repression. The majority of zinc finger proteins contain a Krueppel-type DNA binding domain and a KRAB domain, which is thought to interact with KAP1, thereby recruiting histone modifying proteins. Zinc finger protein 75 (ZNF75), also known as ZNF82, is a 289 amino acid member of the Krueppel C2H2-type zinc finger protein family. Localized to the nucleus, ZNF75 contains five C2H2- type zinc fingers and one KRAB domain through which it is thought to be involved in DNA-binding and transcriptional regulation ...
As a commentator up-thread noted, any slip-and-slide model of sequence-specific DNA binding activity by transcription factors fails the sniff test: how is the activator (or repressor) able to effectively scan the nucleotide side-groups to achive site-specificity when the latter are coated with histones (in most eukaryotes) and with other attendant DNA-binding molecules (in all organisms). The notion that the chromosomal DNA molecule exists in all of its double-helical beauty for all proteins to probe seems rather tired and readily debunked to my mind. Ive been a hesitant skeptic of the histone code as anything other than correlative observations, but given the ubiquitous habit of histone compaction of large chromosomal segments, some portions of which obviously remain accessible to transcription factors, it seems clear to me that were missing some vital pieces of the puzzle.. Delete ...
Recent analysis of a Gal4 mutant (Gap71) carrying three point mutations (S22D, K23Q and K25F) in its DNA-binding domain (DBD), has demonstrated that it cannot occupy GAL promoters efficiently in cells and that it is not mono-ubiquitylated, suggesting a functional link between this modification and stable DNA binding in cells. The mechanistic underpinning of this phenotype is that this protein is hypersensitive to a newly discovered activity of the proteasomal ATPases--their ability to actively dissociate transcription factor-DNA complexes after direct interaction with the activation domain. In this paper, we examine the roles of each of the three point mutations contained in Gap71 individually. These experiments have revealed that serine 22 is a site of phosphorylation in the Gal4 DBD and that lysine 23 is essential for S22 phosphorylation, possibly acting as part of the kinase recognition site. Mutation of either residue blocks Gal4 DBD phosphorylation, its subsequent ubiquitylation and ...
DNA binding capacity of Orf8 and Orf16 by electrophoretic mobility shift assays (EMSAs). Preparation of DNA substrate is graphically shown in panel A. US8 and U
Progression through the cell cycle is essential for the continued existence of all uni- and multicellular organisms. It is crucial for the survival of a cell that its DNA is correctly replicated. In mammals, the onset of DNA replication is regulated by the activity of the heterodimeric E2F-DP transcription factor. The mammalian E2F family contains six proteins (E2F1, E2F2, E2F3, E2F4, E2F5 and E2F6) (Trimarchi and Lees, 2002). All E2Fs have an N-terminally located DNA-binding domain immediately followed by a dimerization domain, allowing them to pair with a dimerization partner (DP1 or DP2). Dimerization of E2F with DP is a prerequisite for high affinity, sequence-specific binding to the E2F consensus DNA-binding site. E2F activity is negatively regulated by retinoblastoma (Rb), which binds to the transcriptional activation domain of the E2F-DP factor, rendering it inactive. Moreover, the recruitment by Rb of DNA-modifying enzymes, such as histone deacetylases and polycomb proteins, leads to ...
Enhancer factor C, EFC, EF-C, MHC class II regulatory factor RFX, MHC class II regulatory factor RFX1, regulatory factor X, 1 (influences HLA class II expression), Regulatory factor X 1, RFX, trans-acting regulatory factor 1, Transcription factor ...
The TET2 DNA dioxygenase regulates gene expression by catalyzing demethylation of 5-methylcytosine, thus epigenetically modulating the genome. TET2 does not contain a sequence-specific DNA-binding domain, and how it is recruited to specific genomic sites is not fully understood. Here we carried out a mammalian two-hybrid screen and identified multiple transcriptional regulators potentially interacting with TET2. The SMAD nuclear interacting protein 1 (SNIP1) physically interacts with TET2 and bridges TET2 to bind several transcription factors, including c-MYC. SNIP1 recruits TET2 to the promoters of c-MYC target genes, including those involved in DNA damage response and cell viability. TET2 protects cells from DNA damage-induced apoptosis dependending on SNIP1. Our observations uncover a mechanism for targeting TET2 to specific promoters through a ternary interaction with a co-activator and many sequence-specific DNA-binding factors. This study also reveals a TET2-SNIP1-c-MYC pathway in ...
DNA-binding protein that preferentially recognizes a curved DNA sequence. It is probably a functional analog of DnaJ; displays overlapping activities with DnaJ, but functions under different conditions, probably acting as a molecular chaperone in an adaptive response to environmental stresses other than heat shock. Lacks autonomous chaperone activity; binds native substrates and targets them for recognition by DnaK. Its activity is inhibited by the binding of CbpM.
Predicted to have DNA-binding transcription factor activity and sequence-specific DNA binding activity. Involved in pericyte cell differentiation and vascular smooth muscle cell development. Predicted to localize to the nucleus. Is expressed in head mesenchyme; pharyngeal arch 1; and pharyngeal arch 2. Orthologous to human FOXF2 (forkhead box F2 ...
The present invention provides a process of transfecting a cell with a polynucleotide mixed with one or more amphipathic compounds and an effective amount of a DNA-binding protein. Exemplary and preferred DNA-binding proteins are H1, H2A, and H2B. Exemplary and preferred amphipathic compounds are cationic amphipathic compounds.
Vol 9: Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
HSSB, MSTP075, MST075, replication protein A 70 kDa DNA-binding subunit, replication protein A1 (70kD), replication protein A1, 70kDa, REPA1RF-A protein 1, Replication factor A protein 1, RF-A, RP-A, RPA70RP-A p70, Single-stranded DNA-binding ...
On the other hand, if the same series of reaction is done not on purified DNA, but rather on DNA that has been allowed to interact with extracts containing DNA-binding proteins, these DNA-binding proteins can, if condition are appropriate, bind specifically to regions of DNA. Such a binding will interfere both with the Maxam-Gilbert sequencing reactions and with the cleavage of DNA by the deoxyribonuclease. As a result, those fragments that are produced by cleavage near a protein-binding site will fail to be formed or be formed at a much lower level leaving a gap in the ladder of reaction products. Such a gap is called a footprint and is evidence for the existence of a specific DNA-binding complex. A similar logic allows the DNA binding regions to be determined by using the Exonuclease III protection* approach. Although the basic idea of doing a footprint is straight forward executing one in practice is more complex because of the difficulty of non-specific binding reactions. DNA is a highly ...
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Although bats are recognized as major reservoir hosts of emerging infectious diseases, Joffrin and colleagues highlight that a significant knowledge gap on transmission mechanisms remains and needs further exploration. They question whether bat bites are the exception rather than the rule, and ask whether other animals can transmit bat-borne pathogens. They conclude by questioning what we can learn from bat-to-bat transmission.. ...
Summary: The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for ,500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes.. Availability: Contact: [email protected] ...
GT:ID BAD55361.1 GT:GENE BAD55361.1 GT:PRODUCT putative DNA-binding protein GT:DATABASE GIB00210CH01 GT:ORG nfar0 GB:ACCESSION GIB00210CH01 GB:LOCATION complement(531217..531633) GB:FROM 531217 GB:TO 531633 GB:DIRECTION - GB:PRODUCT putative DNA-binding protein GB:PROTEIN_ID BAD55361.1 LENGTH 138 SQ:AASEQ MADFAARLNKLFETVHPPGRKPHTNAEVAAALTASGHPISKPYLSQLRSGQRTNPSDETVAALAKFFKVKPDYFFNDIYAAKIDHDLELLSQLQGYGLRRLSSRAFDLSEESQNLLTSMAEKLRASEGLPEIPPDGTE GT:EXON 1,1-138:0, BL:SWS:NREP 1 BL:SWS:REP 1-,69,Y1416_COXBU,7e-04,37.9,58/100, RP:PDB:NREP 1 RP:PDB:REP 6-,104,2ao9A,3e-07,10.1,99/117, HM:PFM:NREP 1 HM:PFM:REP 33-,74,PF01381,4.7e-10,36.1,36/55,HTH_3, RP:SCP:NREP 1 RP:SCP:REP 6-,104,2ao9A1,2e-07,10.1,99/117,a.4.1.17, HM:SCP:REP 39-,77,2a6cA1,0.00055,33.3,39/0,a.35.1.13,1/1,lambda repressor-like DNA-binding domains, OP:NHOMO 42 OP:NHOMOORG 31 OP:PATTERN -------------------------------------------------------------------- ...
High-resolution computational models of genome binding events. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
In living cells, DNA-binding proteins regulate the activity of various genes so that different cells carry out the right tasks at the right time. For this to work, the DNA-binding proteins need to find the right DNA site sufficiently quickly. The research team behind the new study has previously succeeded in determining that it takes only a few minutes for an individual protein molecule to look through the millions of nearly identical binding alternatives and find the right place to bind. This is nevertheless slower than what is predicted by the established theoretical model for how DNA-binding proteins find their way to the proper place by alternating between diffusing in the cell cytoplasm and along DNA strands ...
This motif was first noticed as a feature of the crystal structure of the bacteriophage l Cro protein. The structure of this small regulatory protein contained two a-helices separated by 34 Ã… - the pitch of a DNA double helix. Model building studies showed that these two a-helices would fit into two successive major grooves. As the structures of a number of other bacterial regulatory proteins (the CRP protein and the bacteriophage l cI repressor) were solved, the same structural motif - called a helix-turn-helix - was observed. It consists of two a-helices separated by a short turn (it is not a b turn). One helix binds to recognition elements within the major groove of DNA; the other helps to keep the binding helix properly positioned with respect to the rest of the molecule. This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins ...
The DNA triplets recognized by non-metazoan C2H2-ZF domains are also recognized by metazoan C2H2-ZFs based on experimental B1H data [16], often using identical basecontacting residues
Does anyone use DNA binding proteins expressed in rabbit reticulocyte lysates to do gel shift assays? This system would allow easy and quick expression of a suspected DNA binding protein that I could study (much easier than trying to express and purify the protein). I would specifically like to know if the other proteins in the system or maybe even the DNA added would somehow interfere in a gel shift assay (although I guess its no different than using cell/nuclear extracts). If anyone has experience with this or know of a reference could you please let me know? Thanks. -- Steve Some day I will get the hell out of Wisconsin Rodems Then I am here for the Lee family renioun ... shur-wajo-shur ...
