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.Molecular Sequence Data: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA: 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).Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Amino Acid Sequence: 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.Protein Binding: 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.Promoter Regions, Genetic: 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.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Helix-Turn-Helix Motifs: 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)Repressor Proteins: 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.Zinc Fingers: 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.Nuclear Proteins: 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.Escherichia coli: 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.Bacterial Proteins: Proteins found in any species of bacterium.Viral Proteins: Proteins found in any species of virus.Cloning, Molecular: 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.DNA Replication: The process by which a DNA molecule is duplicated.DNA Helicases: 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.Mutation: 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.Plasmids: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Cell Nucleus: 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)Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Oligodeoxyribonucleotides: 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.Protein Structure, Tertiary: 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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.HeLa Cells: 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.TDP-43 Proteinopathies: Diseases characterized by the presence of abnormally phosphorylated, ubiquitinated, and cleaved DNA-binding protein TDP-43 in affected brain and spinal cord. Inclusions of the pathologic protein in neurons and glia, without the presence of AMYLOID, is the major feature of these conditions, thus making these proteinopathies distinct from most other neurogenerative disorders in which protein misfolding leads to brain amyloidosis. Both frontotemporal lobar degeneration and AMYOTROPHIC LATERAL SCLEROSIS exhibit this common method of pathogenesis and thus they may represent two extremes of a continuous clinicopathological spectrum of one disease.Electrophoretic Mobility Shift Assay: 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.Recombinant Fusion Proteins: 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.Gene Expression Regulation: 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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Y-Box-Binding Protein 1: 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.Replication Protein A: A single-stranded DNA-binding protein that is found in EUKARYOTIC CELLS. It is required for DNA REPLICATION; DNA REPAIR; and GENETIC RECOMBINATION.Deoxyribonuclease I: 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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.NFI Transcription Factors: 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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Oligonucleotide Probes: 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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Frontotemporal Lobar Degeneration: Heterogeneous group of neurodegenerative disorders characterized by frontal and temporal lobe atrophy associated with neuronal loss, gliosis, and dementia. Patients exhibit progressive changes in social, behavioral, and/or language function. Multiple subtypes or forms are recognized based on presence or absence of TAU PROTEIN inclusions. FTLD includes three clinical syndromes: FRONTOTEMPORAL DEMENTIA, semantic dementia, and PRIMARY PROGRESSIVE NONFLUENT APHASIA.Sequence Homology, Nucleic Acid: 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.Consensus Sequence: 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.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Sequence Alignment: 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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Fungal Proteins: Proteins found in any species of fungus.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Oligonucleotides: 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)DNA Footprinting: 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)Protein Conformation: 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).Saccharomyces cerevisiae: 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.Adenoviruses, Human: 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.Chromatography, Affinity: 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)Saccharomyces cerevisiae Proteins: 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.Operator Regions, Genetic: The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Molecular Weight: The sum of the weight of all the atoms in a molecule.DNA-Directed DNA Polymerase: 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.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Genes, Viral: The functional hereditary units of VIRUSES.High Mobility Group Proteins: A family of low-molecular weight, non-histone proteins found in chromatin.Transfection: 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.Leucine Zippers: 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.Kinetics: The rate dynamics in chemical or physical systems.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.DNA Primers: 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.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Binding, Competitive: 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.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Adenovirus E2 Proteins: Proteins transcribed from the E2 region of ADENOVIRUSES. Several of these are required for viral DNA replication.Conserved Sequence: 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.Simplexvirus: A genus of the family HERPESVIRIDAE, subfamily ALPHAHERPESVIRINAE, consisting of herpes simplex-like viruses. The type species is HERPESVIRUS 1, HUMAN.RNA, Messenger: 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.Homeodomain Proteins: 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).CCAAT-Enhancer-Binding Proteins: 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.Repetitive Sequences, Nucleic Acid: 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).Blotting, Southwestern: A method that is used to detect DNA-protein interactions. Proteins are separated by electrophoresis and blotted onto a nitrocellulose membrane similar to Western blotting (BLOTTING, WESTERN) but the proteins are identified when they bind labeled DNA PROBES (as with Southern blotting (BLOTTING, SOUTHERN)) instead of antibodies.Macromolecular Substances: 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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Genetic Complementation Test: 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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Proto-Oncogene Proteins c-myb: Cellular DNA-binding proteins encoded by the myb gene (GENES, MYB). They are expressed in a wide variety of cells including thymocytes and lymphocytes, and regulate cell differentiation. Overexpression of myb is associated with autoimmune diseases and malignancies.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.DNA Primase: A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.Bacteriophage T7: 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.Basic-Leucine Zipper Transcription Factors: A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.Chromatin: 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.Ultraviolet Rays: 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.Drosophila Proteins: 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.Rec A Recombinases: 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.Integration Host Factors: 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.AT Rich Sequence: A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.Deoxyribonucleoproteins: Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.DNA Probes: 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.AT-Hook Motifs: DNA-binding motifs, first described in one of the HMGA PROTEINS: HMG-I(Y) PROTEIN. They consist of positively charged sequences of nine amino acids centered on the invariant tripeptide glycine-arginine-proline. They act to fasten the protein to an AT RICH SEQUENCE in the DNA.Drosophila: 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.Structure-Activity Relationship: 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.Protein Structure, Secondary: 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.Centromere Protein B: A DNA-binding protein that interacts with a 17-base pair sequence known as the CENP-B box motif. The protein is localized constitutively to the CENTROMERE and plays an important role in its maintenance.DNA, Complementary: 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.Temperature: 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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Genes, Reporter: 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.Genes: 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.Chromatin Immunoprecipitation: 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.Erythroid-Specific DNA-Binding Factors: A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.G-Box Binding Factors: A family of transcription factors found primarily in PLANTS that bind to the G-box DNA sequence CACGTG or to a consensus sequence CANNTG.Telomere-Binding Proteins: Proteins that specifically bind to TELOMERES. Proteins in this class include those that perform functions such as telomere capping, telomere maintenance and telomere stabilization.Helix-Loop-Helix Motifs: 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.Templates, Genetic: 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.