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.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
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.
Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.
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)
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.
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).
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
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.
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.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.
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.
Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.
Established cell cultures that have the potential to propagate indefinitely.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
A specificity protein transcription factor that regulates expression of a variety of genes including VASCULAR ENDOTHELIAL GROWTH FACTOR and CYCLIN-DEPENDENT KINASE INHIBITOR P27.
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)
Nucleic acid sequences involved in regulating the expression of genes.
An electrochemical process in which macromolecules or colloidal particles with a net electric charge migrate in a solution under the influence of an electric current.
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.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
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.
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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.
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.
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.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
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.
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.
Ubiquitously expressed basic HELIX-LOOP-HELIX MOTIF transcription factors. They bind CANNTG sequences in the promoters of a variety of GENES involved in carbohydrate and lipid metabolism.
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.
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.
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.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
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.
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.
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.
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.
Proteins found in any species of bacterium.
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.
A family of inhibitory proteins which bind to the REL PROTO-ONCOGENE PROTEINS and modulate their activity. In the CYTOPLASM, I-kappa B proteins bind to the transcription factor NF-KAPPA B. Cell stimulation causes its dissociation and translocation of active NF-kappa B to the nucleus.
A component of NF-kappa B transcription factor. It is proteolytically processed from NF-kappa B p105 precursor protein and is capable of forming dimeric complexes with itself or with TRANSCRIPTION FACTOR RELA. It regulates expression of GENES involved in immune and inflammatory responses.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
A heterotrimeric DNA-binding protein that binds to CCAAT motifs in the promoters of eukaryotic genes. It is composed of three subunits: A, B and C.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
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.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
A subunit of NF-kappa B that is primarily responsible for its transactivation function. It contains a C-terminal transactivation domain and an N-terminal domain with homology to PROTO-ONCOGENE PROTEINS C-REL.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Cellular DNA-binding proteins encoded by the c-jun genes (GENES, JUN). They are involved in growth-related transcriptional control. There appear to be three distinct functions: dimerization (with c-fos), DNA-binding, and transcriptional activation. Oncogenic transformation can take place by constitutive expression of c-jun.
A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.
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).
A protein that has been shown to function as a calcium-regulated transcription factor as well as a substrate for depolarization-activated CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES. This protein functions to integrate both calcium and cAMP signals.
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.
A cell line derived from cultured tumor cells.
A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
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.
Proteins prepared by recombinant DNA technology.
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.
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.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
An early growth response transcription factor that has been implicated in regulation of CELL PROLIFERATION and APOPTOSIS.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Carbamates in which the -CO- group has been replaced by a -CS- group.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
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.
Serum glycoprotein produced by activated MACROPHAGES and other mammalian MONONUCLEAR LEUKOCYTES. It has necrotizing activity against tumor cell lines and increases ability to reject tumor transplants. Also known as TNF-alpha, it is only 30% homologous to TNF-beta (LYMPHOTOXIN), but they share TNF RECEPTORS.
An ets proto-oncogene expressed primarily in adult LYMPHOID TISSUE; BRAIN; and VASCULAR ENDOTHELIAL CELLS.
A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
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.
A cellular transcriptional coactivator that was originally identified by its requirement for the stable assembly IMMEDIATE-EARLY PROTEINS of the HERPES SIMPLEX VIRUS. It is a nuclear protein that is a transcriptional coactivator for a number of transcription factors including VP16 PROTEIN; GA-BINDING PROTEIN; EARLY GROWTH RESPONSE PROTEIN 2; and E2F4 TRANSCRIPTION FACTOR. It also interacts with and stabilizes HERPES SIMPLEX VIRUS PROTEIN VMW65 and helps regulate GENETIC TRANSCRIPTION of IMMEDIATE-EARLY GENES in HERPES SIMPLEX VIRUS.
A 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.
The in vitro fusion of GENES by RECOMBINANT DNA techniques to analyze protein behavior or GENE EXPRESSION REGULATION, or to merge protein functions for specific medical or industrial uses.
Transcription factors that were originally identified as site-specific DNA-binding proteins essential for DNA REPLICATION by ADENOVIRUSES. They play important roles in MAMMARY GLAND function and development.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
A ubiquitously expressed zinc finger-containing protein that acts both as a repressor and activator of transcription. It interacts with key regulatory proteins such as TATA-BINDING PROTEIN; TFIIB; and ADENOVIRUS E1A 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.
DNA locations with the consensus sequence CANNTG. ENHANCER ELEMENTS may contain multiple copies of this element. E-boxes play a regulatory role in the control of transcription. They bind with basic helix-loop-helix (bHLH) type TRANSCRIPTION FACTORS. Binding specificity is determined by the specific bHLH heterodimer or homodimer combination and by the specific nucleotides at the 3rd and 4th position of the E-box sequence.
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
Intracellular receptors that can be found in the cytoplasm or in the nucleus. They bind to extracellular signaling molecules that migrate through or are transported across the CELL MEMBRANE. Many members of this class of receptors occur in the cytoplasm and are transported to the CELL NUCLEUS upon ligand-binding where they signal via DNA-binding and transcription regulation. Also included in this category are receptors found on INTRACELLULAR MEMBRANES that act via mechanisms similar to CELL SURFACE RECEPTORS.
A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
Proteins that are coded by immediate-early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals.
A family of low-molecular weight, non-histone proteins found in chromatin.
A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.
A heterotetrameric transcription factor composed of two distinct proteins. Its name refers to the fact it binds to DNA sequences rich in GUANINE and ADENINE. GA-binding protein integrates a variety of SIGNAL TRANSDUCTION PATHWAYS and regulates expression of GENES involved in CELL CYCLE control, PROTEIN BIOSYNTHESIS, and cellular METABOLISM.
A soluble factor produced by MONOCYTES; MACROPHAGES, and other cells which activates T-lymphocytes and potentiates their response to mitogens or antigens. Interleukin-1 is a general term refers to either of the two distinct proteins, INTERLEUKIN-1ALPHA and INTERLEUKIN-1BETA. The biological effects of IL-1 include the ability to replace macrophage requirements for T-cell activation.
Cellular DNA-binding proteins encoded by the c-fos genes (GENES, FOS). They are involved in growth-related transcriptional control. c-fos combines with c-jun (PROTO-ONCOGENE PROTEINS C-JUN) to form a c-fos/c-jun heterodimer (TRANSCRIPTION FACTOR AP-1) that binds to the TRE (TPA-responsive element) in promoters of certain genes.
In eukaryotes, a genetic unit consisting of a noncontiguous group of genes under the control of a single regulator gene. In bacteria, regulons are global regulatory systems involved in the interplay of pleiotropic regulatory domains and consist of several OPERONS.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.
Biochemical identification of mutational changes in a nucleotide sequence.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
A CCAAT-enhancer-binding protein found in LIVER; INTESTINES; LUNG and ADIPOSE TISSUE. It is an important mediator of INTERLEUKIN-6 signaling.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
An activating transcription factor that regulates expression of a variety of genes including C-JUN GENES and TRANSFORMING GROWTH FACTOR BETA2.
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.
Proteins found usually in the cytoplasm or nucleus that specifically bind steroid hormones and trigger changes influencing the behavior of cells. The steroid receptor-steroid hormone complex regulates the transcription of specific genes.
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.
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.
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).
Deoxyribonucleic acid that makes up the genetic material of bacteria.
A tricyclic pentaglycosidic antibiotic from Streptomyces strains that inhibits RNA and protein synthesis by adhering to DNA. It is used as a fluorescent dye and as an antineoplastic agent, especially in bone and testicular tumors. Plicamycin is also used to reduce hypercalcemia, especially that due to malignancies.