... the protein binds to a non-specific site on the DNA and then it diffuses along the DNA chain until it locates a target site, a ... The in vivo model mentioned above clearly explains 3-D and 1-D diffusion along the DNA strand and the binding of proteins to ... Klenin, Konstantin V.; Merlitz, Holger; Langowski, Jörg; Wu, Chen-Xu (2006). "Facilitated Diffusion of DNA-Binding Proteins". ... 2013), during the process of protein sliding, the protein searches the entire length of the DNA chain using 3-D and 1-D ...
C3orf14-Chromosome 3 open reading frame 14: predicted DNA binding protein.. *C3orf23: encoding protein Uncharacterized protein ... TRAK1: trafficking kinesin-binding protein 1. *TRANK1: encoding protein Tetratricopeptide repeat and ankyrin repeat containing ... ZNF9: zinc finger protein 9 (a cellular retroviral nucleic acid binding protein) ... So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.[5] ...
ion channel binding. • protein binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. • RNA ... ID2, GIG8, ID2A, ID2H, bHLHb26, inhibitor of DNA binding 2, HLH protein, inhibitor of DNA binding 2. ... DNA-binding protein inhibitor ID-2 is a protein that in humans is encoded by the ID2 gene.[5] ... The protein encoded by this gene belongs to the inhibitor of DNA binding (ID) family, members of which are transcriptional ...
Robison, K; McGuire, A. M.; Church, G. M. (1998). "A comprehensive library of DNA-binding site matrices for 55 proteins applied ... "Two DNA-binding proteins," Nature 290:736f, see [5], accessed 4 March 2015. ... G. M. Church, J. L. Sussman & S.-H. Kim, 1977, "Secondary structural complementarity between DNA and proteins," Proc. natn. ... his team has developed use of DNA array (aka DNA chip) synthesizers for combinatorial libraries and assembling large genome ...
Zinc finger Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. Helix- ... Cruciform DNA Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a ... Three or four consecutive amino acid residues form a cation-binding feature. Sequence motif Short linear motif Protein tandem ... D-loop A displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated ...
... , a bacterial histone-like DNA-binding protein. *Wu Hu (disambiguation), an ancient Chinese term for multiple groups in China ...
Wahls WP, Swenson G, Moore PD (June 1991). "Two hypervariable minisatellite DNA binding proteins". Nucleic Acids Research. 19 ( ... Wahls WP, Swenson G, Moore PD (June 1991). "Two hypervariable minisatellite DNA binding proteins". Nucleic Acids Research. 19 ( ... These hotspots are binding sites for the PRDM9 Zinc Finger array. Upon binding to DNA, PRDM9 catalyzes trimethylation of ... minisatelite binding protein 3). This would later turn out to be the same PRDM9 protein independently identified later. In 2005 ...
This list covers DNA-binding proteins. For other protein-related codes, see List of MeSH codes (D12.776). Codes before these ... ccaat-enhancer-binding protein-alpha MeSH D12.776. - ccaat-enhancer-binding protein-beta MeSH D12.776.260.108. ... sterol regulatory element binding proteins MeSH D12.776.260.103.500.750.500 - sterol regulatory element-binding protein 1 MeSH ... sterol regulatory element binding proteins MeSH D12.776. - sterol regulatory element binding protein 1 MeSH ...
sequence-specific DNA binding. • DNA binding. • transcription factor binding. • protein domain specific binding. • RNA ... transcription factor activity, sequence-specific DNA binding. • transcription regulatory region DNA binding. • ... HNF-3G is a member of the forkheadclass of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional ... regulation of transcription, DNA-templated. • transcription, DNA-templated. • spermatogenesis. • positive regulation of ...
sequence-specific DNA binding. • DNA binding. • RNA polymerase II regulatory region sequence-specific DNA binding. • protein ... protein binding. • protein heterodimerization activity. • nucleic acid binding. • transcription regulatory region DNA binding. ... identical protein binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. ... Zinc finger protein Aiolos also known as Ikaros family zinc finger protein 3 is a protein that in humans is encoded by the ...
RNA structure prediction and protein-DNA binding. The first dynamic programming algorithms for protein-DNA binding were ... Recurrent solutions to lattice models for protein-DNA binding. *Backward induction as a solution method for finite-horizon ... at the lowest bound and n. at the highest bound. The second line specifies what happens at the last rank; providing a base case ... Dynamic programming is widely used in bioinformatics for the tasks such as sequence alignment, protein folding, ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... type winged-helix DNA-binding domain, and a conserved N-terminal AT-rich DNA interaction domain-the last domain for which the ... "Nomenclature of the ARID family of DNA-binding proteins". Genomics. 86 (2): 242-51. doi:10.1016/j.ygeno.2005.03.013. PMID ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Research. 7 (4): 273-81. ...
... proteins have weak DNA-binding capacity. Therefore, to effectively bind DNA, NFAT proteins must cooperate with other ... NFAT5 cannot form complexes with AP-1 proteins, however all NFAT proteins recognize similar DNA binding sites in gene ... The best known classes of binding sites for NFAT are the formation of a cooperative complex with AP-1 or other bZIP proteins to ... The best known classes of binding sites for NFAT are the formation of a cooperative complex with AP-1 or other bZIP proteins ...
DNA-binding protein Transcription factor Razaghi, Ali; Huerlimann, Roger; Owens, Leigh; Heimann, Kirsten (1 December 2015). " ... Murguía, José R.; Serrano, Ramón (2012). "New functions of protein kinase Gcn2 in yeast and mammals". IUBMB Life. 64 (12): 971- ... Gcn4 is a highly conserved protein and its mammalian homolog is known as activating transcription factor-4 (ATF4). ... Overexpression of Gcn4 leads to the reduction in protein synthesis capacity which contributes to Gcn4-mediated increase of ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y (Nov 1998). "A novel DNA-binding motif shares structural homology to DNA ... a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs". Genome ... "Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA". Biochemistry. 40 (31): 9142-50. doi:10.1021/bi010476a. ...
... the proteins involved in mRNA transport (RNA-binding proteins, RBPs). DLM1 encodes a Z-DNA binding protein. Z-DNA formation is ... DLM1 then binds to cytosolic Viral DNA using two Z-DNA-binding domains (Zα and Zβ) at its N-terminus along with a DNA binding ... Z-DNA-binding protein 1, also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1, is a protein that in ... "Entrez Gene: ZBP1 Z-DNA binding protein 1". Rathinam VA, Fitzgerald KA (Mar 2011). "Innate immune sensing of DNA viruses". ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs". Genome ... "Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA". Biochemistry. 40 (31): 9142-50. doi:10.1021/bi010476a. ... containing highly conserved putative DNA/chromatin binding motifs is specifically up-regulated in breast cancer". The Journal ...
"MyoD is a sequence-specific DNA binding protein requiring a region of myc homology to bind to the muscle creatine kinase ... "Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection". ... When expressed, the myoD gene produces a protein referred to as MyoD (or MyoD1), which can bind certain DNA sequences, stop ... which is used to find the DNA-binding sites for proteins. Along with chemist Peter Dervan of Caltech and developmental ...
However, the shape feature of these molecules such as DNA and protein have also been studied and proposed to have an equivalent ... Alipanahi, B; Delong, A; Weirauch, MT; Frey, BJ (Aug 2015). "Predicting the sequence specificities of DNA- and RNA-binding ... Since presently-available DNA sequencing technologies are ill-suited for reading long sequences, large pieces of DNA (such as ... Sequence assembly refers to the reconstruction of a DNA sequence by aligning and merging small DNA fragments. It is an integral ...
Phosphocellulose chromatography utilizes the binding affinity of many DNA-binding proteins for phosphocellulose. The stronger a ... It is often used in biochemistry in the purification of proteins bound to tags. These fusion proteins are labeled with ... Fast protein liquid chromatography[edit]. Further information: Fast protein liquid chromatography. Fast protein liquid ... protein's interaction with DNA, the higher the salt concentration needed to elute that protein.[11] ...
The SRY protein, bound to the double helix of DNA. Ridley contemplates evolutionary psychology using the genes SRY on the Y ... The disaster of Creutzfeldt-Jakob disease in humans was found to be caused by the PRP gene which produces a prion protein that ... Recombinant DNA enabled genetic manipulation with restriction enzymes and a ligase. Genetic engineering has been highly ... "see and use the messages in their own DNA as they see fit." Silver describes the book as remarkable for focusing on "pure ...
Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. ... In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" ... In proteinsEdit. In proteins, a structural motif describes the connectivity between secondary structural elements. An ... In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which ...
DNA Research. 7 (1): 65-73. doi:10.1093/dnares/7.1.65. PMID 10718198. "Entrez Gene: chromodomain helicase DNA binding protein 7 ... Chromodomain-helicase-DNA-binding protein 7 also known as ATP-dependent helicase CHD7 is an enzyme that in humans is encoded by ... In GeneReviews CHD7+protein,+human at the US National Library of Medicine Medical Subject Headings (MeSH) Human CHD7 genome ... This protein belongs to a larger group of ATP-dependent chromatin remodeling complexes, the CHD subfamily. Model organisms have ...
Schreiber J, Enderich J, Wegner M (May 1998). "Structural requirements for DNA binding of GCM proteins". Nucleic Acids Res. 26 ... in the process of DNA binding and in the redox regulation of DNA binding. The GCM domain as a new class of Zn-containing DNA- ... binding domain with no similarity to any other DNA-binding domain. The GCM domain consists of a large and a small domain ... Akiyama Y, Hosoya T, Poole AM, Hotta Y (December 1996). "The gcm-motif: a novel DNA-binding motif conserved in Drosophila and ...
Tlusty T, Bar-Ziv R, Libchaber A (December 2004). "High-fidelity DNA sensing by protein binding fluctuations". Phys. Rev. Lett ... During this process, the RecA protein polymerizes along a DNA and this DNA-protein filament searches for a homologous DNA ... DNA damage recognition and repair - a certain DNA repair mechanism utilizes kinetic proofreading to discriminate damaged DNA. ... Bar-Ziv R, Tlusty T, Libchaber A (September 2002). "Protein-DNA computation by stochastic assembly cascade". Proc. Natl. Acad. ...
Chen-Plotkin, Alice S.; Lee, Virginia M.-Y.; Trojanowski, John Q. (2010). "TAR DNA-binding protein 43 in neurodegenerative ... "Prion-like protein seeding and the pathobiology of Alzheimer's disease". Walker LC (2018). In: Protein Folding Disorders in the ... Abnormal proteins and Alzheimer's disease Retrieved 2020-04-16. Die Saat des Vergessens (Article on prion-like protein seeding ... Treatment from Brain Tissue May have Spread Alzheimer's Protein Retrieved 2020-05-04. Corrupted Proteins Spread Disease ...