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.RNA-Binding Protein FUS: A multifunctional heterogeneous-nuclear ribonucleoprotein that may play a role in homologous DNA pairing and recombination. The N-terminal portion of protein is a potent transcriptional activator, while the C terminus is required for RNA binding. The name FUS refers to the fact that genetic recombination events result in fusion oncogene proteins (ONCOGENE PROTEINS, FUSION) that contain the N-terminal region of this protein. These fusion proteins have been found in myxoid liposarcoma (LIPOSARCOMA, MYXOID) and acute myeloid leukemia.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Genes, Bacterial: The functional hereditary units of BACTERIA.Lac Repressors: Bacterial repressor proteins that bind to the LAC OPERON and thereby prevent the synthesis of proteins involved in catabolism of LACTOSE. When lactose levels are high lac repressors undergo an allosteric change that causes their release from the DNA and the resumption of lac operon transcription.Genes, Fungal: The functional hereditary units of FUNGI.Archaeal Proteins: Proteins found in any species of archaeon.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Two-Hybrid System Techniques: 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.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Telomeric Repeat Binding Protein 1: A ubiquitously expressed telomere-binding protein that is present at TELOMERES throughout the CELL CYCLE. It is a suppressor of telomere elongation and may be involved in stabilization of telomere length. It is structurally different from TELOMERIC REPEAT BINDING PROTEIN 2 in that it contains acidic N-terminal amino acid residues.DNA, Superhelical: 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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)DNA Damage: 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.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Bacteriophage T4: Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.DNA Repair: 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.Recombination, Genetic: 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.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Polymerase Chain Reaction: 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.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Response Elements: 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.Sp1 Transcription Factor: 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.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Gene Library: 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.Ikaros Transcription Factor: A transcription factor that plays a role as a key regulator of HEMATOPOIESIS. Aberrant Ikaros expression has been associated with LYMPHOBLASTIC LEUKEMIA.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Antigens, Nuclear: Immunologically detectable substances found in the CELL NUCLEUS.Immunoglobulin J Recombination Signal Sequence-Binding Protein: A ubiquitously expressed sequence-specific transcriptional repressor that is normally the target of signaling by NOTCH PROTEINS.Amyotrophic Lateral Sclerosis: A degenerative disorder affecting upper MOTOR NEURONS in the brain and lower motor neurons in the brain stem and SPINAL CORD. Disease onset is usually after the age of 50 and the process is usually fatal within 3 to 6 years. Clinical manifestations include progressive weakness, atrophy, FASCICULATION, hyperreflexia, DYSARTHRIA, dysphagia, and eventual paralysis of respiratory function. Pathologic features include the replacement of motor neurons with fibrous ASTROCYTES and atrophy of anterior SPINAL NERVE ROOTS and corticospinal tracts. (From Adams et al., Principles of Neurology, 6th ed, pp1089-94)Adenosine Triphosphatases: 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.Tumor Cells, Cultured: 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.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Gene Deletion: 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.Factor For Inversion Stimulation Protein: 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.Telomere: A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs.Nucleosomes: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.Proto-Oncogene Proteins: 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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Virus Replication: 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.Bacteriophage mu: A temperate coliphage, in the genus Mu-like viruses, family MYOVIRIDAE, composed of a linear, double-stranded molecule of DNA, which is able to insert itself randomly at any point on the host chromosome. It frequently causes a mutation by interrupting the continuity of the bacterial OPERON at the site of insertion.DNA Polymerase III: 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 2.7.7.7.Cells, Cultured: 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.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Poly dA-dT: 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.Crithidia fasciculata: A species of monogenetic, parasitic protozoa usually found in insects.Sulfolobus: 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.Baculoviridae: Family of INSECT VIRUSES containing two subfamilies: Eubaculovirinae (occluded baculoviruses) and Nudibaculovirinae (nonoccluded baculoviruses). The Eubaculovirinae, which contain polyhedron-shaped inclusion bodies, have two genera: NUCLEOPOLYHEDROVIRUS and GRANULOVIRUS. Baculovirus vectors are used for expression of foreign genes in insects.Pentoxyl: 5-Hydroxymethyl-6-methyl- 2,4-(1H,3H)-pyrimidinedione. Uracil derivative used in combination with toxic antibiotics to lessen their toxicity; also to stimulate leukopoiesis and immunity. Synonyms: pentoksil; hydroxymethylmethyluracil.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Exodeoxyribonucleases: 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.Models, Biological: 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.HMG-Box Domains: DNA-binding domains present in proteins of the HMG-box superfamily including the archetypal HMGB PROTEINS, a number of sequence specific TRANSCRIPTION FACTORS, and other DNA-BINDING PROTEINS. The domains consist of 70-80 amino acids that form an L-shaped fold from three alpha-helical segments. The domain has the capacity to recognize and/or induce specific DNA structures and effect the accessibility of the DNA to other proteins involved in transcription, recombination, or DNA repair. (Note that not all HIGH MOBILITY GROUP PROTEINS contain this domain.)Cross-Linking Reagents: 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.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Oncogene Proteins v-myb: Transforming proteins coded by myb oncogenes. Transformation of cells by v-myb in conjunction with v-ets is seen in the avian E26 leukemia virus.Blotting, Western: 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.Octamer Transcription Factor-1: A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.T-Phages: 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.Proto-Oncogene Proteins c-ets: A family of transcription factors that share a unique DNA-binding domain. The name derives from viral oncogene-derived protein oncogene protein v-ets of the AVIAN ERYTHROBLASTOSIS VIRUS.Transcription Factor AP-2: A family of DNA binding proteins that regulate expression of a variety of GENES during CELL DIFFERENTIATION and APOPTOSIS. Family members contain a highly conserved carboxy-terminal basic HELIX-TURN-HELIX MOTIF involved in dimerization and sequence-specific DNA binding.Gene Expression Regulation, Developmental: 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.HMGB1 Protein: A 24-kDa HMGB protein that binds to and distorts the minor grove of DNA.TATA Box: 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.Deinococcus: 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.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Inclusion Bodies: A generic term for any circumscribed mass of foreign (e.g., lead or viruses) or metabolically inactive materials (e.g., ceroid or MALLORY BODIES), within the cytoplasm or nucleus of a cell. Inclusion bodies are in cells infected with certain filtrable viruses, observed especially in nerve, epithelial, or endothelial cells. (Stedman, 25th ed)beta-Galactosidase: A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.Bacteriophages: Viruses whose hosts are bacterial cells.Spodoptera: A genus of owlet moths of the family Noctuidae. These insects are used in molecular biology studies during all stages of their life cycle.Models, Genetic: 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.Facilitated Diffusion: The passive movement of molecules exceeding the rate expected by simple diffusion. No energy is expended in the process. It is achieved by the introduction of passively diffusing molecules to an enviroment or path that is more favorable to the movement of those molecules. Examples of facilitated diffusion are passive transport of hydrophilic substances across a lipid membrane through hydrophilic pores that traverse the membrane, and the sliding of a DNA BINDING PROTEIN along a strand of DNA.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.Simian virus 40: A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures.Cyclic AMP Receptor Protein: A transcriptional regulator in prokaryotes which, when activated by binding cyclic AMP, acts at several promoters. Cyclic AMP receptor protein was originally identified as a catabolite gene activator protein. It was subsequently shown to regulate several functions unrelated to catabolism, and to be both a negative and a positive regulator of transcription. Cell surface cyclic AMP receptors are not included (CYCLIC AMP RECEPTORS), nor are the eukaryotic cytoplasmic cyclic AMP receptor proteins, which are the regulatory subunits of CYCLIC AMP-DEPENDENT PROTEIN KINASES.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Replication Origin: 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)Viral Regulatory and Accessory Proteins: A broad category of viral proteins that play indirect roles in the biological processes and activities of viruses. Included here are proteins that either regulate the expression of viral genes or are involved in modifying host cell functions. Many of the proteins in this category serve multiple functions.