The relationship between the dose of an administered drug and the response of the organism to the drug.
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.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A phorbol ester found in CROTON OIL with very effective tumor promoting activity. It stimulates the synthesis of both DNA and RNA.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A subfamily of nuclear receptors that regulate GENETIC TRANSCRIPTION of a diverse group of GENES involved in the synthesis of BLOOD COAGULATION FACTORS; and in GLUCOSE; CHOLESTEROL; and FATTY ACIDS metabolism.
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.
A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.
The rate dynamics in chemical or physical systems.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A sub-family of steroid receptor-related orphan nuclear receptors that have specificity for a variety of DNA sequences related to AGGTCA. COUP transcription factors can heterodimerize with a variety of factors including RETINOIC ACID RECEPTORS; THYROID HORMONE RECEPTORS; and VITAMIN D RECEPTORS.
A subtype of RETINOIC ACID RECEPTORS that are specific for 9-cis-retinoic acid which function as nuclear TRANSCRIPTION FACTORS that regulate multiple signaling pathways.
A family of transcription factors that contain regions rich in basic residues, LEUCINE ZIPPER domains, and HELIX-LOOP-HELIX MOTIFS.
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.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
Proteins in the nucleus or cytoplasm that specifically bind RETINOIC ACID or RETINOL and trigger changes in the behavior of cells. Retinoic acid receptors, like steroid receptors, are ligand-activated transcription regulators. Several types have been recognized.
Lipid-containing polysaccharides which are endotoxins and important group-specific antigens. They are often derived from the cell wall of gram-negative bacteria and induce immunoglobulin secretion. The lipopolysaccharide molecule consists of three parts: LIPID A, core polysaccharide, and O-specific chains (O ANTIGENS). When derived from Escherichia coli, lipopolysaccharides serve as polyclonal B-cell mitogens commonly used in laboratory immunology. (From Dorland, 28th ed)
Compounds or agents that combine with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
Elements of limited time intervals, contributing to particular results or situations.
Proteins found in any species of virus.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
Specific high affinity binding proteins for THYROID HORMONES in target cells. They are usually found in the nucleus and regulate DNA transcription. These receptors are activated by hormones that leads to transcription, cell differentiation, and growth suppression. Thyroid hormone receptors are encoded by two genes (GENES, ERBA): erbA-alpha and erbA-beta for alpha and beta thyroid hormone receptors, respectively.
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.
A signal transducer and activator of transcription that mediates cellular responses to INTERFERONS. Stat1 interacts with P53 TUMOR SUPPRESSOR PROTEIN and regulates expression of GENES involved in growth control and APOPTOSIS.
Caustic extract from the roots of Podophyllum peltatum and P. emodi. It contains PODOPHYLLOTOXIN and its congeners and is very irritating to mucous membranes and skin. Podophyllin is a violent purgative that may cause CNS damage and teratogenesis. It is used as a paint for warts, skin neoplasms, and senile keratoses.
An interferon regulatory factor that binds upstream TRANSCRIPTIONAL REGULATORY ELEMENTS in the GENES for INTERFERON-ALPHA and INTERFERON-BETA. It functions as a transcriptional activator for the INTERFERON TYPE I genes.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
A forkhead transcription factor that regulates expression of metabolic GENES and is involved in EMBRYONIC DEVELOPMENT. Mutations in HNF-3beta have been associated with CONGENITAL HYPERINSULINISM.
Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.
An increase in the rate of synthesis of an enzyme due to the presence of an inducer which acts to derepress the gene responsible for enzyme synthesis.
A signal transducer and activator of transcription that mediates cellular responses to INTERLEUKIN-6 family members. STAT3 is constitutively activated in a variety of TUMORS and is a major downstream transducer for the CYTOKINE RECEPTOR GP130.
A member of the CXC chemokine family that plays a role in the regulation of the acute inflammatory response. It is secreted by variety of cell types and induces CHEMOTAXIS of NEUTROPHILS and other inflammatory cells.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.
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.
Difficulty in walking from place to place.
A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.
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.
A family of transcription factors characterized by the presence of highly conserved calcineurin- and DNA-binding domains. NFAT proteins are activated in the CYTOPLASM by the calcium-dependent phosphatase CALCINEURIN. They transduce calcium signals to the nucleus where they can interact with TRANSCRIPTION FACTOR AP-1 or NF-KAPPA B and initiate GENETIC TRANSCRIPTION of GENES involved in CELL DIFFERENTIATION and development. NFAT proteins stimulate T-CELL activation through the induction of IMMEDIATE-EARLY GENES such as INTERLEUKIN-2.
Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
Transport proteins that carry specific substances in the blood or across cell membranes.
A superfamily of PROTEIN-SERINE-THREONINE KINASES that are activated by diverse stimuli via protein kinase cascades. They are the final components of the cascades, activated by phosphorylation by MITOGEN-ACTIVATED PROTEIN KINASE KINASES, which in turn are activated by mitogen-activated protein kinase kinase kinases (MAP KINASE KINASE KINASES).
An essential GATA transcription factor that is expressed primarily in HEMATOPOIETIC STEM CELLS.
Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.
One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.
A CALCIUM-independent subtype of nitric oxide synthase that may play a role in immune function. It is an inducible enzyme whose expression is transcriptionally regulated by a variety of CYTOKINES.
Deoxyribonucleic acid that makes up the genetic material of viruses.
Single pavement layer of cells which line the luminal surface of the entire vascular system and regulate the transport of macromolecules and blood components.
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
An activating transcription factor that regulates expression of a variety of GENES including C-JUN GENES; CYCLIN A; CYCLIN D1; and ACTIVATING TRANSCRIPTION FACTOR 3.
An inducibly-expressed subtype of prostaglandin-endoperoxide synthase. It plays an important role in many cellular processes and INFLAMMATION. It is the target of COX2 INHIBITORS.
A family of zinc finger transcription factors that share homology with Kruppel protein, Drosophila. They contain a highly conserved seven amino acid spacer sequence in between their ZINC FINGER MOTIFS.
A transcription factor that controls the expression of variety of proteins including CYTOCHROME C and 5-AMINOLEVULINATE SYNTHETASE. It plays an important role in maintenance of the RESPIRATORY CHAIN of MITOCHONDRIA.
Hepatocyte nuclear factor 1-alpha is a transcription factor found in the LIVER; PANCREAS; and KIDNEY that regulates HOMEOSTASIS of GLUCOSE.
A cytokine that stimulates the growth and differentiation of B-LYMPHOCYTES and is also a growth factor for HYBRIDOMAS and plasmacytomas. It is produced by many different cells including T-LYMPHOCYTES; MONOCYTES; and FIBROBLASTS.
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.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
A family of transcription factors that control expression of a variety of nuclear GENES encoding proteins that function in the RESPIRATORY CHAIN of the MITOCHONDRIA.
Retrovirus-associated DNA sequences (jun) originally isolated from the avian sarcoma virus 17 (ASV 17). The proto-oncogene jun (c-jun) codes for a nuclear protein which is involved in growth-related transcriptional control. Insertion of c-jun into ASV-17 or the constitutive expression of the c-jun protein produces tumorgenicity. The human c-jun gene is located at 1p31-32 on the short arm of chromosome 1.
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.
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.
Fushi tarazu transcription factors were originally identified in DROSOPHILA. They are found throughout ARTHROPODS and play important roles in segmentation and CENTRAL NERVOUS SYSTEM development.
The sum of the weight of all the atoms in a molecule.
Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
A transcription factor and member of the nuclear receptor family NR5 that is expressed throughout the adrenal and reproductive axes during development. It plays an important role in sexual differentiation, formation of primary steroidogenic tissues, and their functions in post-natal and adult life. It regulates the expression of key steroidogenic enzymes.
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.
A family of transcription factors characterized by the presence of a bipartite DNA-binding domain known as the POU domain. The POU domain contains two subdomains, a POU-specific domain and a POU-homeodomain. The POU domain was originally identified as a region of approximately 150 amino acids shared between the Pit-1, Oct-1, Oct-2, and Unc-86 transcription factors.
Eukaryotic cell line obtained in a quiescent or stationary phase which undergoes conversion to a state of unregulated growth in culture, resembling an in vitro tumor. It occurs spontaneously or through interaction with viruses, oncogenes, radiation, or drugs/chemicals.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.
A CELL LINE derived from human T-CELL LEUKEMIA and used to determine the mechanism of differential susceptibility to anti-cancer drugs and radiation.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
A GATA transcription factor that is expressed in the MYOCARDIUM of developing heart and has been implicated in the differentiation of CARDIAC MYOCYTES. GATA4 is activated by PHOSPHORYLATION and regulates transcription of cardiac-specific genes.
Cellular DNA-binding proteins encoded by the rel gene (GENES, REL). They are expressed predominately in hematopoietic cells and may play a role in lymphocyte differentiation. Rel frequently combines with other related proteins (NF-KAPPA B, I-kappa B, relA) to form heterodimers that regulate transcription. Rearrangement or overexpression of c-rel can cause tumorigenesis.

Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. (1/4336)

The ordered assembly of immunoglobulin and TCR genes by V(D)J recombination depends on the regulated accessibility of individual loci. We show here that the histone tails and intrinsic nucleosome structure pose significant impediments to V(D)J cleavage. However, alterations to nucleosome structure via histone acetylation or by stable hSWI/SNF-dependent remodeling greatly increase the accessibility of nucleosomal DNA to V(D)J cleavage. Moreover, acetylation and hSWI/SNF remodeling can act in concert on an individual nucleosome to achieve levels of V(D)J cleavage approaching those observed on naked DNA. These results are consistent with a model in which regulated recruitment of chromatin modifying activities is involved in mediating the lineage and stage-specific control of V(D)J recombination.  (+info)

An RNA-binding chameleon. (2/4336)

The arginine-rich RNA binding motif is found in a wide variety of proteins, including several viral regulatory proteins. Although related at the primary sequence level, arginine-rich domains from different proteins adopt different conformations depending on the RNA site recognized, and in some cases fold only in the context of RNA. Here we show that the RNA binding domain of the Jembrana disease virus (JDV) Tat protein is able to recognize two different TAR RNA sites, from human and bovine immunodeficiency viruses (HIV and BIV, respectively), adopting different conformations in the two RNA contexts and using different amino acids for recognition. In addition to the conformational differences, the JDV domain requires the cyclin T1 protein for high-affinity binding to HIV TAR, but not to BIV TAR. The "chameleon-like" behavior of the JDV Tat RNA binding domain reinforces the concept that RNA molecules can provide structural scaffolds for protein folding, and suggests mechanisms for evolving distinct RNA binding specificities from a single multifunctional domain.  (+info)

Activation of telomerase rna gene promoter activity by NF-Y, Sp1, and the retinoblastoma protein and repression by Sp3. (3/4336)