Červenák F, Juríková K, Nosek J, Tomáška L (2017). "Double-stranded telomeric DNA binding proteins: Diversity matters". Cell ... TRF1 (Telomere Repeat binding Factor 1): TRF1 is a homodimeric protein that binds to the double-stranded TTAGGG region of the ... RAP1 (Repressor / Activator Protein 1): RAP1 is a stabilizing protein associated with TRF2. RAP1 inhibits DNA repair. POT1 ( ... thereby bridging units attached to double-stranded DNA and units attached to single-stranded DNA. There are two main DNA-damage ...
androgen receptor binding. • RNA binding. • ubiquitin protein ligase binding. • transcription regulatory region DNA binding. • ... tubulin binding. • metal ion binding. • enzyme binding. • zinc ion binding. • damaged DNA binding. • ligação a proteínas ... ubiquitin-protein transferase activity. • DNA binding. • transferase activity. • RNA polymerase II transcription coactivator ... RNA polymerase binding. • identical protein binding. Componente celular. • BRCA1-BARD1 complex. • condensed nuclear chromosome ...
... which in turn are often brought to the promoter DNA by an activator protein's binding to its own DNA binding site nearby.. In ... Identifying a Protein Binding Sites on DNA molecule YouTube tutorial video. *Pleiades Promoter Project - a research project ... In the case of a transcription factor binding site, there may be a single sequence that binds the protein most strongly under ... initial reversible binding of RNA polymerase, conformational changes in RNA polymerase, conformational changes in DNA, binding ...
Each protein contains three DNA-binding motifs, known as AT-hooks, that bind in the minor groove of AT tracts in DNA. Multiple ... HMG-I proteins are DNA-binding proteins thought to affect the formation and function of transcription complexes. ... Multivalent DNA-binding properties of the HMG-1 proteins. J F Maher and D Nathans ... we demonstrate that high-affinity binding uses two or three appropriately spaced AT tracts as a single multivalent binding site ...
... employing ten different recombinant plant bZIP proteins demonstrated that nucleotides flanking the ACGT core affected binding ... Plant bZIP proteins exhibit a relaxed DNA-binding specificity for DNA sequence motifs containing an ACGT core. Gel mobility ... Plant bZIP proteins exhibit a relaxed DNA-binding specificity for DNA sequence motifs containing an ACGT core. Gel mobility ... Group 1 proteins exhibit a stronger binding affinity for G-box elements, group 2 proteins bind both G-box and C-box motifs with ...
I need to purify some proteins which bind to DNA. I use DNA binding protein purification kit from Boerhinger with long ... DNA binding protein purification. Joel Baguet Joel.Baguet at Mon Dec 14 11:37:15 EST 1998 *Previous message: Thank ... The protein-binding conditions are those for gel retardation assay. The results are very poor (about 1% with 35S in vitro ... concatamers of protein-binding oligonucleotide (obtainrd using self-primed PCR technique) ligated streptavidin magnetic ...
WT-DNA,. wild-type DNA;. MT-DNA,. mutant DNA;. BD,. binding domain;. HD,. homeodomain;. AD,. activation domain;. SAAB,. ... A) WT-DNA and MT-DNA binding sites were used as probes. (B) T7-KN1 was incubated with WT-DNA probe (W) or MT-DNA probe (M). (C ... KN1 and T7-KIP were mixed together in DNA binding assays at 1 ng or 10 ng of each protein per reaction. DNA-binding specificity ... This half site is also critical for DNA binding of the MEIS protein. Slight variations in these TALE HD DNA-binding motifs ...
The DNA-binding specificity of SOX9 and other SOX proteins.. Mertin S1, McDowall SG, Harley VR. ... How different SOX proteins achieve specific regulation of target genes is not known. We determined the DNA-binding specificity ... The optimal SOX9 binding sequence, AGAACAATGG, contained a core DNA-binding element AACAAT, flanked by 5 AG and 3 GG ... Our studies support the notion that SOX proteins achieve DNA sequence specificity through subtle preferences for flanking ...
When PB transposase is fused to a DNA-binding protein, it causes PB to integrate into the genome near the binding sites for ... "Calling Cards" for DNA-Binding Proteins in Mammalian Cells. Haoyi Wang, David Mayhew, Xuhua Chen, Mark Johnston and Robi David ... "Calling Cards" for DNA-Binding Proteins in Mammalian Cells. Haoyi Wang, David Mayhew, Xuhua Chen, Mark Johnston and Robi David ... "Calling Cards" for DNA-Binding Proteins in Mammalian Cells. Haoyi Wang, David Mayhew, Xuhua Chen, Mark Johnston and Robi David ...
... binds with high affinity to single-stranded DNA but does not bind well to double-stranded ... E. coli Single-Stranded DNA Binding Protein (SSB) consists of four identical 18.9kDa subunits that cooperatively bind to single ... This protein is involved in DNA replication and in recombination in vivo. ... Studying DNA replication and recombination. *DNA sequencing using the primer walking strategy with contiguous oligonucleotides ...
Proteins that bind DNA using small contiguous helix-turn-helix (HTH) motifs comprise a significant number of all DNA-binding ... A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data ... Using structural motif templates to identify proteins with DNA binding function.. Jones S1, Barker JA, Nobeli I, Thornton JM. ... A threshold value is indicated at 1.6 Å, below which a protein is predicted to contain a DNA-binding HTH motif. ...
... Itisam Sarangi via (by itisam.sarangi from ... Dear all Presently I am trying to purifying a DNA binding protein from E.coli..and trying to remove the contaminating DNA... I ... Previous message: [Protein-analysis] PREDITOP *Next message: [Protein-analysis] Re: Protocol needed from study the protein ... Previous message: [Protein-analysis] PREDITOP *Next message: [Protein-analysis] Re: Protocol needed from study the protein ...
They bind DNA without sequence specificity, but have a high affinity for bent or distorted DNA, and bend linear DNA. The ... contain two DNA-binding HMG-box domains (A and B) and a long acidic C-terminal domain. ... high mobility group proteins 1 and 2; renamed HMGB1 and 2) ... HMG1 and 2: architectural DNA-binding proteins Biochem Soc ... They bind DNA without sequence specificity, but have a high affinity for bent or distorted DNA, and bend linear DNA. The ...
DNA damage-binding protein 2ARBA annotation. ,p>Information which has been generated by the UniProtKB automatic annotation ... Damage-specific DNA-binding protein 2ARBA annotation. Automatic assertion according to rulesi ... tr,A0A3B4GCD4,A0A3B4GCD4_9CICH DNA damage-binding protein 2 OS=Pundamilia nyererei OX=303518 PE=3 SV=1 ... to allow unambiguous identification of a protein.,p>,a href=/help/protein_names target=_top>More...,/a>,/p>Protein namesi. ...
... we transplanted the DNA-binding region of MyoD intro helix 3 of protein Z. MyoD is a bHLH domain DNA-binding protein [17]. The ... MD Simulations of the Protein-DNA Complex. Simulations of the protein-DNA complexes were performed using Amber 10 [25]. Protein ... Protein Z and MyoD. Protein Z is derived from staphylococcal protein A and holds an IgG Fc-binding domain. It consists of a ... As mentioned before, four Amber simulations were performed to check the models DNA-binding abilities. Protein-DNA interactions ...
... the number of known DNA-binding proteins is very small compared to the large non-DNA-binding proteins and unknown proteins. DNA ... Among them, 525 are DNA-binding and 550 are non-DNA-binding protein sequences. All the protein sequences were taken from PDB [ ... K. K. Kumar, G. Pugalenthi, and P. N. Suganthan, "DNA-prot: identification of DNA binding proteins from protein sequence ... 17] constructed this independent dataset consisting of 93 DNA-binding and 93 non-DNA-binding protein sequences. They used ...
... a mono-ubiquitin-binding protein. FAN1 has a DNA branch-specific nuclease activity that is required for the removal and ... The nuclease FAN1 acts with Fanconi anemia proteins to help repair damaged DNA. ... The nuclease FAN1 acts with Fanconi anemia proteins to help repair damaged DNA. ... Mutations in 13 different genes implicated in repairing damaged DNA are known to be involved in the disease. Liu et al. have ...
The nuclease FAN1 acts with Fanconi anemia proteins to help repair damaged DNA. ... The nuclease FAN1 acts with Fanconi anemia proteins to help repair damaged DNA. ...
Proteins that bind to DNA can be divided into two groups: those that bind to a specific DNA sequence and those that bind non- ... The point is that even for a highly specific DNA binding protein like lac repressor, most of the protein is bound to other ... Now, heres the important point: all specific DNA binding proteins also bind DNA non-specifically. In many cases its part of ... the protein binds to any old place on the DNA molecule and slides along the DNA searching for a specific binding sequence. ...
We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their ... InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... protein]-cysteine S-methyltransferase, DNA binding (IPR014048). Key Species. Key species. Number of proteins. FASTA. Protein ... unclassified sequences unclassified sequences 262 proteins, FASTA , Protein IDs * Viruses Viruses 20 proteins, FASTA , Protein ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex ... Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under ... Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN * ... The Protein Feature View requires a browser that supports SVG (Scalable Vector Graphics). Mouse over tracks and labels for more ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex ... "single-stranded DNA-binding protein", "single-stranded DNA binding protein 1", "single-stranded DNA binding protein 1, ... White boxes represent UTRs (untranslated regions). Orange: protein coding regions. The black lines connecting boxes represent ...
Tyrosine phosphorylation of DNA binding proteins by multiple cytokines. By AC Larner, M David, GM Feldman, K Igarashi, RH ... Tyrosine phosphorylation of DNA binding proteins by multiple cytokines. By AC Larner, M David, GM Feldman, K Igarashi, RH ... Tyrosine phosphorylation of DNA binding proteins by multiple cytokines Message Subject. (Your Name) has forwarded a page to you ... activated DNA binding proteins that recognized the IFN-gamma response region (GRR) located in the promoter of the Fc gamma RI ...
... is effected in part by changes in the DNA binding status of transcriptional activators. Distinct DNA binding proteins are also ... Genome-Wide Location and Function of DNA Binding Proteins. By Bing Ren, François Robert, John J. Wyrick, Oscar Aparicio, Ezra G ... Genome-Wide Location and Function of DNA Binding Proteins. By Bing Ren, François Robert, John J. Wyrick, Oscar Aparicio, Ezra G ... which has been previously used to study protein-DNA interactions at a small number of specific DNA sites (7), with DNA ...