*  Browsing HMS Scholarly Articles by Subject "DNA-binding proteins"

... 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/ ...

*  DNA binding protein purification

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 ens-lyon.fr 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 ...

*  "Calling Cards" for DNA-Binding Proteins in Mammalian Cells |...

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 ...

*  EMSA for non-DNA binding protein - Protein and Proteomics

EMSA for non-DNA binding protein - (Jan/23/2008 ). im trying to perform an EMSA for a protein that is part of a transcriptional ... well, when you do an EMSA you probe with an oligo corresponding to the DNA binding sequence recognized by your TF.. I'm ... complex but does not bind DNA directly. is this possible/difficult? any experience anyone? ...

*  Sandwalk: Slip Slidin' Along - How DNA Binding Proteins Find Their Target

1. DNA-binding protein reaches a piece of DNA by regular 3D diffusion and binds to it ('non-specifically' - which isn't really ... It's important to realize that DNA binding proteins interact with the DNA double helix and not with unwound DNA where the ... and other similar DNA binding proteins) sticks non-specifically to DNA then slides along the DNA molecule looking for a target ... repressor (and other similar DNA binding proteins) sticks non-specifically to DNA then slides along the DNA molecule looking ...

*  RCSB PDB - Protein Feature View - DNA-binding protein inhibitor ID-3 - Q02535 (ID3 HUMAN)

The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex ... Inhibits the binding of E2A-containing protein complexes to muscle creatine kinase E-box enhancer. Regulates the circadian ... Transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the basic helix-loop-helix (bHLH) ... transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. Implicated in ...

*  DNA-binding protein - Wikipedia

A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, ... DNA-binding proteins are proteins composed of DNA-binding domains and thus have a specific or general affinity for either ... Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or ... Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, ...

*  Bacterial DNA binding protein - Wikipedia

DNA-binding domain DNA-binding protein DNA-binding protein from starved cells Transcription factor Drlica K, Rouviere-Yaniv J ( ... Following elution, the protein readily binds DNA, indicating the protein's high affinity for DNA. Histone-like proteins were ... bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known ... In DNA replication at the lagging strand site, DNA polymerase III removes nucleotides individually from the DNA binding protein ...

*  Single-strand DNA-binding protein - Wikipedia

Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli (E. coli) bacteria, that binds to single- ... DNA-binding protein Single-stranded binding protein Comparison of nucleic acid simulation software Oakley, A.J. "Intramolecular ... "Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined ... As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved ...

*  Inhibitor of DNA-binding protein - Wikipedia

Inhibitor of DNA-binding/differentiation proteins, also known as ID proteins comprise a family of proteins that heterodimerize ... ID proteins can bind E-proteins, preventing them from binding bHLH proteins and halting transcription, a case often seen in ... transcription factors to inhibit DNA binding of bHLH proteins. ID proteins also contain the HLH-dimerization domain but lack ... The first helix-loop-helix proteins identified were named E-proteins because they bind to Ephrussi-box (E-box) sequences. In ...

*  SAND DNA-binding protein domain - Wikipedia

The precise function of the protein domain SAND remains to be determined. Nevertheless, it is thought to be a DNA binding ... Henceforth, this suggests that the SAND domain is the DNA-binding region of DEAF-1. The structure of this protein domain ... In molecular biology, the protein domain SAND is named after a range of proteins in the protein family: Sp100, AIRE-1, NucP41/ ... Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 ...

*  TAR DNA-Binding Protein 43 (TDP-43) - Pipeline Review, H1 2016 : ReportsnReports

Global Markets Direct's, 'TAR DNA-Binding Protein 43 (TDP-... ... Check for Discount on TAR DNA-Binding Protein 43 (TDP-43) - ... TAR DNA-Binding Protein 43 (TDP-43) - Products under Development by Stage of Development 7 TAR DNA-Binding Protein 43 (TDP-43 ... TAR DNA-Binding Protein 43 (TDP-43) - Dormant Projects 33 TAR DNA-Binding Protein 43 (TDP-43) - Featured News & Press Releases ... TAR DNA-Binding Protein 43 (TDP-43) - Products under Development by Indication 9 TAR DNA-Binding Protein 43 (TDP-43) - Pipeline ...

*  DNA-binding protein from starved cells - Wikipedia

"Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells. A ferritin-like DNA-binding ... "Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells. A ferritin-like DNA-binding ... DNA-binding proteins from starved cells (DPS) are proteins that belong to the ferritin superfamily and are characterized by ... Chiancone, E.; Ceci, P. (2010). "Role of Dps (DNA-binding proteins from starved cells) aggregation on DNA". Frontiers in ...

*  A novel DNA-binding protein modulating methicillin resistance in staphylococcus aureus - Zurich Open Repository and Archive

RESULTS: Analysis of proteins binding to a DNA fragment containing the mec operator region identified a novel, putative helix- ... RESULTS: Analysis of proteins binding to a DNA fragment containing the mec operator region identified a novel, putative helix- ... Ender, M; Berger-Bächi, B; McCallum, N (2009). A novel DNA-binding protein modulating methicillin resistance in staphylococcus ... turn-helix DNA-binding protein, SA1665. Nonpolar deletion of SA1665, in heterogeneously methicillin resistant S. aureus (MRSA) ...

*  Transactive response DNA-binding protein 43 burden in familial Alzheimer disease and Down syndrome - Zurich Open Repository...

CONCLUSIONS: Transactive response DNA-binding protein 43 pathology occurs in FAD and DS, similar to that observed in sporadic ... CONCLUSIONS: Transactive response DNA-binding protein 43 pathology occurs in FAD and DS, similar to that observed in sporadic ... Transactive response DNA-binding protein 43 burden in familial Alzheimer disease and Down syndrome ... OBJECTIVE: To assess the transactive response DNA-binding protein 43 (TDP-43) burden in familial forms of Alzheimer disease ( ...

*  Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii - Nottingham ePrints

Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. The roles of ... Stroud, A. L. (2012) Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii. PhD thesis, University ... Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii ... To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA.. Haloferax volcanii encodes ...

*  DNA Binding Proteins

... Below are examples of different types of DNA-binding proteins. The most common and best studied DNA- ... binding proteins are the Zinc finger proteins, the Helix-turn-helix proteins, and the Leucine zipper proteins. ... This protein is somewhat unusual in that its TBP-binding domain binds to the minor groove of DNA. ... This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins. ...

*  DNA-Protein Binding Assay Kit (Colorimetric) (ab117139) Protocols

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 ...

*  Chromodomain-helicase-DNA-binding protein 1

Data indicate that chromodomain-helicase-DNA-binding protein CHD1, neoplasm protein GREB1 and karyopherin alpha 2 protein KPNA2 ... Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.. ... Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to ... The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain.. ...

*  Chromodomain-helicase-DNA-binding protein 8

The autism-associated gene chromodomain helicase DNA-binding protein 8 (CHD8) regulates noncoding RNAs and autism-related genes ... Frequent disruption of chromodomain helicase DNA-binding protein 8 (CHD8) and functionally associated chromatin regulators in ... This gene encodes a DNA helicase that functions as a transcription repressor by remodeling chromatin structure. It binds beta- ... DNA helicase that acts as a chromatin remodeling factor and regulates transcription. Acts as a transcription repressor by ...