Expression of the human telomerase RNA component gene, hTERC is essential for telomerase activity. The hTERC gene is expressed during embryogenesis and then downregulated during normal development, leaving most adult somatic cells devoid of hTERC expression. During oncogenesis, however, hTERC is re-expressed consequently contributing to the unrestricted proliferative capacity of many human cancers. Thus the identification of the molecular basis for the regulation of the telomerase RNA component gene in normal cells and its deregulation in cancer cells is of immediate interest. We have previously cloned the hTERC promoter and in this study have identified several transcription factors that modulate the expression of hTERC. We demonstrate that NF-Y binding to the CCAAT region of the hTERC promoter is essential for promoter activity. Sp1 and the retinoblastoma protein (pRb) are activators of the hTERC promoter and Sp3 is a potent repressor. These factors appear to act in a species-specific manner. Whereas Sp1 and Sp3 act on the human, bovine, and mouse TERC promoters, pRb activates only the human and bovine promoter, and NF-Y is only essential for the human TERC gene.  (+info)

Opposing regulation of choline deficiency-induced apoptosis by p53 and nuclear factor kappaB. (4/4336)

We have previously shown that fetal rat brain cells, preneuronal (PC12), and hepatocyte (CWSV-1) cells undergo apoptosis during choline deficiency (CD). The PC12 and epithelial cell culture models were used to determine the molecular mechanism by which CD induces apoptosis. Our data indicate that CD leads to both growth arrest and apoptosis in a subpopulation of cells, which correlate with the up-regulation of the tumor suppressor protein p53 and concurrent up-regulation of the cyclin-dependent kinase-inhibitor p21(WAF1/CIP1). Additionally, CD induced both a G1/S and a G2/M arrest. Transient transfection of a dominant negative p53 (p53DN) construct into PC12 cells, which inhibited endogenous p53 activation, significantly reduced the induction of apoptosis associated with CD. Interestingly, CD also induced the persistent activation of the transcription factor NF-kappaB. Activation of NF-kappaB has been shown to promote cell survival and proposed to antagonize p53. Consistent with this, expression of a super-repressor form of IkappaBalpha (SR-IkappaBalpha) that functions to strongly inhibit NF-kappaB activation, profoundly enhanced cell death during CD. In summary, these results suggest that the effects of CD on apoptosis and subsequent cell survival are mediated through two different signaling pathways, p53 and NF-kappaB, respectively. Taken together, our data demonstrates the induction of opposing mechanisms associated with nutrient deficiency that may provide a molecular mechanism by which CD promotes carcinogenesis.  (+info)

Induction of the transcriptional repressor Yin Yang-1 by vascular cell injury. Autocrine/paracrine role of endogenous fibroblast growth factor-2. (5/4336)

Yin Yang-1 (YY1) is a multifunctional transcription factor that can repress the expression of many growth factor, hormone, and cytokine genes implicated in atherogenesis. YY1 expression is activated in rat vascular smooth muscle cells shortly after injury. YY1 DNA binding activity paralleled elevated protein levels in the nucleus. Smooth muscle cell injury triggered the rapid extracellular release of immunoreactive fibroblast growth factor-2 (FGF-2). YY1 induction after injury was blocked by neutralizing antibodies directed against FGF-2. This growth factor increased YY1 mRNA and protein expression and stimulated YY1 binding and transcriptional activity. Overexpression of YY1 inhibited smooth muscle cell replication. Immunohistochemical analysis demonstrated YY1 staining in medial smooth muscle cells, coincident with FGF-2 expression. Proliferating cell nuclear antigen staining, in contrast, was confined mainly to the atherosclerotic intima. This is the first demonstration that YY1 is induced by either injury or FGF-2, is differentially expressed in normal and diseased human arteries, and that its overexpression inhibits vascular smooth muscle but not endothelial cell replication.  (+info)

Ingenol esters induce apoptosis in Jurkat cells through an AP-1 and NF-kappaB independent pathway. (6/4336)

BACKGROUND: Ingenol derivatives have received constant and multidisciplinary attention on account of their pleiotropic pattern of biological activity. This includes activation of protein kinase C (PKC), tumour-promotion, anticancer, and anti-HIV properties, and the possibility of dissecting co-cancerogenic and clinically useful activities has been demonstrated. Certain ingenol esters show powerful anticancer activity, and a structure-activity relationship model to discriminate between their apoptotic and non-apoptotic properties has been developed. RESULTS: The polyhydroxylated southern region of ingenol was selectively modified, using the anticancer and PKC activator ingenol 3,20-dibenzoate (IDB) as a lead compound. The evaluation of IDB analogues in apoptosis assays showed strict structure-activity relationships, benzoylation of the 20-hydroxyl being required to trigger apoptosis through a pathway involving caspase-3 and occurring at the specific cell cycle checkpoint that controls the S-M phase transition. Conversely, a study on the activation of the PKC-dependent transcription factors AP-1 and NF-kappaB by IDB analogues showed significant molecular flexibility, including tolerance to changes at the 3- and 20-hydroxyls. IDB-induced apoptosis was independent of activation of PKC, since it was not affected by treatment with the non-isoform-selective PKC inhibitor GF 109230X0. CONCLUSIONS: Remarkable deviations from the tumour-promotion pharmacophore were observed for both the apoptotic and the PKC-activating properties of IDB analogues, showing that ingenol is a viable template to selectively target crucial pathways involved in tumour promotion and development. Since the apoptotic and the PKC-activating properties of ingenoids are mediated by different pathways and governed by distinct structure-activity relationships, it is possible to dissect them by suitable chemical modification. In this context, the esterification pattern of the 5- and 20-hydroxyls is critical.  (+info)

CCAAT/enhancer-binding proteins alpha and beta negatively influence the capacity of tumor necrosis factor alpha to up-regulate the human cytomegalovirus IE1/2 enhancer/promoter by nuclear factor kappaB during monocyte differentiation. (7/4336)