... scientists at the Gladstone Institutes discovered that proteins must rely on another clue to know where to bind: the DNAs ... with a given protein only binding to a specific sequence of letters. In a new study, published in Cell Systems, ... Scientists have traditionally thought that DNA binding proteins use patterns in the genomes code of As, Cs, Ts, and Gs to ... made a major discovery about how these proteins bind to DNA.. Scientists have traditionally thought that DNA binding proteins ...
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes ... "DNA-Binding Proteins" by people in Harvard Catalyst Profiles by year, and whether "DNA-Binding Proteins" was a major or minor ... "DNA-Binding Proteins" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... Single-Stranded DNA Binding Proteins*Single-Stranded DNA Binding Proteins. *Single Stranded DNA Binding Proteins ...
DNA damage-binding protein 2ARBA annotation. ,p>Information which has been generated by the UniProtKB automatic annotation ... Damage-specific DNA-binding protein 2ARBA annotation. Automatic assertion according to rulesi ... DNA damage-binding protein 2. DNA damage-binding protein 2 (Damage-specific DNA-binding protein 2) ... DNA damage-binding protein 2. DNA damage-binding protein 2 (Damage-specific DNA-binding protein 2) ...
Abcam provides general protocols for DNA-Protein Binding Assay Kit (Colorimetric) (ab117139). Please download our pdf protocol ... Proteins and Peptides. Proteomics tools. Agonists, activators, antagonists and inhibitors. Lysates. Multiplex miRNA assays. By ... Epigenetics and Nuclear Signaling Chromatin Binding Proteins DNA / RNA binding Share by email ...
Understanding when and where proteins bind to DNA may be the ticket to identifying cancer at the cellular level, according to ... Study identifies link between DNA-protein binding, cancer onset. Understanding when and where proteins bind to DNA may be the ... The DNA within a cells nucleus is tightly wound together with certain proteins into a threadlike structure known as chromatin ... The vast amount of genetic research is focused on the 2 percent of our DNA that is used to create proteins. In the current ...
... DSpace/Manakin Repository. * DASH Home ... Differential Disruption of EWS-FLI1 Binding by DNA-Binding Agents Chen, Changmin; Wonsey, Diane R.; Lemieux, Madeleine E.; Kung ... CCAAT/Enhancer-Binding Protein \(\gamma\) Is a Critical Regulator of IL-1\(\beta\)-Induced IL-6 Production in Alveolar ... Cyclic AMP Responsive Element Binding Proteins Are Involved in Emergency Granulopoiesis through the Upregulation of CCAAT/ ...
The assay effectively detected blotted DNA-binding proteins. At least 17 gonococcal DNA-binding proteins were identified; ... lacked DNA-binding activity at the 11-kDa protein in BI. The segregation of DNA-binding proteins within BI and BII correlates ... Certain DNA-binding proteins had varied affinities for single- and double-stranded DNA, and the intact transformation uptake ... DNA-binding proteins in cells and membrane blebs of Neisseria gonorrhoeae. Message Subject (Your Name) has forwarded a page to ...
KW - DNA binding protein. KW - DNA compaction. KW - HMG-box containing protein. KW - mitochondrial DNA (mtDNA). KW - Holliday ... keywords = {DNA binding protein; DNA compaction; HMG-box containing protein; mitochondrial DNA (mtDNA); Holliday junction; ... DNA binding protein; DNA compaction; HMG-box containing protein; mitochondrial DNA (mtDNA); Holliday junction; mitochondrial ... DNA. In fact, ScAbf2p and YlMhb1p bind quantitatively to this substrate only at very high protein to DNA ratios and CpGcf1p ...
... Autoři. PALEČEK, Emil, Daniel VLK, Veronika STAŇKOVÁ, ... Tumor suppresor protein p53 binds preferentially to supercoiled DNA. Oncogene. Basingstoke: Macmillan Press, 1997, roč. 18, č. ... TI - Tumor suppresor protein p53 binds preferentially to supercoiled DNA. JF - Oncogene. VL - 18. IS - 15. SP - 2201-2009. EP ... title = {Tumor suppresor protein p53 binds preferentially to supercoiled DNA},. volume = {18},. year = {1997}. }. ...
  • Studies using a panel of G-box and C-box oligonucleotides differing in their flanking sequences identified high affinity binding sites. (
  • however, the affinity is greatly increased when they cooperatively bind to their appropriate DNA sequences as a heterodimer ( 17 - 21 , 26 ). (
  • Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (
  • Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (
  • HMMBinder uses monogram and bigram features extracted from the HMM profiles of the protein sequences. (
  • Proteins that bind to specific DNA sequences are often activators or repressors involved in regulating gene expression. (
  • Since most activators will be bound to random DNA sequences most of the time, the chances of accidentally recruiting RNA polymerase to begin a spurious transcript are quite high. (
  • There are actually three different operator sequences to which lac repressor can bind but that doesn't make much different for the point I trying to make. (
  • Transcriptional activators, for example, bind to specific promoter sequences and recruit chromatin modifying complexes and the transcription apparatus to initiate RNA synthesis ( 1-3 ). (
  • To test their theory, the researchers adapted a common machine learning algorithm typically used to identify the letter sequences proteins bind to, except now they were looking for patterns in shape. (
  • First, proteins that bind to multiple different letter sequences turn out to be homing in on the same spatial pattern, and second, proteins that appear to share letter sequences are in fact attaching to very different shapes. (
  • Western immunoblots of whole-cell and bleb proteins from transformation-competent and DNA-uptake-deficient (dud) mutants were probed with single- or double-stranded gonococcal DNA, pBR322, or synthetic DNA oligomers containing intact or altered gonococcal transformation uptake sequences. (
  • Although these proteins are some of the fastest evolving components of mtnucleoids, it is not known whether the divergence of mtHMG proteins on the level of their amino acid sequences is accompanied by diversification of their biochemical properties. (
  • The GAF protein bound more than 100 different locations in the genome, most commonly at repetitive DNA sequences in the regulatory regions of genes. (
  • In contrast, other proteins have evolved to bind to specific DNA sequences. (
  • Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that have these sequences near their promoters. (
  • The effects on nuclear protein binding to NF- kB DNA consensus sequences were examined using an electrophoretic mobility shift assay. (
  • In-vitro treatment with crocidolite caused significant dose related increases in p65 binding to NF-kB consensus DNA sequences in both RLE and RPM cells. (
  • Screen for polypeptides that bind nucleic acid sequences of interest. (
  • In practice, the binding sites (operators) differ slightly in their sequences. (
  • Binding of myc proteins to canonical and noncanonical DNA sequences. (
  • Using an in vitro binding-site selection assay, we have demonstrated that c-Myc-Max complexes bind not only to canonical CACGTG or CATGTG motifs that are flanked by variable sequences but also to noncanonical sites that consist of an internal CG or TG dinucleotide in the context of particular variations in the CA--TG consensus. (
  • We show that operator binding by many proteins such as LexA-Myc, LexA-Fos, and LexA-Bicoid is severely impaired, while binding of other LexA-derivative proteins, such as those that carry bacterially encoded acidic sequences ("acid blobs"), is not. (
  • Proteins that have the ability to recognise and bind DNA sequences can be classified either according to their DNA-binding motif or based on the sequence of the target nucleotides. (
  • The extraordinary specificity of the TAL proteins for their target DNA sequences enables their exploitation for precise genome engineering. (
  • In the region upstream of the achaete gene of the AS-C, we have identified three 'E box' consensus sequences that are bound specifically in vitro by hetero-oligomeric complexes consisting of the da protein and an AS-C protein. (
  • HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. (
  • However, the detailed nucleotide sequences of cis-acting elements and presence of DNA-binding proteins related to Cah1 regulation have not been identified. (
  • These factors generally recognize and bind to unique 10-15 bp DNA sequences in or near the promoter regions and these bindings cause a change in DNA conformation to enhance the transcription by RNA polymerase complex. (
  • Yeast one hybrid system is one of the most widely used systems in many studies to isolate and characterize transcription factors which can directly bind to target DNA sequences, but there are several disadvantages in this system. (
  • First of all, this system is only fit for a 10-15 bp short DNA sequences, but completely not for a comprehensive screening of the transcription factors using a whole part of the target promoter region. (
  • Assuming that only high affinity bZIP binding sites are likely to function in vivo, identification of these sites will allow us to predict which genes are activated by a particular bZIP protein. (
  • The knox gene family was the first group of plant genes identified that encodes homeodomain (HD) proteins ( 14 ). (
  • How different SOX proteins achieve specific regulation of target genes is not known. (
  • Genes bound by SP1 are more likely to be expressed in the HCT116 cell line we used, and SP1-bound CpG islands show a strong preference to be unmethylated. (
  • Mutations in 13 different genes implicated in repairing damaged DNA are known to be involved in the disease. (
  • Interferon-activated protein complexes bind enhancers present in the promoters of early response genes such as the high-affinity Fc gamma receptor gene (Fc gamma RI). (
  • This is achieved in part by the action of "DNA binding proteins" that latch onto the human genome at particular places to turn genes on or off. (
  • The research focuses on chromatin, the DNA-protein complex where all genes reside. (
  • Specifically, it evaluates chromatin's relationship to transcription factors - proteins that play a crucial role in managing which genes are activated within cells. (
  • Certain genes are turned on or off based on how transcription factors bind to specific parts of the chromatin. (
  • The binding of proteins to DNA controls many essential functions in cells, from switching genes on and off to repairing DNA to packaging DNA into chromosomes. (
  • The researchers found that each protein bound to a distinct set of genes. (
  • HP-1 bound to a handful of genes previously identified as binding targets. (
  • The third protein, Sir2, can silence genes in yeast, but it appears to have a different role in Drosophila . (
  • Larger arrays with genomic DNA could provide a more detailed picture of how enhancer and promoter regions influence the activity of genes, the researchers write in Nature Genetics . (
  • This system employed the Su(Hw) DNA-binding domain (ZnF) to direct PcG proteins to transposons that carried the white and yellow reporter genes. (
  • CHD6 is a chromatin remodeling protein characterized to play a role in transcriptional repression of genes and viruses. (
  • The lac repressor, for example, binds to a specific DNA site that blocks transcription of the genes required for lactose uptake and utilization. (
  • In the bottom picture the lac genes have been "induced" and the repressor isn't bound specifically to DNA. (
  • induced the lac genes and then allowed the lac repressor to re-bind to its target site. (
  • The ram and chp genes specify hydrophobic structural components required for aerial hyphae to escape surface tension and grow into the air, while the majority of bld genes encode regulatory proteins ( 16 ). (
  • We demonstrated that the GCC box, which is an 11-bp sequence (TAAGAGCCGCC) conserved in the 5' upstream region of ethylene-inducible pathogenesis-related protein genes in Nicotiana spp and in some other plants, is the sequence that is essential for ethylene responsiveness when incorporated into a heterologous promoter. (
  • 2009) The Mycoplasma pneumoniae MPN490 and Mycoplasma genitalium MG339 Genes Encode RecA Homologs That Promote Homologous DNA Strand Exchange. (