*  High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein

Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA ... High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein. ... High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein ' Extremophiles , vol 21 , no. 2 , pp. 369 ... SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to ...

*  DNA damage-binding protein - Wikipedia

DNA damage-binding protein or UV-DDB is a protein complex that is responsible for repair of UV-damaged DNA. This complex is ... "Damage-specific DNA binding protein 1 (DDB1): a protein with a wide range of functions" (PDF). The International Journal of ... for the p127 and p48 subunits of a human damage-specific DNA binding protein". Genomics. 29 (1): 62-9. doi:10.1006/geno. ... DDB1 moves from the cytosol to the nucleus and binds to DDB2, thus forming the UV-DDB complex. This complex functions in ...

*  CMR1 - DNA damage-binding protein CMR1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) - CMR1 gene &...

... and double-stranded DNA. Binds preferentially to UV-damaged DNA in vitro (PubMed:22367945). May be involved in DNA-metabolic ... DNA-binding protein that binds to both single- ... DNA-binding protein that binds to both single- and double- ... "Saccharomyces cerevisiae Cmr1 protein preferentially binds to UV-damaged DNA in vitro.". Choi D.H., Kwon S.H., Kim J.H., Bae S. ... "Saccharomyces cerevisiae Cmr1 protein preferentially binds to UV-damaged DNA in vitro.". Choi D.H., Kwon S.H., Kim J.H., Bae S. ...

*  Protein-analysis] one-to-one protein-to-DNA binding

... Emily Arturo via proteins%40net.bio.net (by ecakbd from missouri.edu). Sun ... DNA complexes. I now have some spectroscopic data of DNA binding to a Trp-containing protein and am having a rough time finding ... I have read several papers by Lohman & company on multi-site binding of SSB protein to DNA, but these analyses are ... Previous message: [Protein-analysis] Re: Enthalpy of protein *Next message: [Protein-analysis] Re: ELISA HELP NEEDED Cant Get ...

*  RAD54抗体[Rad54 4E3/1]|Abcam中国|Anti-RAD54抗体[Rad54 4E3/1]

DNA repair and recombination protein RAD54 like antibody. *DNA repair and recombination protein RAD54-like antibody ... Contains 1 helicase ATP-binding domain.. Contains 1 helicase C-terminal domain. ... Involved in DNA repair and mitotic recombination. Functions in the recombinational DNA repair (RAD52) pathway. Dissociates ... The cells were then incubated in 1x PBS / 10% normal goat serum / 0.3M glycine to block non-specific protein-protein ...

DNA-binding proteinColes PhillipsSymmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Pituitary-specific positive transcription factor 1: POU domain, class 1, transcription factor 1 (Pit1, growth hormone factor 1), also known as POU1F1, is a transcription factor for growth hormone.Sticky and blunt ends: DNA end or sticky end refers to the properties of the end of a molecule of DNA or a recombinant DNA molecule. The concept is important in molecular biology, especially in cloning or when subcloning inserts DNA into vector DNA.DNA binding site: DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Proximity ligation assay: Proximity ligation assay (in situ PLA) is a technology that extends the capabilities of traditional immunoassays to include direct detection of proteins, protein interactions and modifications with high specificity and sensitivity. Protein targets can be readily detected and localized with single molecule resolution and objectively quantified in unmodified cells and tissues.GC box: In molecular biology, a GC box is a distinct pattern of nucleotides found in the promoter region of some eukaryotic genes upstream of the TATA box and approximately 110 bases upstream from the transcription initiation site. It has a consensus sequence GGGCGG which is position dependent and orientation independent.Eukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Helix-turn-helix: 200px|thumb|The λ repressor of [[bacteriophage lambda employs a helix-turn-helix (left; green) to bind DNA (right; blue and red).]]Repressor: In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. A DNA-binding repressor blocks the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes into messenger RNA.Zinc fingerList of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.DNA re-replication: DNA re-replication (or simply rereplication) is an undesirable and possibly fatal occurrence in eukaryotic cells in which the genome is replicated more than once per cell cycle. Rereplication is believed to lead to genomic instability and has been implicated in the pathologies of a variety of human cancers.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Triparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.CpG OligodeoxynucleotideFERM domain: In molecular biology, the FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane.Hypersensitive site: In genetics a hypersensitive site is a short region of chromatin and is detected by its super sensitivity to cleavage by DNase I and other various nucleases (DNase II and micrococcal nucleases). In a hypersensitive site, the nucleosomal structure is less compacted, increasing the availability of the DNA to binding by proteins, such as transcription factors and DNase I.Reaction coordinateNucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.Allele-specific oligonucleotide: An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay.Frontotemporal lobar degeneration: Frontotemporal lobar degeneration (FTLD) is a pathological process that occurs in frontotemporal dementia. It is characterized by atrophy in the frontal lobe and temporal lobe of the brain, with sparing of the parietal and occipital lobes.Enhancer (genetics)CS-BLASTAbscription: During normal transcription, RNA polymerase transcribes a number of short nonproductive oligonucleotides, and this process is called abortive transcription. The trapped RNAPs have been named abscriptases and the synthesis of specific length oligonucleotides called abscription.Database of protein conformational diversity: The Database of protein conformational diversity (PCDB) is a database of diversity of protein tertiary structures within protein domains as determined by X-ray crystallography. Proteins are inherently flexible and this database collects information on this subject for use in molecular research.Zuotin: Z-DNA binding protein 1, also known as Zuotin, is a Saccharomyces cerevisiae yeast gene.Adenovirus genome: Adenovirus genomes are linear, non-segmented double-stranded (ds) DNA molecules that are typically 26-46 Kbp long, containing 23-46 protein-coding genes. The example used for the following description is Human adenovirus E, a mastadenovirus with a 36 Kbp genome containing 38 protein-coding genes.Affinity chromatography: Affinity chromatography is a method of separating biochemical mixtures based on a highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.Operator (biology): In genetics, an operator is a segment of DNA to which a transcription factor binds to regulate gene expression. The transcription factor is a repressor, which can bind to the operator to prevent transcription.Escherichia coli (molecular biology): Escherichia coli (; commonly abbreviated E. coli) is a gammaproteobacterium commonly found in the lower intestine of warm-blooded organisms (endotherms).Molar mass distribution: In linear polymers the individual polymer chains rarely have exactly the same degree of polymerization and molar mass, and there is always a distribution around an average value. The molar mass distribution (or molecular weight distribution) in a polymer describes the relationship between the number of moles of each polymer species (Ni) and the molar mass (Mi) of that species.T7 DNA polymerase: T7 DNA polymerase is an enzyme used during the DNA replication of the T7 bacteriophage. During this process, the DNA polymerase “reads” existing DNA strands and creates two new strands that match the existing ones.Chemically induced dimerization: Chemically Induced Dimerization (CID) is a biological mechanism in which two proteins bind only in the presence of a certain small molecule, enzyme or other dimerizing agent. Genetically engineered CID systems are used in biological research to control protein localization, to manipulate signalling pathways and to induce protein activation.High mobility group protein HMG14 and HMG17: High mobility group protein HMG14 and HMG17 also known as nucleosomal binding domain is a family of evolutionarily related proteins.RNA transfection: RNA transfection is the process of deliberately introducing RNA into a living cell. RNA can be purified from cells after lysis or synthesized from free nucleotides either chemically, or enzymatically using an RNA polymerase to transcribe a DNA template.Zipper (BDSM): In BDSM terms, a zipper is a string of clothespins or other clips, held together loosely by a cord or light chain.Burst kinetics: Burst kinetics is a form of enzyme kinetics that refers to an initial high velocity of enzymatic turnover when adding enzyme to substrate. This initial period of high velocity product formation is referred to as the "Burst Phase".WIN 56,098: WIN 56,098 is a chemical that is considered to be an aminoalkylindole derivative. It is a tricyclic aryl derivative that acts as a competitive antagonist at the CB2 cannabinoid receptor.Margaret Jope: Margaret Jope (1913–2004) was a Scottish biochemist, born as Henrietta Margaret Halliday in Peterhead, Scotland.Mature messenger RNA: Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, it consists exclusively of exons, with all introns removed.Iroquois homeobox factor: Iroquois homeobox factors are a family of homeodomain transcription factors that play a role in many developmental processes.Direct repeat: Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence.Primase: DNA primase, also called as DNA primerase, is an enzyme involved in the replication of DNA. DNA primase is a type of RNA polymerase which creates an RNA primer (later this RNA piece is removed by a 5' to 3' exonuclease); next, DNA polymerase uses the RNA primer to replicate ssDNA.Bivalent chromatin: Bivalent chromatin are segments of DNA, bound to histone proteins, that have both repressing and activating epigenetic regulators in the same region. These regulators work to enhance or silence the expression of genes.UVB-induced apoptosis: UVB-induced apoptosis is the programmed cell death of cells that become damaged by ultraviolet rays. This is notable in skin cells, to prevent melanoma.BESS domain: In molecular biology, the BESS domain is a protein domain which has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32), Suvar(3)7 and Stonewall ). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain.