Recently we demonstrated that the ability of tumor necrosis factor alpha (TNFalpha) to stimulate the human cytomegalovirus (HCMV) IE1/2 enhancer/promoter activity in myeloid progenitor-like cells decreases when these cells differentiate into promonocytic cells. In addition, TNFalpha stimulation in the progenitor-like cell line HL-60 was shown to be mediated by nuclear factor kappaB (NF-kappaB) activation and its binding to the 18-base pair sequence motifs of the IE1/2 enhancer. We demonstrate here that the cell differentiation-dependent reduction of TNFalpha stimulation is not due to insufficient NF-kappaB activation but correlates with increased synthesis of the monocyte differentiation-associated factors CCAAT/enhancer-binding protein (C/EBP) alpha and beta. Overexpression of C/EBPalpha/beta in HL-60 cells, which normally produce only very small amounts of C/EBP, stimulated the basal activity of the promoter in the absence of NF-kappaB but suppressed the stimulatory effect of TNFalpha. A novel C/EBP-binding site was identified in the IE1/2 enhancer directly downstream of a NF-kappaB site. In order to understand the mechanisms of interaction, we used an IE1/2 promoter mutant that failed to bind C/EBP at this position and several constructs that contained exclusively NF-kappaB- and/or C/EBP-binding sites upstream of the minimal IE1/2 promoter. We could demonstrate that C/EBPalpha/beta interacts with NF-kappaB p65 and displays inhibitory activity even in the absence of direct DNA binding by forming p65-C/EBP-containing protein complexes bound to the NF-kappaB site. Moreover, C/EBP binding to the DNA adjacent to NF-kappaB supports the down-regulatory effect of C/EBPs possibly due to stabilization of a multimeric NF-kappaB-C/EBP complex. Our results show that cell differentiation factors may interfere with TNFalpha-induced human cytomegalovirus gene (re)activation.  (+info)

Cloning and characterization of a novel mouse AP-2 transcription factor, AP-2delta, with unique DNA binding and transactivation properties. (8/4336)

AP-2 transcription factors are sequence-specific DNA-binding proteins expressed in neural crest and other tissues during mammalian development. Three mammalian genes, AP-2alpha, AP-2beta, and AP-2gamma, have been reported previously. A partial predicted AP-2 gene was identified in tandem with AP-2beta on human chromosome 6p12-p21.1. The orthologous mouse gene, which we named Ap-2delta, was identified from a fetal mouse head cDNA library. Northern analysis revealed two transcripts in embryonic and newborn mouse brain, with markedly higher steady-state levels in the former. The predicted Ap-2delta protein comprised 452 amino acids and was highly similar to other AP-2 proteins across the DNA-binding and dimerization domains. Ap-2delta formed homodimers and heterodimers in vitro, bound an optimized AP-2 consensus DNA sequence, and transactivated gene expression in eukaryotic cells. Ap-2delta dimers bound poorly to an AP-2 binding sequence from the human metallothionein IIa promoter in vitro, revealing a sequence specificity not previously observed among other AP-2 proteins. The PY motif and critical residues in the transactivation domain, which are highly conserved in the AP-2 family and believed necessary for transactivation, were divergent in Ap-2delta. The unique protein sequence and functional features of Ap-2delta suggest mechanisms, besides tissue-specific AP-2 gene expression, for specific control of target gene activation.  (+info)