  • On binding to the estrogen response elements (EREs) in the target genes the ERs undergo DNA-induced changes in conformation. (
  • Although it does not bind directly to DNA, by binding basic helix-loop-helix transcription factors through its HLH motif, ID2 may control tissue-specific genes related to cell growth, proliferation and differentiation (Hara et al. (
  • Proteins encoded by the daughterless (da) gene and three genes of the achaete-scute complex (AS-C) act positively in the determination of the sensory organ precursor cell fate, while the extramacrochaetae (emc) and hairy (h) gene products act as negative regulators. (
  • A particularly intriguing case concerns the thermophilic acidophile Thermoplasma acidophilum, which lacks histone genes but instead encodes a protein named HTa ( H istone-like protein of T hermoplasma a cidophilum ). (
  • Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. (
  • Plant bZIP proteins exhibit a relaxed DNA-binding specificity for DNA sequence motifs containing an ACGT core. (
  • These ten different bZIP proteins could be categorized into three groups according to their qualitative and quantitative specificity for G-box and C-box elements. (
  • Information provided by our systematic analysis of plant bZIP DNA binding specificity can be used to identify high affinity binding sites for the plant bZIP proteins studied here. (
  • The DNA-binding specificity of SOX9 and other SOX proteins. (
  • We determined the DNA-binding specificity of SOX9 using a random oligonucleotide selection assay. (
  • Our studies support the notion that SOX proteins achieve DNA sequence specificity through subtle preferences for flanking nucleotides and that this is likely to be dictated by signature amino acids in their HMG domains. (
  • Furthermore, the related HMG domains of SOX9 and Sox17 have similar optimal binding sites that differ from those of SRY and Sox5, suggesting that SOX factors may co-evolve with their DNA targets to achieve specificity. (
  • They bind DNA without sequence specificity, but have a high affinity for bent or distorted DNA, and bend linear DNA. (
  • The specificity and sensitivity of a nonradioactive DNA-binding protein assay was evaluated, and the assay was used to visualize DNA-protein complexes on the blots. (
  • The complexes were then characterized by molecular mass, DNA-binding specificity, and expression in bleb fractions. (
  • The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to read the DNA sequence. (
  • Mathematical descriptions of protein-DNA binding taking into account sequence-specificity, and competitive and cooperative binding of proteins of different types are usually performed with the help of the lattice models. (
  • Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era. (
  • Substitution of an arginine that is conserved in these proteins into MyoD (MyoD-R) changes its binding specificity so that it recognizes CACGTG instead of the MyoD cognate sequence (CAGCTG). (
  • The model resolves the apparent paradox, and accounts for the observed speed, specificity, and stability in protein-DNA interactions. (
  • The functional specificity of the DCX E3 ubiquitin- protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. (
  • These data confirm that the interactions between E1 and DNA polymerase alpha-primase do not exhibit cell-type specificity, as had already been suggested by data from in vivo and in vitro replication assays, but they imply that other cellular proteins may affect the level of E1-dependent replication. (
  • We describe a method for permanently recording protein-DNA interactions in mammalian cells. (
  • But mapping the transcriptional networks that control cell-fate decisions is difficult given the limitations of the tools available to measure protein-DNA interactions. (
  • The genome-wide location analysis method we have developed allows protein-DNA interactions to be monitored across the entire yeast genome ( 6 ). (
  • The method combines a modified ch romatin i mmuno p recipitation (ChIP) procedure, which has been previously used to study protein-DNA interactions at a small number of specific DNA sites ( 7 ), with DNA microarray analysis. (
  • Because little is known about the interactions between DNA and blebs, studies were initiated to identify specific proteins that bind DNA in elaborated membrane blebs. (
  • Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. (
  • Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. (
  • These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. (
  • Protein-DNA interactions occur when a protein binds a molecule of DNA, often to regulate the biological function of DNA, usually the expression of a gene. (
  • The role of single-stranded DNA binding (SSB) protein during DNA replication in Escherichia coli cells has been studied, specifically the interactions between SSB and the χ subunit of DNA polymerase III in environments of varying salt concentrations. (
  • Summary Developed at Harvard Medical School, this invention provides nucleic acid arrays specifically designed for the assay of DNA-dependent protein:protein binding and/or physical interactions between proteins and nucleic acid molecules. (
  • Identify nucleotides or amino acids that mediate specific DNA:protein or protein:protein interactions. (
  • These results suggest the need to reevaluate some previous studies of activation that employed LexA derivatives and modifications to recent experimental approaches that use LexA and GAL4 derivatives to detect and study protein-protein interactions. (
  • DNA-protein interactions govern several high fidelity cellular processes like DNA-replication, transcription, DNA repair, etc. (
  • Electrophoretic mobility shift assay (EMSA) is an in vitro approach allowing for the visualization of these protein-DNA interactions. (
  • In our efforts to identify novel interactions with the DNA-bound receptor, we have isolated several proteins that interact with the A2 ERE-bound ERalpha using DNA pull-down and agarose gel shift assays. (
  • Recent studies from the ENCODE project have confirmed that disease-associated variants are enriched in regulatory DNA and that promoters and distal elements engage in multiple long-range interactions to form complex networks ( 7 - 10 ). (
  • To address the underlying mechanism of Erlotinib resistance, we investigated additional mechanisms related to mode-of-drug-action, by multiple protein-binding interactions, besides EGFR by using drug affinity responsive target stability (DARTS) and liquid chromatography-mass spectrometry (LC-MS/MS) methods with non-labeled Erlotinib. (
  • HMG-I proteins are DNA-binding proteins thought to affect the formation and function of transcription complexes. (
  • HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair. (
  • Although tyrosine phosphorylation was required for the assembly of each of these GRR binding complexes, only those formed as a result of treatment with IFN-gamma or IL-10 contained p91. (
  • Instead, complexes activated by IL-3 or GM-CSF contained a tyrosine-phosphorylated protein of 80 kilodaltons. (
  • Within chromosomes, DNA is held in complexes with structural proteins. (
  • Three PcG fusion proteins, ZnF-PC, ZnF-SCM, and ZnF-ESC, were studied, since biochemical analyses place these PcG proteins in distinct complexes. (
  • CHD6 is localized to the nucleus and is found in large multi-protein chromatin remodeling complexes, including the Nrf2 transcription factor (Nioi et al. (
  • PHD zinc-finger motifs are thought to play roles in chromatin-associated transcriptional regulation, whereas chromodomains are frequently observed in proteins involved in recruitment of transcriptional regulatory complexes. (
  • Formation of SDBP and DNA complexes was observed by agarose gel electrophoresis. (
  • The SDBPs with dysopsonin properties and DNA complexes may be further modified and ultimately be developed into a novel DNA carrier system favorable for systemic gene delivery. (
  • however, probes between 100-500 bp work well in providing optimal resolution of DNA-protein complexes without requiring extensively long gel running times. (
  • Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. (
  • Identification of the components of these complexes reveal proteins involved in several cell processes including, transcription, DNA repair and replication, G-protein modulation, and scavengers of superoxide radicals. (
  • Under the conditions of our experiments, the emc protein, but not the h protein, is able to antagonize specifically the in vitro DNA-binding activity of da/AS-C and putative da/da protein complexes. (
  • We interpret these results as follows: the heterodimerization capacity of the emc protein (conferred by its HLH domain) allows it to act in vivo as a competitive inhibitor of the formation of functional DNA-binding protein complexes by the da and AS-C proteins, thereby reducing the effective level of their transcriptional regulatory activity within the cell. (
  • The KN1-KIP complex, however, binds specifically to this DNA-binding motif with high affinity, indicating that the association of KN1 and KIP may function in transcriptional regulation. (
  • The ability to chronicle transcription-factor binding events throughout the development of an organism would facilitate mapping of transcriptional networks that control cell-fate decisions. (
  • The reprogramming of gene expression that occurs as cells move through the cell cycle, or when cells sense changes in their environment, is effected in part by changes in the DNA binding status of transcriptional activators. (
  • im trying to perform an EMSA for a protein that is part of a transcriptional complex but does not bind DNA directly. (
  • The integration host factor (IHF), a dimer of closely related chains which is suggested to function in genetic recombination as well as in translational and transcriptional control is found in Enterobacteria and viral proteins including the African swine fever virus protein A104R (or LMW5-AR). (
  • CHD6 protein is expected to function as a transcriptional repressor and it has been shown to be interact with RNA Pol II proteins (Lutz et al. (
  • SNF2 domains are commonly observed in, although not restricted to, proteins involved in chromatin unwinding, DNA repair and recombination, and transcriptional regulation. (
  • Subcloning and sequencing showed that bldC encodes a member of a previously unrecognized family of small (58- to 78-residue) DNA-binding proteins, related to the DNA-binding domains of the MerR family of transcriptional activators. (
  • Rgg proteins comprise a family of transcriptional regulators widespread among the Firmicutes. (
  • Collectively, these findings identify CNBP as a novel DNA binding protein that acts as a transcriptional regulator controlling the inflammatory program in macrophages. (
  • Nuclear transcription factor Y (NF‑Y) specifically bound the non‑risk allele of the SNP rs2074196 region and stimulated the transcriptional activity of an artificial promoter containing SNP rs2074196 in an allele‑specific manner. (
  • On the basis of these results, the relationship between the transcriptional regulation of Cah1 and protein-binding to the enhancer elements in the 5′-upstream region of Cah1 is discussed. (
  • In this paper, we describe a conserved DNA sequence in the two enhancer elements involved in the transcriptional activation of Cah1 under low-CO 2 conditions and the presence of DNA-binding proteins that interact with the enhancer elements in nuclear extracts. (
  • Proteins in the latter category include those required for DNA replication, repair, and recombination, as well as packaging proteins like the histones. (
  • Spurious initiation of DNA replication is generally a major disaster for the cell. (
  • Distinct DNA binding proteins are also associated with origins of DNA replication, centromeres, telomeres, and other sites, where they regulate chromosome replication, condensation, cohesion, and other aspects of genome maintenance ( 4 , 5 ). (
  • BRD4 prevents the accumulation of R-loops and protects against transcription-replication collision events and DNA damage. (
  • In contrast, the proteins exhibit much higher preference for recombination intermediates such as Holliday junctions and replication forks. (
  • Therefore, we hypothesize that the roles of the yeast mtHMG proteins in maintenance and compaction of mtDNA in vivo are in large part mediated by their binding to recombination/replication intermediates. (