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

(8/69904) 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.

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)



helicase DNA binding

  • Data indicate that chromodomain-helicase-DNA-binding protein CHD1, neoplasm protein GREB1 and karyopherin alpha 2 protein KPNA2 as critical mediators of miR-26a and miR-26b elicited cell growth. (nih.gov)
  • Chromodomain-helicase-DNA-binding protein 7 also known as ATP-dependent helicase CHD7 is an enzyme that in humans is encoded by the CHD7 gene. (wikipedia.org)
  • Chromodomain-helicase-DNA-binding protein 3 is an enzyme that in humans is encoded by the CHD3 gene. (wikipedia.org)
  • The gene CHD8 encodes the protein chromodomain helicase DNA binding protein 8, which is a chromatin regulator enzyme that is essential during fetal development. (wikipedia.org)

single-stranded

  • A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. (wikipedia.org)
  • These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases. (wikipedia.org)
  • In these high salt concentrations, the eukaryotic histone protein is eluted from a DNA solution in which single stranded DNA is bound covalently to cellulose. (wikipedia.org)
  • 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. (wikipedia.org)
  • Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli (E. coli) bacteria, that binds to single-stranded regions of deoxyribonucleic acid (DNA). (wikipedia.org)
  • Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. (wikipedia.org)
  • As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved in all of these processes. (wikipedia.org)
  • Binding of single-stranded DNA to the tetramer can occur in different "modes", with SSB occupying different numbers of DNA bases depending on a number of factors, including salt concentration. (wikipedia.org)
  • Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. (nottingham.ac.uk)
  • The roles of RPA include stabilising and protecting single- stranded DNA from nuclease degradation during DNA replication and repair. (nottingham.ac.uk)
  • To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA. (nottingham.ac.uk)
  • Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. (st-andrews.ac.uk)
  • Single-stranded DNA-binding protein 3 is a protein that in humans is encoded by the SSBP3 gene. (wikipedia.org)

vitro

  • The results are very poor (about 1% with 35S in vitro synthetized proteins). (bio.net)
  • For example, the (SSB)65 binding mode, in which approximately 65 nucleotides of DNA wrap around the SSB tetramer and contact all four of its subunits, is favoured at high salt concentrations in vitro. (wikipedia.org)
  • Dps dodecamers can condense DNA in vitro through a cooperative binding mechanism. (wikipedia.org)
  • Gel shift assays are often performed in vitro concurrently with DNase footprinting, primer extension, and promoter-probe experiments when studying transcription initiation, DNA replication, DNA repair or RNA processing and maturation, as well as pre-mRNA splicing. (wikipedia.org)
  • Once DNA-protein binding is determined in vitro, a number of algorithms can narrow the search for identification of the transcription factor. (wikipedia.org)
  • The in vitro model, which is a very well known method of facilitated diffusion, that takes place outside of a living cell, explains the 3-dimensional pattern of diffusion in the cytosol and the 1-dimensional diffusion along the DNA contour. (wikipedia.org)
  • After analyzing the process for the time it takes for TF's to diffuse across the contour and cytoplasm of the bacteria's DNA, it was concluded that in vitro and in vivo are similar in that the association and dissociation rates of TF's to and from the DNA are similar in both. (wikipedia.org)

residues

  • 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. (wikipedia.org)
  • 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. (wikipedia.org)
  • This protein domain has a conserved region of around 80 residues. (wikipedia.org)
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
  • Three consecutive amino acid residues form an anion-binding concavity. (wikipedia.org)
  • Three or four consecutive amino acid residues form a cation-binding feature. (wikipedia.org)
  • The ARID2 protein contains two conserved C-terminal C2H2 zinc fingers motifs, a region rich in the amino acid residues proline and glutamine, a RFX (regulatory factor X)-type winged-helix DNA-binding domain, and a conserved N-terminal AT-rich DNA interaction domain-the last domain for which the protein is named. (wikipedia.org)
  • When the protein is not acetylated, it stays in the nucleus, but hyperacetylation on lysine residues causes it to translocate into the cytosol. (wikipedia.org)

Regulates

  • Transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the basic helix-loop-helix (bHLH) transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. (rcsb.org)
  • Regulates negatively DNA replication. (nih.gov)
  • DNA helicase that acts as a chromatin remodeling factor and regulates transcription. (nih.gov)
  • It binds beta-catenin and negatively regulates Wnt signaling pathway, which plays a pivotal role in vertebrate early development and morphogenesis. (nih.gov)
  • This nuclear protein organizes the DNA and regulates transcription. (wikipedia.org)
  • HMGB1 is an intracellular protein that can translocate to the nucleus where it binds DNA and regulates gene expression. (wikipedia.org)

helix-loop-

  • bZIP domain Comparison of nucleic acid simulation software DNA-binding domain Helix-loop-helix Helix-turn-helix HMG-box Leucine zipper Lexitropsin (a semi-synthetic DNA-binding ligand) Single-strand binding protein Zinc finger Created from PDB 1LMB Created from PDB 1RVA Travers, A. A. (1993). (wikipedia.org)
  • Inhibitor of DNA-binding/differentiation proteins, also known as ID proteins comprise a family of proteins that heterodimerize with basic helix-loop-helix (bHLH) transcription factors to inhibit DNA binding of bHLH proteins. (wikipedia.org)
  • The first helix-loop-helix proteins identified were named E-proteins because they bind to Ephrussi-box (E-box) sequences. (wikipedia.org)
  • The ID homologue gene in Drosophila is called extramacrochaetae (EMC) and encodes a transcription factor of the helix-loop-helix family that lacks a DNA binding domain. (wikipedia.org)
  • Helix-loop-helix: Consists of alpha helices bound by a looping stretch of amino acids. (wikipedia.org)