Profacgen offers professional Electrophoretic Mobility Shift Assay (EMSA) service to help your study on DNA-protein interaction, RNA-protein interaction, and even DNA-RNA interaction.
Capillary electrophoretic mobility shift assay for binding of DNA with NFAT3, a transcription factor from H9c2 cardiac myoblast cells ...
TY - JOUR. T1 - Protein-deoxyribonucleic acid interactions linked to gene expression. T2 - electrophoretic mobility shift assay.. AU - Javed, Amjad. AU - Zaidi, Sayyed K.. AU - Gutierrez, Soraya E.. AU - Lengner, Christopher J.. AU - Harrington, Kimberly S.. AU - Hovhannisyan, Hayk. AU - Cho, Brian C.. AU - Pratap, Jitesh. AU - Pockwinse, Shirwin M.. AU - Montecino, Martin. AU - van Wijnen, André J.. AU - Lian, Jane B.. AU - Stein, Janet L.. AU - Stein, Gary S.. PY - 2004. Y1 - 2004. UR - http://www.scopus.com/inward/record.url?scp=5444248659&partnerID=8YFLogxK. M3 - Article. C2 - 15269397. AN - SCOPUS:5444248659. VL - 285. SP - 45. EP - 55. JO - Methods in molecular biology (Clifton, N.J.). JF - Methods in molecular biology (Clifton, N.J.). SN - 1064-3745. ER - ...
Die elektrophoretische Mobilität Shift-Assay (EMSA) ist eine biochemische Verfahren zur Bindung zwischen Proteinen und Nukleinsäuren zu erhellen. In dieser...
هنا نقدم بروتوكول لتحليل التفاعلات RNA / البروتين. ويستند هذا التحول فحص التنقل الكهربي (EMSA) ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
In article ,39t6d7$ja2 at nuscc.nus.sg,, sci30828 at leonis.nus.sg (C G PADMASHREE) writes: ,I am an inexperienced undergraduate who has been assigned a project on ,gel mobility shift assays involving binding of steroid hormones to their ,receptors.I request for help to find suitable references on this ,subject.Early help would be greatly appreciated.Thank you. , Try a reference availablr in most molecular biology labs: Ausubel et.al. (eds) Current protocols in Molecular Biology (Red Book) Volume 2, Chapter 12 DNA-Protein interactions Emmanuel ...
Kyle Tamshen, Robert Kousnetsov, and Amanda Dewey use electrophoretic mobility shift assays to analyze the interactions between protein LIN-31 and DNA from lin-39.. ...
Studying nucleic acid interactions with proteins can be accomplished using a rapid and efficient electrophoretic mobility shift assay (EMSA). This method is essentially an agarose gel electrophoresis technique that detects protein:nucleic acid interactions, as the mobility of the labeled nucleic acid will be retarded if bound to a protein (compared to unbound DNA). A lesser-known…. ...
Event Electromobility & Low Carbon Vehicles 2016-17. This course provides an understanding of the policy background and principles behind the concept of electromobility. Youll gain an understanding of the latest changes in research, legislation, ...
Furthermore, the examination of DNA-bound FOXO3a by electrophoretic mobility-shift assay demonstrated a marked increase in nuclear, DNA bound FOXO3a in GK rats with MI compared to Sham-GK and corresponding post-MI Wistar controls (Figure 5D). ...
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This kit is not sensitive enough for a complex mixuture of protein and RNA. This kit has most optimum results when used with a more purified sample. The analysis of a complex solution with low concentrations of the actual target molecule requires more sensitivity than fluorescence can provide. From Molecular Probes technical assistance ...
Gel shift assay: (aka gel mobility shift assay (GMSA), band shift assay (BSA), electrophoretic mobility shift assay (EMSA)) A method by which one can determine whether a particular protein preparation contains factors which bind to a particular DNA fragment. When a radiolabeled DNA fragment is run on a gel, it shows a characteristic mobility. If it is first incubated with a cellular extract of proteins (or with purified protein), any protein-DNA complexes will migrate slower than the naked DNA - a shifted band.. Gene: A unit of DNA which performs one function. Usually, this is equated with the production of one RNA or one protein. A gene contains coding regions, introns, untranslated regions and control regions.. Genome: The total DNA contained in each cell of an organism. Mammalian genomic DNA (including that of humans) contains 6x109 base pairs of DNA per diploid cell. There are somewhere in the order of a hundred thousand genes, including coding regions, 5 and 3 untranslated regions, ...
DNA binding capacity of Orf8 and Orf16 by electrophoretic mobility shift assays (EMSAs). Preparation of DNA substrate is graphically shown in panel A. US8 and U
Separation of antigens of low electrophoretic mobility by the method of immunofiltration 的翻译是:采用免疫渗滤法分离电泳迁移率较低的抗原 是什么意思?英文翻译中文,中文翻译英文,怎么说?-我要翻译网
Gentaur molecular products has all kinds of products like :search , Signosis 2011 \ GAS_ISRE EMSA Kit \ GS-0017 for more molecular products just contact us
Mobility & Seniors - |p|There is nothing nicer than seeing your horse or pony striding out soundly whether they are five or twenty five, but there may be periods when their mobility is not so good and this can be influenced by a number
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Hypocrea jecorina (anamorph Trichoderma reesei) is a filamentous ascomycete of industrial importance due to its hydrolases (e.g., xylanases and cellulases). The regulation of gene expression can influence the composition of the hydrolase cocktail, and thus, transcription factors are a major target of current research. Here, we design an approach for identifying a repressor of a xylanase-encoding gene. We used streptavidin affinity chromatography to isolate the Xylanase promoter-binding protein 1 (Xpp1). The optimal conditions and templates for the chromatography step were chosen according to the results of an electrophoretic mobility shift assay performed under repressing conditions, which yielded a DNA-protein complex specific to the AGAA-box (the previously identified, tetranucleotide cis-acting element). After isolating AGAA-box binding proteins, the eluted proteins were identified with Nano-HPLC/tandem MS-coupled detection. We compared the identified peptides to sequences in the H. jecorina genome
ERRα interacts with the mouse Sirt3 promoter in vitro and in vivo.A, Electrophoretic mobility shift assay was executed using a biotin probe. Biotin-labeled dou
Whether you purchased your mobility product from us or not, SpinLife® can help you locate and purchase the exact part you need! ...
EMSA troubleshooting - posted in Molecular Biology: Hi All, I am trying to optimize an EMSA to look at DNA binding by NF-kB. I started with 293T cells treated with TNF for either 30 or 60 minutes. I extracted the nuclear fraction using high salt buffer (420mM) with glycerol and checked for cytoplasmic contamination by western prior to performing the EMSA. The protein concentration of each sample was normalized using high salt buffer (i.e. the salt concentration in the binding reacti...
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Confused by the difference between mobility work & stretching? Learn how to properly structure a mobility plan and increase your performance.
As people age, they might suffer mobility issues. Discover how a proactive approach to improving mobility can prevent future complications in the Elderly.
Global Mobility - For almost two decades, Deloitte has taken a leadership role in advancing the World Economic Forums objective of
Global Mobility - For almost two decades, Deloitte has taken a leadership role in advancing the World Economic Forums objective of