  • In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. (
  • in these processes, bacterial DNA binding proteins have an architectural role, maintaining structural integrity as transcription, recombination, replication, or any other DNA-dependent process proceeds. (
  • In DNA replication at the lagging strand site, DNA polymerase III removes nucleotides individually from the DNA binding protein. (
  • An unstable SSB/DNA system would result in rapid disintegration of the SSB, which stalls DNA replication. (
  • Research has shown that the ssDNA is stabilized by the interaction of SSB and the χ subunit of DNA polymerase III in E. coli, thus preparing for replication by maintaining the correct conformation that increases the binding affinity of enzymes to ssDNA. (
  • Furthermore, binding of SSB to DNA polymerase III at the replication fork prevents dissociation of SSB, consequently increasing the efficiency of DNA polymerase III to synthesize a new DNA strand. (
  • HU is a protein that plays a role in various bacterial processes including compaction, transcription and replication of the genome. (
  • DNA tumor viruses proliferate by hijacking their host cell's DNA replication machinery. (
  • This protein corrupts the cellular checkpoint mechanisms that guard cell division and the transcription, replication and repair of DNA. (
  • Drs. Clurman and Welcker suspect that by acting as a decoy and binding to Fbw7, T antigen protects cellular Fbw7 targets that facilitate viral replication and tumorigenesis. (
  • DNA mismatch repair (MMR) is responsible for the maintenance of DNA fidelity upon replication. (
  • DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. (
  • Background and purpose: Single-stranded DNA-binding proteins participate in all stages of DNA metabolism that involve single-stranded DNA, from replication, recombination, repair of DNA damage, to natural competence in species such as Bacillus subtilis. (
  • A class of proteins called mycobacterial histone-like proteins has been associated with regulation of replication and latency, but their precise role in the infection process has yet to be uncovered. (
  • However, as other proteins involved in DNA replication, bacterial SSB proteins are clearly different from those found in Archaea and Eukaryotes. (
  • Bovine papillomavirus E1 protein binds specifically DNA polymerase alpha but not replication protein A. (
  • Extracts prepared from either mouse cells or monkey cells were examined for the ability to support in vitro bovine papillomavirus type 1 (BPV1) DNA replication, and they were used in parallel as a source of host replication proteins for affinity chromatography. (
  • In contrast to previous observations, we found that low levels of E1 were highly efficient in initiating DNA replication in the absence of the BPV1 transcription factor E2. (
  • Surprisingly, COS-1 cell extract allowed a high rate of BPV1 DNA replication, supporting an efficient production of mature circular DNA molecules, whereas in mouse cell extracts, the replication products mostly consisted of replicative intermediates. (
  • Furthermore, replication protein A was not retained on E1 affinity columns, even when E2 was complexed with E1. (
  • The results are very poor (about 1% with 35S in vitro synthetized proteins). (
  • The KN1 DNA-binding sequence, TGACAG(G/C)T, was biochemically identified, and in vitro DNA-binding assays show that individually KN1 and the HD of KIP bind specifically to this motif with low affinity. (
  • There have been a wide variety of experimental methods such as in vitro methods [ 4 , 5 ] like filter binding assays, chromatin immunoprecipitation on microarrays (ChIP-chip) genetic analysis, and X-ray crystallography which are used to predict DNA-binding proteins. (
  • To directly investigate this issue, we compared operator binding by a series of LexA-derivative proteins to operator binding by native LexA, by using both in vivo and in vitro assays. (
  • EMSA analysis of Rgg protein activity has facilitated in vitro confirmation of regulatory targets, identification of precise DNA binding sites via DNA probe mutagenesis, and characterization of the mechanism by which some cognate signaling peptides modulate Rgg protein function ( e.g. interruption of DNA-binding in some cases). (
  • The detected phosphorylation site was assessed for its influence on DNA-binding in vitro, using electrophoretic mobility shift assays. (
  • The in vitro assays demonstrated that SsbA is preferentially phosphorylated by the B. subtilis Hanks-type kinase YabT, and phosphorylation of threonine 38 leads to enhanced cooperative binding to DNA. (
  • The EE-1- and EE-2-binding proteins interacted with the EECs contained in both of the two enhancer elements in vitro. (
  • We endow transcription factors with the ability to deposit a transposon into the genome near to where they bind. (
  • By harvesting the transposon calling cards along with their flanking genomic DNA, a genome-wide map of transcription factor binding can be obtained. (
  • We developed a microarray method that reveals the genome-wide location of DNA-bound proteins and used this method to monitor binding of gene-specific transcription activators in yeast. (
  • Many proteins bind to specific sites in the genome to regulate genome expression and maintenance. (
  • Our understanding of these proteins and their functions is limited by our knowledge of their binding sites in the genome. (
  • If the grooves on the protein don't match those on the genome, the key won't fit. (
  • They discovered that over 80 percent of proteins bind to a specific shape pattern in the genome. (
  • The researchers say that although the proteins are frequently not reading the alphabetical code of the genome, the sequence of the letters is still vital to dictating where these proteins bind, but because it defines the genome's shape. (
  • What's more, proteins that frequently bind to the genome as a pair are attracted to specific shapes that can differ from the shapes they recognize when they bind alone. (
  • Identifying binding sites in the genome is difficult and laborious. (
  • Now, American and Dutch researchers have used DNA microarrays, or gene chips, to simultaneously tag and map the location in the genome of hundreds of these binding sites. (
  • This protein also bound to 13 transposons, or stretches of DNA that 'jump' throughout the genome. (
  • These segments are labeled with a fluorescent dye and read by DNA microarrays, providing researchers with the location in the genome of each methyl group, and thus each binding site. (
  • These DNA targets can occur throughout an organism's genome. (
  • HU-type proteins have been found in a variety of bacteria (including cyanobacteria) and archaea, and are also encoded in the chloroplast genome of some algae. (
  • How does a DNA binding protein like lac repressor find its specific site in the genome? (
  • This method of searching for the target site depends on the number of proteins, the size of the genome, and the on-off rates for specific and non-specific binding. (
  • Since the DNA of the genome doesn't move around very much, the bound molecule appears as a stable, yellow, spot. (
  • This study can serve as a basis for annotation and distribution of DNA-binding proteins in genome(s) of interest. (
  • GeneArt Precision TALs Products and Services provide researchers with custom DNA-binding proteins (encoded in Gateway compatible entry clones) for accurate DNA targeting, providing a means of editing specific loci throughout the genome. (
  • GeneArt Precision TALs provide custom DNA-binding proteins fused to effector domains for accurate DNA targeting and precise genome editing. (
  • In contrast, the predictability with which Precision TALs bind to an exact DNA sequence makes it possible to target any locus in the genome with a known sequence. (
  • Double-strand DNA breaks can be created at a customer-specified locus in the genome using a pair of GeneArt Precision TALs that have been fused to the Fok1 nuclease ( Figure 1A ). (
  • Much like the cut-and-paste feature on a computer, Precision TALs can cleave a DNA sequence to induce gene silencing or insert an exogenous DNA fragment into an exact location in the genome. (
  • Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. (
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (
  • The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. (
  • In molecular biology, bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins. (
  • Functional analyses of alanine mutants in P2 Cox argue for the importance of key residues for protein function. (
  • The DNA binding domain was identified within a region of 59 amino acid residues that was common to all four deduced EREBPs. (
  • B. subtilis single-stranded DNA-binding proteins have previously been found to be phosphorylated on tyrosine and arginine residues. (
  • Conclusions: Our findings contribute to the emerging picture that bacterial proteins, exemplified here by SsbA, undergo phosphorylation at multiple residues. (
  • Dissociation constant values (Kd values) of these bZIP proteins for high affinity G-box and C-box elements and reciprocal competition gel mobility shift assays confirmed our classification scheme. (
  • The specific interaction between SOX9 and AGAACAATGG was confirmed by mobility shift assays, DNA competition and dissociation studies. (
  • Regardless of the method of purification, it should be mentioned that it is preferable to generate affinity-tagged Rgg's in such a way as to allow for removal the affinity tag from Rgg prior to use in EMSA assays, thereby helping to ensure that the tag is not interfering with the DNA-binding activity of the protein. (
  • Competitive gel retardation assays showed DNA binding activities to be specific to the GCC box sequence in tobacco nuclear extracts. (
  • Gel mobility shift assays indicated that nuclear extracts purified from cells grown under low-CO 2 conditions in light contained DNA-binding proteins specifically interacting with EE-1 and EE-2. (
  • Gel mobility shift assays using mutant oligonucleotide probes revealed that the protein binding to EE-1 preferentially recognized a 9-bp sequence stretch (A GA T TT T C A) of EE-1, containing a conserved sequence motif named EEC, GANTTNC, which is also present in EE-2. (
  • DNA polymerase alpha subunit B (POLA2) was identified as a new Erlotinib binding protein that was validated by the DARTS platform, complemented with cellular thermal shift assays. (
  • Certain DNA-binding proteins had varied affinities for single- and double-stranded DNA, and the intact transformation uptake sequence competitively displaced the altered sequence from a BI protein at 11 kilodaltons (kDa). (
  • We found that all three proteins exhibit relatively weak binding to intact double-stranded (ds) DNA. (
  • DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. (
  • The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. (
  • Here, we use atomic force microscopy to study the effect of HU on the stiffness and supercoiling of double-stranded DNA. (
  • Many proteins bind to double-stranded DNA and most of them bind specifically to a particular target site. (
  • If you look closely at the structure shown above, you can see how parts of the protein lie in the grove of double-stranded DNA where they can detect the sequence by "reading" the chemical groups on the edges of the base pairs. (
  • I think we can safely conclude that most specific DNA binding proteins find their target sites by binding non-specifically to DNA then sliding along the double-stranded helix until they find their specific binding site. (
  • 1. The two sites are inverted relative to each other so that each subunit is, in theory, binding to exactly the same piece of double-stranded DNA. (
  • It involves incubation of nuclear extract proteins with 5'biotinylated double-stranded DNA probes and streptavidin-agarose beads. (
  • Each protein contains three DNA-binding motifs, known as AT-hooks, that bind in the minor groove of AT tracts in DNA. (
  • Group 1 proteins exhibit a stronger binding affinity for G-box elements, group 2 proteins bind both G-box and C-box motifs with comparable binding affinity, whereas the group 3 proteins display a stronger binding affinity for C-box oligonucleotides. (
  • In contrast to the situation observed for G-box elements, C-box motifs displayed a very much more stringent flanking nucleotide requirement for binding activity. (