Genes

  • 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. (genetics.org)
  • 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. (wikipedia.org)
  • Haloferax volcanii encodes three RPAs - RPA1, RPA2 and RPA3, of which rpa1 and rpa3 are in operons with genes encoding associated proteins (APs). (nottingham.ac.uk)
  • CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. (nih.gov)
  • The changes among protein-coding genes involved genes that are enriched in neuronal development and in previously identified autism candidate genes. (nih.gov)

Genomics

  • Application of this method to 2235 structural genomics targets uncovered 37 as DNA binding proteins, 27 (73%) of which are putatively DNA binding and only 1 protein whose annotated functions do not contain DNA binding, while the remaining proteins have unknown function. (edu.au)

family of proteins

  • The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. (nih.gov)

oligonucleotide

  • I use DNA binding protein purification kit from Boerhinger with long concatamers of protein-binding oligonucleotide (obtainrd using self-primed PCR technique) ligated streptavidin magnetic particles. (bio.net)
  • SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. (st-andrews.ac.uk)
  • Often, an extra lane is run with a competitor oligonucleotide to determine the most favorable binding sequence for the binding protein. (wikipedia.org)
  • A Southwestern blot is based on Southern blotting and is used to identify and characterize DNA-binding proteins by their ability to bind to specific oligonucleotide probes. (wikipedia.org)

replication

  • 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. (wikipedia.org)
  • 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. (wikipedia.org)
  • In DNA replication at the lagging strand site, DNA polymerase III removes nucleotides individually from the DNA binding protein. (wikipedia.org)
  • An unstable SSB/DNA system would result in rapid disintegration of the SSB, which stalls DNA replication. (wikipedia.org)
  • 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. (wikipedia.org)
  • 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. (wikipedia.org)
  • The protein has been implicated in DNA replication, recombination, and repair. (wikipedia.org)
  • SSB protein domains in bacteria are important in its function of maintaining DNA metabolism, more specifically DNA replication, repair, and recombination. (wikipedia.org)

recombination

  • 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). (wikipedia.org)
  • PRDM9 is responsible for positioning recombination hotspots during meiosis by binding a DNA sequence motif encoded in its zinc finger domain. (wikipedia.org)

Escherichia

  • DNA extracted from yeast colonies was introduced into Escherichia coli and the plasmid was isolated. (genetics.org)
  • 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. (wikipedia.org)
  • In Escherichia coli Dps protein is Induced by rpoS and IHF in the early stationary phase. (wikipedia.org)

transcriptional

  • 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. (genetics.org)
  • But mapping the transcriptional networks that control cell-fate decisions is difficult given the limitations of the tools available to measure protein-DNA interactions. (genetics.org)

double-stranded

  • DNA-binding proteins are proteins composed of DNA-binding domains and thus have a specific or general affinity for either single or double stranded DNA. (wikipedia.org)
  • The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. (wikipedia.org)
  • DNA-binding protein that binds to both single- and double-stranded DNA. (uniprot.org)

Zinc

  • 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. (wikipedia.org)
  • The most common and best studied DNA-binding proteins are the Zinc finger proteins, the Helix-turn-helix proteins, and the Leucine zipper proteins. (studentreader.com)
  • Zinc finger: Two beta strands with an alpha helix end folded over to bind a zinc ion. (wikipedia.org)
  • PR domain zinc finger protein 9 is a protein that in humans is encoded by the Prdm9 gene. (wikipedia.org)
  • PRDM9 has multiple domains including KRAB domain, SSXRD, PR/SET domain (H3K4 & H3K36 trimethyltransferase), and an array of C2H2 Zinc Finger domains (DNA binding). (wikipedia.org)
  • These hotspots are binding sites for the PRDM9 Zinc Finger array. (wikipedia.org)

transcription factors

  • We endow transcription factors with the ability to deposit a transposon into the genome near to where they bind. (genetics.org)
  • 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. (wikipedia.org)
  • 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. (wikipedia.org)
  • The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. (wikipedia.org)
  • Alternatively, transcription factors can bind enzymes that modify the histones at the promoter. (wikipedia.org)
  • 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. (wikipedia.org)
  • ID proteins also contain the HLH-dimerization domain but lack the basic DNA-binding domain and thus regulate bHLH transcription factors when they heterodimerize with bHLH proteins. (wikipedia.org)
  • In normal development, E proteins form dimers with other bHLH transcription factors, allowing transcription to occur. (wikipedia.org)
  • One vital role of facilitated diffusion is that it is the main mechanism behind the binding of Transcription Factors (TFs) to designated target sites on the DNA molecule. (wikipedia.org)

bHLH

  • E proteins are members of the class I bHLH family and form dimers with bHLH proteins from class II to regulate transctiption. (wikipedia.org)
  • ID proteins can bind E-proteins, preventing them from binding bHLH proteins and halting transcription, a case often seen in cancerous phenotypes. (wikipedia.org)
  • 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. (hindawi.com)

encodes

  • This gene encodes a DNA helicase that functions as a transcription repressor by remodeling chromatin structure. (nih.gov)
  • CHD8 encodes for a DNA helicase that function as a transcription repressor by remodeling chromatin structure by altering the position of nucleosomes. (wikipedia.org)

molecule

  • DNA is a negatively charged molecule due to the phosphate found in its backbone. (wikipedia.org)
  • The report provides comprehensive information on the TAR DNA-Binding Protein 43 (TDP-43), targeted therapeutics, complete with analysis by indications, stage of development, mechanism of action (MoA), route of administration (RoA) and molecule type. (reportsnreports.com)
  • Single molecule studies have shown that Dps-DNA complexes can get trapped in long-lived metastable states that exhibit hysteresis. (wikipedia.org)
  • the other helps to keep the binding helix properly positioned with respect to the rest of the molecule. (studentreader.com)
  • In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules. (wikipedia.org)
  • This procedure can determine if a protein or mixture of proteins is capable of binding to a given DNA or RNA sequence, and can sometimes indicate if more than one protein molecule is involved in the binding complex. (wikipedia.org)
  • Single-molecule imaging is an imaging technique which provides an ideal resolution necessary for the study of the Transcription factor binding mechanism in living cells. (wikipedia.org)