FT is a complex trait with polygenic inheritance. While the genetic basis of FT has been widely studied in cereals by bi-parental linkage mapping and expression profiling, exploitation of the allelic and phenotypic variation of FT in rye by association studies has lagged behind [20, 21, 24]. This study reports the first candidate gene-based association studies in rye examining the genetic basis of FT.. Statistically significant SNP-FT associations were identified in nine candidate genes hypothesized to be involved in the frost responsive network among which the transcription factor Ice2 is one of the key factors. The function of Ice2 was characterized both in wheat and Arabidopsis [25, 26]. Over-expression of TaIce2 and AtIce2 in transgenic Arabidopsis plants resulted in increased FT of transgenic plants and was associated with higher expression levels of the Cbf gene family. Using electrophoresis mobility shift assays, Badawi et al. [25] further showed that TaIce2 binds to the promoter region ...
Epicatechin and cocoa metabolites caused an increase in ApoAI expression in HepG2 cells. Electrophoretic mobility shift assays revealed the involvement of Sites A and B of the ApoAI promoter in the induction of ApoAI mRNA upon incubation with cocoa metabolites. Using supershift assays, we demonstrated the binding of HNF-3β, HNF-4, ER-α, and RXR-α to Site A and the binding of HNF-3β, NFY, and Sp1 to Site B. Luciferase assays performed with a construct containing Site B confirmed its role in the upregulation of ApoAI by cocoa metabolites. Incubation with 3-methyl-epicatechin led to an increase in HNF-3β mRNA, HNF-3β, ER-α, Sp1, and NFY protein levels and the activation of ApoAI transcription mediated by NFY, Sp1, and ER-α. ...
MATERIALS AND METHODS: To this end, first, the MMPs inhibition factor was purified from an alkali-solubilized fraction of RJ (Apis mellifera) by C18 reverse-phase column chromatography and identified as 10-hydroxy-2-decenoic acid (10H2DA) by LTQ XL analysis. Next, examination was made of why 10H2DA could inhibit the activity of MMPs: With RASFs isolated from Rheumatoid tissues by enzymatic digestion, cultures in monolayers were treated with 10H2DA (0. 5, 1, 2mM) or PBS for 2h followed by stimulation with TNF-alpha (10ng/ml) for 2h, mRNA. Protein levels of MMP-1, MMP-3 were measured by real-time PCR and enzyme-linked immunosorbent assay(ELISA), the DNA binding activity of activator protein-1(AP-1) and nuclear factor kappaB (NF-kappaB) by electrophoretic mobility shift assay(EMSA), and the protein kinase activity of p38, ERK and JNK by kinase assay ...
How UL44 binds to DNA and the role of DNA binding in processivity function have not been yet elucidated. To begin to understand these mechanism, we characterized the interaction of UL44 with DNA by means of filter-binding assays and electrophoretic mobility shift assays (EMSA). We found that, similar to HSV-1 UL42, UL44 binds directly to DNA with nanomolar affinity in a manner that does not require ATP hydrolysis or accessory proteins. UL44 binds DNA as a dimer in a sequence-non specific manner and displays higher affinity for ds DNA compared to ss DNA. Affinity of UL44 for ds DNA decreases with increasing ionic strength and this effect is mediated by ion release, suggesting that DNA binding entails electrostatic interactions between the negatively charged phosphates on DNA backbone and the positive charge of basic residues on the back face and disordered loops of UL44 ...
The structure of Cas9 bound to AcrIIA4 suggested that the inhibitor competes for the initial DNA recognition event of PAM binding. However, we previously found that Cas9 binds so tightly to target DNA that its off-rate is negligible (7, 8). This implies an unusual nonequilibrium mode of inhibition, in which AcrIIA4 requires access to Cas9-sgRNA before formation of the Cas9-sgRNA-DNA complex. To test this prediction, we used biolayer interferometry (BLI) to measure the binding of catalytically inactivated Cas9 (dCas9) to a DNA target in the presence of an inhibitor. These experiments were performed under stoichiometric binding conditions in which Cas9 was present at concentrations greater than the dissociation constant of the Cas9-AcrIIA4 interaction. Preincubation of Cas9 with AcrIIA4 markedly inhibited Cas9 binding to DNA (on-rate) in a dose-dependent fashion, including complete prevention of target engagement (Fig. 3C and fig. S7). An electrophoretic mobility shift assay (EMSA) further ...
Methods The antitumor effect of C. crepidioides was evaluated in S-180-cell-bearing mice. Cell growth was assessed using a colorimetric assay. Nitrite and nitrate levels were measured by colorimetry. The expression levels of inducible NO synthase (iNOS) in murine RAW264.7 macrophages was assessed by reverse transcriptase-polymerase chain reaction. Activation of iNOS promoter was detected by reporter gene. Activation of nuclear factor-κB (NF-κB) was evaluated by electrophoretic mobility shift assay. The role of NF-κB signaling was analyzed using inhibitors of NF-κB and dominant-negative mutants, and Western blot analysis ...
Jurkat nuclear extract (1 day growth) for use in WB and EMSA. For studies related to T cells, viral infection (e.g HIV), cytokines, differentiation, and cancer.
In further experiments, EA.hy 926 cells were transiently transfected with different pGl3-Basic-derived constructs containing fragments of 1.6-kb to 0.33-kb of the human eNOS promoter cloned before a luciferase reporter gene. The 1.6-kb-eNOS-promoter-luciferase construct showed a significant (,7.5-fold) increase in (basal) promoter activity compared with pGl3-Basic. The nonstimulated activities of the shorter promoter fragments did not differ significantly from those of p-eNOS-1600-Hu-Luc: p-eNOS-1111-Hu-Luc had 118% ± 21% of p-eNOS-1600-Hu-Luc, p-eNOS-633-Hu-Luc 78% ± 20%, and p-eNOS-326-Hu-Luc 143% ± 37% (n = 3, each). The transfected cells were incubated for 24 h with either ethanol (1.25%, v/v) or the French wine L.Chevaliers (10%, v/v). The wine increased the activities of the 1.6-kb-, 1.1-kb-, and the 0.6-kb-promoter fragments more than 2.5-fold; the activity of the 0.3-kb-promoter fragment was still increased 1.7-fold (Fig. 5B).. Using electrophoretic mobility shift assay, we tested ...
Use near-infrared fluorescent oligonucleotides in EMSA applications. Then image on the Odyssey Infrared Imagers for faster, safer gel shift assay imaging.
Buy our human hepatocellular liver carcinoma cell line nuclear lysate, acetaldehyde treated. ab14661 has been validated in electrophoretic mobility shift…
A single-nucleotide polymorphism (C/A) located within an E-box at the −20 position of the human angiotensinogen (AGT) promoter may regulate transcriptional activation through differential recruitment of the transcription factors upstream stimulatory factor (USF) 1 and 2. To study the contribution of USF1 on AGT gene expression, mice carrying a (−20C) human AGT (hAGT) transgene were bred with mice harboring a USF1 gene trap allele designed to knock down USF1 expression. USF1 mRNA was reduced relative to controls in liver (9±1%), perigenital adipose (16±3%), kidney (17±1%), and brain (34±2%) in double-transgenic mice. This decrease was confirmed by electrophoretic mobility shift assay. Chromatin immunoprecipitation analyses revealed a decrease in USF1, with retention of USF2 binding at the hAGT promoter in the liver of male mice. hAGT expression was reduced in the liver and other tissues of female but not male mice. The decrease in endogenous AGT expression was insufficient to alter ...