  • Among the proteins that bind to DNA are transcription factors that activate or repress gene expression by binding to DNA motifs and histones that form part of the structure of DNA and bind to it less specifically. (
  • PcG proteins form a family based upon their common role in gene expression rather than extensive shared homologies or structural motifs. (
  • Our results also show that DNA binding by LexA derivatives that contain the LexA carboxy-terminal dimerization domain (amino acids 88 to 202) is considerably stronger than binding by fusions that lack it and that heterologous dimerization motifs cannot substitute for the LexA88-202 function. (
  • The gene for datin (the DAT gene) encodes a 248‐residue protein which contains a number of repeated sequence motifs. (
  • The human DNA topoisomerase II-binding protein 1 (TopBP1) protein contains eight BRCA1 COOH terminus motifs and shares similarities with Cut5, a yeast checkpoint Rad protein. (
  • Some of these proteins function independently to regulate target gene expression, while others have now been demonstrated to function as effectors of cell-to-cell communication, having regulatory activitiesthat that are modulated via direct interaction with small signaling peptides. (
  • The DNA within a cell's nucleus is tightly wound together with certain proteins into a threadlike structure known as chromatin, and that chromatin is further coiled to form a larger structure called a chromosome. (
  • When a transcription factor finds an available section of chromatin and binds to it, that region of the DNA sequence unzips, allowing transcription to occur. (
  • As Chang explained, ATAC-seq is like spray-painting your DNA but only the accessible chromatin gets painted, giving researchers a fast and easy way to identify key protein-binding areas. (
  • One finding showed that mutations can occur within the chromatin sequence, thereby creating a new and accessible site where a transcription factor can bind. (
  • When the team performed ATAC-seq on the tissue, they noticed that a chromatin mutation created a new protein-binding site that was associated with a strong increase in the activity of a neighboring genethat regulates cell size, motility and shape - all of which are classic factors in cancer growth. (
  • Chromatin profiling using targeted DNA adenine methyltransferase. (
  • These proteins organize the DNA into a compact structure called chromatin. (
  • Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or distorted DNA. (
  • Chromatin remodeling, transcription co-factor binding, suppression of gene expression. (
  • CHD family proteins are thought to play a role in chromatin remodeling. (
  • Furthermore, Chromatin Immunoprecipitation experiments revealed that CNBP itself bound the IL12 promoter and c-Rel binding to this promoter was compromised in CNBP-deficient macrophages. (
  • In contrast, a single group of proteins has come to dominate chromatin in eukaryotes: histones. (
  • HU proteins are often abundant constituents of bacterial chromatin. (
  • They share at least 50% homology in their HMG domains, which bind the DNA element AACAAT. (
  • However, analogous proteins may have structural homology although this is not a prerequisite. (
  • At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. (
  • In this study, we demonstrate that high-affinity binding uses two or three appropriately spaced AT tracts as a single multivalent binding site. (
  • Protein/DNA binding experiments using scanning mutants of a high affinity G-box element and G-box/C-box hybrid elements demonstrated that bZIP protein binding activity depends upon the affinity of protein dimer subunits for ACGT half-sites. (
  • The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets, including four-way junctions, but not distorted DNA minicircles, to which the proteins bind with very high affinity. (
  • Following elution, the protein readily binds DNA, indicating the protein's high affinity for DNA. (
  • Solubility of expressed Rgg proteins varies greatly between homologs, necessitating individual optimization of buffer composition and affinity tag utilization. (
  • Blue-light irradiation of the hybrid protein leads to enhanced conformational dynamics of the cPYP portion and a two-fold enhancement of the DNA binding affinity of the zENG domain. (
  • oligo(dT) DNA for high affinity binding. (
  • Submitting the extracts to affinity chromatography allowed specific binding of DNA polymerase alpha-primase to E1 protein, up to a total depletion of the extract, regardless of the origin of the cell extract. (
  • The individual A and B boxes (which, although broadly similar, show both structural and functional differences) exhibit many of the structure-specific properties of the whole protein. (
  • In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. (
  • In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. (
  • When H-NS is bound with RNA Polymerase to the promoter region, there are structural differences in the DNA that are accessible. (
  • This thesis includes structural biochemical work in combination with mutational and functional studies of proteins from both human and virus. (
  • Human tetraspanins are integral membrane proteins grouped by their conserved structural features. (
  • Our observations can be rationalized in terms of the formation of a nucleoprotein filament followed by a structural rearrangement of the bound HU on DNA. (
  • Thus this protein exists as a structural heterodimer, explaining why only one of the partners in the eukaryotic heterodimers determines which mismatch is bound. (
  • Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (
  • We have collated the DNA-binding families by integrating information from both protein sequence family and structural databases. (
  • The DNA-binding families, with no structural information, were clustered together into potential superfamilies based on sequence associations. (
  • SSB proteins share common structural characteristics and have been suggested to descend from an ancestor polypeptide. (
  • Functional studies demonstrated that, despite the structural and amino acid sequence differences from bacterial SSBs, Orf14(bIL67) protein complements the conditional lethal ssb-1 mutation of Escherichia coli. (
  • Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the bacteriophage T4. (
  • To date, however, despite having learned a good deal about the protein's biochemistry over the years, scientists have been unable to "see" the protein ?using the tools of structural biology ?bound to DNA in its naturally occurring form. (
  • We knew there had to be a structural rearrangement of the core domains to allow p53 to bind DNA as a dimer. (
  • These are proteins that interact with a short, well-defined, nucleotide sequence found near the start site for transcription. (
  • We think the proteins dock onto DNA as a 3D structure, just like when they interact with other proteins or with chemicals. (
  • Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. (
  • It's important to realize that DNA binding proteins interact with the DNA double helix and not with unwound DNA where the individual bases are exposed. (
  • Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. (
  • DNAbound transactivators recruit transcription coactivators or repressors and an array of associated proteins that interact with the basal transcription factors, thereby activating the transcription machinery. (
  • Date: February 24, 2021 Time: 7:00am (PST) Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. (
  • The UV- DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. (
  • Deletion of the nucleotide sequence encoding the PEST sequence between the two initiation codons unusually reduced the protein molecular size on SDS-polyacrylamide gel-electrophoresis. (
  • DNA-binding proteins can incorporate such domains as the zinc finger, the helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid. (
  • The single-stranded-nucleic acid binding (SSB) protein superfamily includes proteins encoded by different organisms from Bacteria and their phages to Eukaryotes. (
  • DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. (
  • A gene on chromosome 6q22.1 that belongs to the regulatory factor X gene family, which encode transcription factors that contain a highly conserved winged-helix DNA-binding domain. (
  • A gene on chromosome 2q11.2 that belongs to the regulatory factor X gene family, the protein product of which is thought to be a transcription factor. (
  • Interferon-alpha (IFN-alpha) and IFN-gamma regulate gene expression by tyrosine phosphorylation of several transcription factors that have the 91-kilodalton (p91) protein of interferon-stimulated gene factor-3 (ISGF-3) as a common component. (
  • Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. (
  • Currently, many more functions of bacteria DNA binding proteins have been discovered, including the regulation of gene expression by histone-like nucleoid-structuring protein, H-NS. (
  • these proteins are likely to represent global regulators of gene expression. (
  • In bacteria, interaction of various proteins with DNA is essential for the regulation of specific target gene expression. (
  • The bottom line is that we now have a detailed picture of how p53 binds DNA," says Ronen Marmorstein, Ph.D., a professor in the Gene Expression and Regulation Program at Wistar and senior author on the study. (
  • Binding of nuclear transactivators to sequence-specific regulatory elements on the promoter regions is of fundamental importance in gene expression and regulation. (
  • This method has the potential to trace transcription-factor binding throughout cellular and organismal development in a way that has heretofore not been possible. (
  • DNA-binding proteins play a vital role in various cellular processes. (
  • Understanding when and where proteins bind to DNA may be the ticket to identifying cancer at the cellular level, according to researchers at Stanford. (
  • Thus, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. (
  • These proteins are also some of the most broadly acting cellular oncogenes, and include cyclin E, c-Myc, Notch, and c-Jun," noted Dr. Clurman. (
  • The study of DNA tumors viruses has been an extremely important tool in understanding the cellular pathways that regulate cell division and are disrupted in cancer. (
  • There were several control experiments and additional experiments showing that the presence of other cellular proteins on the DNA didn't have much of an effect. (
  • Transcription activator-like (TAL) effector proteins are used by certain plant pathogens to manipulate cellular processes and suppress immunity in their host cells. (
  • Background: DNA-binding proteins are vital cellular components, and their identification is important for the understanding of biological processes. (
  • HMGB1 and HMGB2 proteins have been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. (
  • Interaction between KN1 and KIP is mediated by conserved domains in the N termini of both proteins. (
  • In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones. (
  • These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. (
  • Alternatively, transcription factors can bind enzymes that modify the histones at the promoter. (
  • Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. (
  • Histone-like proteins were unknown to be present in bacteria until similarities between eukaryotic histones and the HU-protein were noted, particularly because of the abundancy, basicity, and small size of both of the proteins. (
  • Upon further investigation, it was discovered that the amino acid composition of HU resembles that of eukaryotic histones, thus prompting further research into the exact function of bacterial DNA binding proteins and discoveries of other related proteins in bacteria. (
  • The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. (
  • Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea. (
  • Proteins which make bond with DNA in both eukaryotes and prokaryotes while performing like activators or repressors are DNA-binding proteins. (
  • In 2006, TAR DNA-binding protein 43 (TDP-43), a highly conserved nuclear protein, was identified as the major disease protein in amyotrophic lateral sclerosis (ALS) and in the most common variant of frontotemporal lobar degeneration (FTLD), FTLD-U, which is characterized by cytoplasmic inclusions that stain positive for ubiquitin but negative for tau and alpha-synuclein. (