structural

  • Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. (wikipedia.org)
  • Within chromosomes, DNA is held in complexes with structural proteins. (wikipedia.org)
  • When H-NS is bound with RNA Polymerase to the promoter region, there are structural differences in the DNA that are accessible. (wikipedia.org)
  • 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. (studentreader.com)
  • Motivation: Template-based prediction of DNA binding proteins requires not only structural similarity between target and template structures but also prediction of binding affinity between the target and DNA to ensure binding. (edu.au)
  • Results: We showed that this energy function together with the structural alignment program TM-align achieves the Matthews correlation coefficient (MCC) of 0.76 with an accuracy of 98%, a precision of 93% and a sensitivity of 64%, for predicting DNA binding proteins in a benchmark of 179 DNA binding proteins and 3797 nonbinding proteins. (edu.au)
  • However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
  • In proteins, a structural motif describes the connectivity between secondary structural elements. (wikipedia.org)
  • In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. (wikipedia.org)
  • Sequence motif Short linear motif PROSITE Database of protein families and domains SCOP Structural classification of Proteins CATH Class Architecture Topology Homology FSSP FSSP PASS2 PASS2 - Protein Alignments as Structural Superfamilies SMoS SMoS - Database of Structural Motifs of Superfamily S4 S4: Server for Super-Secondary Structure Motif Mining Chiang YS, Gelfand TI, Kister AE, Gelfand IM (2007). (wikipedia.org)

bacterial

  • Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. (wikipedia.org)
  • 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. (wikipedia.org)
  • Initially, bacterial DNA binding proteins were thought to help stabilize bacterial DNA. (wikipedia.org)
  • HU is a small (10 kDa) bacterial histone-like protein that resembles the eukaryotic Histone H2B. (wikipedia.org)
  • DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. (wikipedia.org)
  • This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins. (studentreader.com)
  • The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. (st-andrews.ac.uk)
  • Bauer & Metzler (2013) therefore carried out an experiment using a bacterial genome in which they investigated the average time for TF - DNA binding to occur. (wikipedia.org)

Chromosome

  • 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 protected from diverse damages. (wikipedia.org)

complexes

  • Inhibits the binding of E2A-containing protein complexes to muscle creatine kinase E-box enhancer. (rcsb.org)
  • Hello, I got some advice a while ago from DK on storage of protein:DNA complexes. (bio.net)

regulate transcription

  • However, in cancerous phenotypes, ID proteins can regulate transcription by binding E proteins, so no dimers can be formed and transcription is inactive. (wikipedia.org)

sequence

  • 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. (wikipedia.org)
  • 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. (wikipedia.org)
  • 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. (wikipedia.org)
  • The GCN4 transcription activator in yeast is a dimer in which the leucine zipper region helps to position the two basic regions that bind to the DNA recognition sequence. (studentreader.com)
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" structure. (wikipedia.org)
  • In 1991 a protein binding to the minisatelite consensus sequence 5′-CCACCTGCCCACCTCT-3′ was detected and partially purified (named Msbp3 - minisatelite binding protein 3). (wikipedia.org)
  • If the starting concentrations of protein and probe are known, and if the stoichiometry of the complex is known, the apparent affinity of the protein for the nucleic acid sequence may be determined. (wikipedia.org)
  • The use of different oligonucleotides of defined sequence allows the identification of the precise binding site by competition (not shown in diagram). (wikipedia.org)
  • Consensus sequence oligonucleotides for the transcription factor of interest will be able to compete for the binding, eliminating the shifted band, and must be confirmed by supershift. (wikipedia.org)
  • If the predicted consensus sequence fails to compete for binding, identification of the transcription factor may be aided by Multiplexed Competitor EMSA (MC-EMSA), whereby large sets of consensus sequences are multiplexed in each reaction, and where one set competes for binding, the individual consensus sequences from this set are run in a further reaction. (wikipedia.org)
  • A Southern blot is a method routinely used in molecular biology for detection of a specific DNA sequence in DNA samples. (wikipedia.org)

affinity

  • Following elution, the protein readily binds DNA, indicating the protein's high affinity for DNA. (wikipedia.org)
  • With an α-helical hydrophobic core and two positively charged β-ribbon arms, HU binds non-specifically to dsDNA with low affinity but binds to altered DNA-such as junctions, nicks, gaps, forks, and overhangs-with high affinity. (wikipedia.org)
  • Here, we propose to predict protein- DNA binding affinity by introducing a new volume-fraction correction to a statistical energy function based on a distance-scaled, finite, ideal-gas reference (DFIRE) state. (edu.au)
  • An electrophoretic mobility shift assay (EMSA) or mobility shift electrophoresis, also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel retardation assay, is a common affinity electrophoresis technique used to study protein-DNA or protein-RNA interactions. (wikipedia.org)
  • While isotopic DNA labeling has little or no effect on protein binding affinity, use of non-isotopic labels including flurophores or biotin can alter the affinity and/or stoichiometry of the protein interaction of interest. (wikipedia.org)

sequences

  • In contrast, other proteins have evolved to bind to specific DNA sequences. (wikipedia.org)
  • 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. (hindawi.com)
  • 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 ]. (hindawi.com)
  • The Reverse Northern blot differs from both Northern and Southern blotting in that DNA is first immobilized on a blotting matrix and specific sequences are detected with labeled RNA probes. (wikipedia.org)

posttranslational modifications

  • The Eastern blot is used for the detection of specific posttranslational modifications of proteins. (wikipedia.org)
  • Proteins are separated by gel electrophoresis before being transferred to a blotting matrix whereupon posttranslational modifications are detected by specific substrates (cholera toxin, concanavalin, phosphomolybdate, etc.) or antibodies. (wikipedia.org)

damage-binding

  • DNA damage-binding protein or UV-DDB is a protein complex that is responsible for repair of UV-damaged DNA. (wikipedia.org)

nucleus

  • Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. (wikipedia.org)
  • When cells are exposed to UV radiation, DDB1 moves from the cytosol to the nucleus and binds to DDB2, thus forming the UV-DDB complex. (wikipedia.org)

biological

  • Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions. (wikipedia.org)
  • p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
  • In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
  • Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions. (wikipedia.org)
  • Facilitated diffusion (also known as facilitated transport or passive-mediated transport) is the process of spontaneous passive transport (as opposed to active transport) of molecules or ions across a biological membrane via specific transmembrane integral proteins. (wikipedia.org)

interact

  • The double chromodomains of CHD1 adopt an 'open pocket' to interact with the free N-terminal amine of H3K4, and the open pocket permits the NS1 mimic to bind in a distinct conformation. (nih.gov)

interactions

  • We describe a method for permanently recording protein-DNA interactions in mammalian cells. (genetics.org)
  • Similar to a Western blot, the Far-Western blot uses protein-protein interactions to detect the presence of a specific protein immobilized on a blotting matrix. (wikipedia.org)
  • Northern blot for RNA Reverse Northern blot for RNA Western blot for proteins Far-Western blot for protein-protein interactions Eastern blotting for posttranslational modification Far-Eastern blot for glycolipids Dot blot Immunoscreening Towbin et al. (wikipedia.org)

processes

  • Thus, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. (wikipedia.org)

eukaryotes

  • In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones. (wikipedia.org)