  • Measurement of DNA Methylation and Nuclear Organization with Nanopore. (
  • DNA fragments encompassing SNPs, and risk or non‑risk alleles were immobilized onto the novel nanobeads and DNA‑binding proteins were purified from the nuclear extracts of pancreatic β cells using these DNA‑immobilized nanobeads. (
  • This observation suggests that the MEIS and KNOX proteins were derived from a common ancestral gene, and that these domains may have similar biochemical functions. (
  • The biochemical function of the MEINOX domain in MEIS proteins is to mediate heterodimerization with another group of TALE HD proteins, PBX in vertebrates and extradenticle (EXD) in Drosophila ( 17 - 21 ). (
  • In biochemical terms we say that it's bound half-life is 20 minutes. (
  • In this study we performed a comparative biochemical analysis of yeast mtHMG proteins from Saccharomyces cerevisiae (ScAbf2p), Yarrowia lipolytica (YlMhb1p) and Candida parapsilosis (CpGcf1p). (
  • We here present the first structure from the Cox protein family and, together with previous biochemical observations, propose that P2 Cox achieves its various functions by specific binding of DNA while wrapping the DNA around its helical oligomer. (
  • Biochemical studies of proteins are crucial for a more detailed view of the world around us. (
  • We have used this DNA-binding activity to investigate the biochemical basis of the negative regulatory function of emc. (
  • It has been observed that the percentages of prokaryotes and eukaryotes protein that can bind to DNA are only 2-3% and 4-5%, respectively [ 2 , 3 ]. (
  • The HD is a conserved structure that contains three α helices, and a sequence motif in the third helix recognizes and binds to the appropriate DNA sequence ( 15 ). (
  • Fbw7 recognizes a destruction signal on certain proteins that need to be degraded and brings them in close proximity to the enzymes that attach ubiquitin. (
  • The studies discussed in this thesis unify experimental and theoretical techniques, both established and novel, in investigating the problem of how a protein that binds specific sites on DNA translocates to, recognizes, and stably binds to its target site or sites. (
  • Winter, E. and Varshavsky, A. (1989), A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts. (
  • Practically, the number of known DNA-binding proteins is very small compared to the large non-DNA-binding proteins and unknown proteins. (
  • Treatment of human peripheral blood monocytes or basophils with interleukin-3 (IL-3), IL-5, IL-10, or granulocyte-macrophage colony-stimulating factor (GM-CSF) activated DNA binding proteins that recognized the IFN-gamma response region (GRR) located in the promoter of the Fc gamma RI gene. (
  • In E. coli, H-NS binds to a P1 promoter decreasing rRNA production during stationary and slow growth periods. (
  • It has been found that H-NS and RNA polymerase both bind to the P1 promoter and form a complex. (
  • ZnF-PcG proteins tethered as far as 3.0 kb away from the target promoter produced silencing, indicating that these effects were long range. (
  • RFX6 activates transcription by forming a heterodimer with RFX3 and binding to the X-box in the target gene's promoter region. (
  • This method has been shown to be useful in determining the regulation of binding of transactivators, p300/CBP, and associated proteins to the cyclooxygenase-2 (COX-2) promoter. (
  • As a proof of this principle, we tried to isolate transcription factors which specifically bind to the promoter region of the Arabidopsis thaliana AtGST11 gene. (
  • Two obtained candidates, RING zinc finger protein and AtHB6, showed DNA binding activity to the AtGST11 promoter region. (
  • Chromodomains are highlighted in purple, the highly conserved SNF2-like ATPase region is indicated in light blue, and the DNA binding domain (green oval) contains BRK binding sights, indicated by the red diamonds. (
  • This mutation is situated in a highly conserved region of the T-box domain and alters the ability of the T protein to bind to its consensus DNA target. (
  • Here we have identified a highly conserved Zinc finger DNA binding protein CNBP (also called ZNF9) upregulated in myeloid cells exposed to lipopolysaccharide. (
  • The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. (
  • Comparative analysis of the allele-specific DNA-binding proteins indicated that the affinities of several proteins for the examined SNPs differed between the alleles. (
  • Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. (
  • Initially, bacterial DNA binding proteins were thought to help stabilize bacterial DNA. (
  • HU is a small (10 kDa) bacterial histone-like protein that resembles the eukaryotic Histone H2B. (
  • Many studies of transcription activation employ fusions of activation domains to DNA binding domains derived from the bacterial repressor LexA and the yeast activator GAL4. (
  • TALs are bacterial proteins identified in Xanthomonas bacteria, a genus of plant pathogens responsible for the natural spread of disease via their type III secretion system [1]. (
  • Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin. (
  • In order to reduce TDP-43 pathology, we generated single-chain (scFv) antibodies against the RNA recognition motif 1 (RRM1) of TDP-43, which is involved in abnormal protein self-aggregation and interaction with p65 NF-κB. (
  • 2002). Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified Box H/ACA snoRNP protein GAR1. (
  • Repression by ZnF-SCM required a protein interaction domain, the SPM domain, which suggests that this domain is not primarily used to direct SCM to chromosomal loci. (
  • If it isn't, the interaction is much weaker and the protein falls off quickly so it can check out another potential site. (
  • It can scan about 50 bp of DNA in a single interaction and this form of "facilitated diffusion" leads to a much quicker search for the target sequence. (
  • To address this problem, we elaborate a model of protein-DNA interaction in which the protein may bind DNA in either a search (S) mode or a recognition (R) mode. (
  • Investigation of the association of ERalpha with the DNA repair protein, 3-methyadenine DNA glycosylase (MPG) reveals that this interaction modulates estrogen responsiveness and alters DNA repair. (
  • We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (
  • SV40 T antigen contains a motif that mimics the destruction signal found in these proteins. (
  • neither did the deduced proteins contain a basic leucine zipper or zinc finger motif. (
  • These dinoflagellate histone-like proteins replace histone in some dinoflagellates and package DNA into a liquid-crystalline state. (
  • Histone-like proteins are present in many Eubacteria, Cyanobacteria, and Archaebacteria. (
  • So we decided that we needed to somehow lock the protein into a conformation that's compatible with the dimer binding to DNA. (
  • The functional domains of the chromodomain-helicase-DNA binding protein 5 (CHD5) are shown above. (
  • These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases. (
  • Examples include the HU protein in Escherichia coli, a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. (
  • Functional mismatch repair is dependent on recognition of mismatches by a dimeric MutS protein, a homodimer in bacteria but a heterodimer in humans (MSH2/MSH6 or MSH2/MSH3). (
  • Bacteria typically encode multiple small basic proteins that are dynamically expressed and fulfill a variety of architectural roles by bridging, wrapping, or bending DNA ( Dillon and Dorman, 2010 ). (
  • Outside bacteria, HU proteins are comparatively rare ( Figure 2a ). (
  • The protein-binding conditions are those for gel retardation assay. (
  • The assay effectively detected blotted DNA-binding proteins. (
  • Commonly used techniques to determine DNA-protein binding such as the electrophoretic mobility shift assay (EMSA) have limited value for analyzing simultaneously a large number of proteins in the complex. (
  • We describe here a streptavidin-agarose pulldown assay that is capable of analyzing quantitatively binding of an array of proteins to DNA probes. (
  • DNA extracted from yeast colonies was introduced into Escherichia coli and the plasmid was isolated. (
  • N2 - Yeast mitochondrial DNA (mtDNA) is compacted into nucleoprotein structures called mitochondrial nucleoids (mt-nucleoids). (
  • T antigen also inactivates some of the most important proteins that protect cells against malignant transformation, including tumor suppressor proteins p53 and pRb. (
  • In the Journal of Biological Chemistry paper, Dr. Welcker and Dr. Bruce Clurman report that T antigen also binds to another tumor suppressor, Fbw7. (
  • Structure determined for p53 tumor suppressor protein as bound to DNA for anti-cancer activity ( More than half of human cancers involve. (
  • More than half of human cancers involve mutations in the p53 tumor-suppressor gene, suggesting the critical role played by the normal p53 protein in defending against cancer. (
  • SOX (SRY-related HMG box) proteins are transcription factors that have critical roles in the regulation of numerous developmental processes. (
  • The segregation of DNA-binding proteins within BI and BII correlates with their distinct protein profiles and suggests that these vesicles may play different roles. (
  • The proteins recognized by Fbw7 play key roles in cell division, cell growth, differentiation, and cell death. (
  • Dear all Presently I am trying to purifying a DNA binding protein from E.coli. (
  • Garner, M. M.and Revzin, A. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. (
  • Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions. (
  • These proteins, collectively referred to as MEIS, include the myeloid ecotropic viral integration site (MEIS) and pre-B cell homeobox (PBX)-regulating protein 1 (PREP1) family in vertebrates and Homothorax (HTH) in Drosophila ( 16 ). (
  • Bas van Steensel, of the University of Amsterdam, and colleagues tested their strategy in the fruit fly Drosophila melanogaster by pinpointing the binding sites of the three fly proteins HP-1, GAF and Sir2 that bind DNA. (
  • TDP-43 is a multi-functional RNA/DNA-binding protein well-conserved among many species including mammals and Drosophila. (
  • In Drosophila, a group of regulatory proteins of the helix-loop-helix (HLH) class play an essential role in conferring upon cells in the developing adult epidermis the competence to give rise to sensory organs. (
  • This protein is part of a ubiquitin ligase complex that adds ubiquitin to proteins to mark them for destruction by the cell. (
  • The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases. (
  • The results show that, in remarkable contrast to other phage SSBs, the Orf14(bIL67)-like proteins form a distinct, self-contained and well supported phylogenetic group connected to the archaeal SSBs. (
  • All methods supported the recognition of these phage proteins as a new family within the SSB superfamily. (
  • Here we introduce a new approach for the screening of DNA binding proteins, using a phage library based on a phage display technique. (
  • In principal, a complementary DNA (cDNA) library based on the recombinant bacteriophage T7 expressing target proteins on its capsid (phage display) is constructed. (
  • These phage particles are hybridized with a biotinylated target DNA fragment which is immobilized on the surface of streptavidin paramagnetic particle (SA-PMP). (
  • The phage particles are released from the target DNA fragment by a nuclease treatment and the recovered phages are used to the next round of hybridization. (
  • We could validate that our new application of phage display is a superior method for isolation of DNA binding proteins with a broad range of potential applications. (
  • The physical ends of eukaryotic chromosomes form a specialized nucleoprotein complex composed of DNA and DNA binding proteins. (
  • These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes. (
  • DNA-binding protein prediction is often modeled as a binary class classification problem where given a protein sequence as input the task is to predict whether the protein is DNA-binding or not. (
  • Further, sequence domain families were mapped to structures in the protein databank (PDB) and the protein domain structure classification database (SCOP). (