conformation

  • Larger molecules are transported by transmembrane carrier proteins, such as permeases, that change their conformation as the molecules are carried across (e.g. glucose or amino acids). (wikipedia.org)

interaction

  • Under the correct experimental conditions, the interaction between the DNA (or RNA) and protein is stabilized and the ratio of bound to unbound nucleic acid on the gel reflects the fraction of free and bound probe molecules as the binding reaction enters the gel. (wikipedia.org)

polymerase

  • This alters the accessibility of the DNA template to the polymerase. (wikipedia.org)
  • the protein is involved in stabilizing the lagging strand as well as interacting with DNA polymerase III. (wikipedia.org)
  • It has been found that H-NS and RNA polymerase both bind to the P1 promoter and form a complex. (wikipedia.org)

molecular biology

  • In molecular biology, the protein domain SAND is named after a range of proteins in the protein family: Sp100, AIRE-1, NucP41/75, DEAF-1. (wikipedia.org)
  • A blot, in molecular biology and genetics, is a method of transferring proteins, DNA or RNA, onto a carrier (for example, a nitrocellulose, polyvinylidene fluoride (PVDF) or nylon membrane). (wikipedia.org)

Nonpolar

  • Hence, no nonpolar molecules are transported by proteins in the form of transmembrane channels. (wikipedia.org)

Inhibits

  • citation needed] Spermidine's known actions include: Inhibits neuronal nitric oxide synthase (nNOS) Binds and precipitates DNA Polyamine plant growth regulator Good dietary sources of spermidine are aged cheese, mushrooms, soy products, legumes, corn, and whole grains. (wikipedia.org)

coli

  • In E. coli, H-NS binds to a P1 promoter decreasing rRNA production during stationary and slow growth periods. (wikipedia.org)
  • In prokaryotic bacteria cells such as E. coli, facilitated diffusion is required in order for regulatory proteins to locate and bind to target sites on DNA base pairs. (wikipedia.org)

DDB2

  • This complex is composed of two protein subunits, a large subunit DDB1 (p127) and a small subunit DDB2 (p48). (wikipedia.org)
  • Damaged DNA-binding protein 2 DDB2 protects against UV irradiation in human cells and Drosophila - Descarga este documento en PDF. (duhnnae.com)
  • BackgroundWe observed previously that cisplatin-resistant HeLa cells were cross-resistant to UV light due to accumulation of DDB2, a protein implicated in DNA repair. (duhnnae.com)
  • More recently, we found that cFLIP, which represents an anti-apoptotic protein whose level is induced by DDB2, was implicated in preventing apoptosis induced by death-receptor signaling. (duhnnae.com)
  • In addition, the cFLIP protein could be induced by stable expression of DDB2 in these cells. (duhnnae.com)

nucleotides

  • At lower salt concentrations, the (SSB)35 binding mode, in which about 35 nucleotides bind to only two of the SSB subunits, tends to form. (wikipedia.org)

electrophoretic

  • A mobility shift assay is electrophoretic separation of a protein-DNA or protein-RNA mixture on a polyacrylamide or agarose gel for a short period (about 1.5-2 hr for a 15- to 20-cm gel). (wikipedia.org)

dissociation

  • Variants of the competition assay are useful for measuring the specificity of binding and for measurement of association and dissociation kinetics. (wikipedia.org)

subunit

  • The TATA box binding protein is a subunit of the eukaryotic transcription factor, TFIID. (studentreader.com)

fragment

  • RESULTS: Analysis of proteins binding to a DNA fragment containing the mec operator region identified a novel, putative helix-turn-helix DNA-binding protein, SA1665. (uzh.ch)
  • The control lane (DNA probe without protein present) will contain a single band corresponding to the unbound DNA or RNA fragment. (wikipedia.org)
  • However, assuming that the protein is capable of binding to the fragment, the lane with protein present will contain another band that represents the larger, less mobile complex of nucleic acid probe bound to protein which is 'shifted' up on the gel (since it has moved more slowly). (wikipedia.org)
  • When using a biotin label, streptavidin conjugated to an enzyme such as horseradish peroxidase is used to detect the DNA fragment. (wikipedia.org)
  • Southern blotting combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization. (wikipedia.org)

minor groove

  • This protein is somewhat unusual in that its TBP-binding domain binds to the minor groove of DNA. (studentreader.com)

purification

  • May be used for purification of DNA-binding proteins. (wikipedia.org)

differentiation

  • both proteins cooperate in myoblast differentiation (By similarity). (rcsb.org)
  • ID proteins are key regulators of development where they function to prevent premature differentiation of stem cells. (wikipedia.org)
  • By inhibiting the formation of E-protein dimers that promote differentiation, ID proteins can regulate the timing of differentiation of stem cells during development. (wikipedia.org)

leucine zipper

  • A variation of the leucine zipper, the basic DNA-binding helices are connected to the dimerization helices by a short loop. (studentreader.com)

novel

  • Here we searched for novel proteins binding to the mec operator, in an attempt to identify new factor(s) controlling methicillin resistance phenotypes. (uzh.ch)
  • Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)
  • Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (hindawi.com)

motif

  • This motif was first noticed as a feature of the crystal structure of the bacteriophage l Cro protein. (studentreader.com)

locates

  • There are 2 main steps involved: 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 process referred to as sliding. (wikipedia.org)

eukaryotic

  • They are commonly referred to as histone-like and have many similar traits with the eukaryotic histone proteins. (wikipedia.org)
  • 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. (wikipedia.org)
  • This domain is common in eukaryotic DNA-binding proteins. (studentreader.com)
  • This domain is an important feature of many eukaryotic regulatory proteins. (studentreader.com)

Deletion

  • The rpa3, rpa3ap and the rpa3 operon deletion mutants showed sensitivity to DNA damage but only a slight growth defect. (nottingham.ac.uk)
  • The double rpa1 rpa3 operon deletion was difficult to generate but unexpectedly lacked a significant DNA damage sensitivity and growth defect. (nottingham.ac.uk)

signal transduction

  • HMGB1-LPS complex activates TLR4, and causes the binding of adapter proteins (MyD88 and others), leading to signal transduction and the activation of various signaling cascades. (wikipedia.org)

regulatory

  • The structure of this small regulatory protein contained two a-helices separated by 34 Ã… - the pitch of a DNA double helix. (studentreader.com)

targets

  • These DNA targets can occur throughout an organism's genome. (wikipedia.org)
  • ID proteins could be potential targets for systemic cancer therapies without inhibiting the functioning of most normal cells because they are highly expressed in embryonic stem cells, but not in differentiated adult cells. (wikipedia.org)
  • Also, on the DNA contour, the motion is slower and target sites are easy to localize while in the cytoplasm, the motion is faster but the TF's are not sensitive to their targets and so binding is restricted. (wikipedia.org)

ssDNA

  • One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. (st-andrews.ac.uk)
  • Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. (st-andrews.ac.uk)

gene expression

  • 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. (wikipedia.org)
  • Helix-turn-helix: Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression. (wikipedia.org)

histones

  • Like the histones, HMGB1 is among the most important chromatin proteins. (wikipedia.org)
  • This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. (wikipedia.org)