978 TGFβ is a proliferation suppressor in untransformed epithelial cells. However, in solid tumors, particularly at later stages of disease, increased TGFβ production by the tumor cells contributes to cancer progression through paracrine stimulation of cells in the tumor micro-environment. We therefore proposed that the blockade of TGFβ1 production by the tumor cells would lead to suppression of tumor growth. In this study we investigated the potential components critical for signaling pathways mediating TGFβ1 production using an siRNA approaches, electrophoretic mobility shift assays (EMSA), EMSA super-shift analysis, and TGFβ1 promoter AP-1 luciferase reporter assays. A TGFβ-sensitive, untransformed rat intestinal epithelial cell line, IEC4-1, and a human colon carcinoma (HCC) cell line, FET, were employed in these studies. FET cells stably transfected with tetracycline-controllable dominant-negative mutants of TGFβ type II receptors (DN RII) were also utilized. Our results indicate ...
BACKGROUND. The prostrate cancer (PCa) susceptibility gene glycine N-methyltransferase (GNMT) is associated with the metastasis potential of PCa cells. Androgens, which participate in transcriptional regulation via an androgen receptor (AR), play an important role in PCa development. Our two goals were to determine whether GNMT is regulated by androgen, and to map androgen response elements (AREs).. METHODS. Real-time PCR was used to evaluate GNMT mRNA expression levels after LNCaP and DU145 cells were treated with R1881 (a synthetic AR agonist). Putative AREs were identified and tested using the MatInspector program and a luciferase reporter assay respectively. Electrophoretic mobility shift assay and chromatin immunoprecipitation were used to verify the binding properties of the GNMT-ARE motif.. RESULTS. Results from real-time PCR analyses indicate that R1881 is capable of inducing significant GNMT mRNA levels in AR-positive LNCaP cells, but not in AR-negative DU145 cells. According to ...
|i|Background:|/i| Interleukin-1 (IL-1), an inflammatory cytokine whose levels are elevated in inflamed mucosa, causes part of its effect on intestinal epithelial cells (IEC) through inducing ceramide production.|i|Aim:|/i| To study the role of nuclear factor-κB (NF-κB), a pro-inflammatory and anti-apoptotic factor, in IL-1- treated IEC.|i|Methods:|/i| NF-κB activity and levels of apoptotic proteins were assessed by electrophoretic mobility shift assay and RNA-protection assay, respectively.|i|Results:|/i| IL-1 and ceramide, which have been shown to partially mediate IL-l effects on IEC, activated NF-κB levels significantly. This activation was due to a decrease in IκB-α and IκB-β protein levels. Moreover, the ratio of mRNA levels of anti-apoptotic to pro-apoptotic proteins was significantly increased in IL-1-treated IEC.|i| Conclusion:|/i| NF-κB may play a key role in the regulation of the expression of pro-inflammatory and/or apoptotic genes in inflammatory bowel disease, making this protein
The CCD-11Lu human lung fibroblast cell line was used as an in vitro model. Cells were pretreated with CAPE followed by stimulation with interleukin-4 and tumor necrosis factor alpha. The levels of eotaxin in cultured supernatants were measured by enzyme-linked immunosorbent assay. The amounts of STAT6 and phosphorylated STAT6 in cellular nuclear protein extracts were determined by Western blot analysis. STAT6 DNA binding activities were detected by electrophoretic mobility shift assay. ...
OBJECTIVE: Genetic variants in the region of tumor necrosis factor-induced protein 3-interacting protein 1 (TNIP1) are associated with autoimmune disease and reduced TNIP1 gene expression. The aim of this study was to define the functional genetic mechanisms driving TNIP1 hypomorphic expression imparted by the systemic lupus erythematosus-associated TNIP1 H1 risk haplotype. METHODS: Dual luciferase expression and electrophoretic mobility shift assays were used to evaluate the allelic effects of 11 risk variants on enhancer function and nuclear protein binding in immune cell line models (Epstein-Barr virus [EBV]-transformed human B cells, Jurkat cells, and THP-1 cells), left in a resting state or stimulated with phorbol 12-myristate 13-acetate/ionomycin. HiChIP was used to define the regulatory 3-dimensional (3-D) chromatin network of the TNIP1 haplotype by detecting in situ long-range DNA contacts associated with H3K27ac-marked chromatin in EBV B cells. Then, quantitative reverse ...
All possible two-, three-, and C646 datasheet four-way SNP interactions were tested using 20-fold cross-validation in an exhaustive search (considering all possible SNP combinations). The conditional logistic regression analysis was performed using SPSS (v16.0) to confirm the reported interactive effects in MDR, which may be caused by the main effects from the component loci instead of the epistatic interactions. A logistic regression analysis with P < 0.05 could support the corresponding significant MDR interaction model. Electrophoretic mobility shift assay The human complementary DNA clone of CDX1 (pCMV6-CDX1) was produced by OriGene (OriGene Technologies,. Rockville, MD, USA). CDX1 protein preparation was made by transfecting pCMV6-CDX1 construct into HEK293 cells using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). Cells were harvested 48-h post-transfection, and nuclear extractions were performed. using a nuclear extraction kit (Panomics, Fremont, CA, USA). Protein concentration was ...
As more of the world’s cities become congested and polluted, new business models and technologies are emerging to solve the mobility challenge.
The regulation of macrophage activator protein-1 (AP-1) gene expression by LPS and cytokines is of potentially crucial importance in the pathogenesis of several diseases. The action of LPS and four cytokines on AP-1 gene expression in the murine macrophage J774.2 cell line was, therefore, studied. Exposure of the cells to IL-6 produced no changes in the mRNA levels of all AP-1 members studied. In contrast, the expression of JunB, c-jun and c-fos, but not JunD, was increased by LPS, TNF-α, IFN-γ and IL-1, albeit with different kinetics and magnitude of induction. Electrophoretic mobility shift assays showed a close correlation between the expression of the AP-1 genes and the functional AP-1 DNA binding activity and, additionally, demonstrated the participation of heterodimeric interactions between the different members. These studies provide insights into the potential mechanisms that may be involved in the mediator-specific modulation of AP-1 regulated macrophage gene expression.. ...
Aberrant regulation of the Wnt/β-catenin pathway plays important roles in colorectal carcinogenesis, with over 90% of cases of sporadic colon cancer featuring β-catenin accumulation. While ubiquitination-mediated degradation is widely accepted as a major route for β-catenin protein turnover, little is known about the regulation of β-catenin in transcriptional level. …Elf3, a member of the E-twenty-six family of transcription factors, drives β-catenin transactivation and associates with poor survival of colorectal cancer (CRC) patients. … first found recurrent amplification and upregulation of Elf3 in CRC tissues, and further Gene Set Enrichment Analysis identified significant association between Elf3 expression and activity of WNT/β-catenin pathway. Chromatin immunoprecipitation and electrophoretic mobility shift assay consistently revealed that Elf3 binds to and transactivates β-catenin promoter. Ectopic expression of Elf3 induces accumulation of β-catenin in both nucleus and ...
Tumor suppressor protein p53 possesses two DNA-binding sites. One that is located within its core domain is responsible for sequence-specific DNA binding of the protein, non-specific binding to internal segments of single- or double-stranded DNA, and to certain kinds of non-B DNA structures. The other that is contained in the C-terminus of the protein binds to damaged DNA. Binding of active, latent, and in vitro-activated p53 protein to DNA fragments modified by antitumor cisplatin was studied using electrophoretic mobility shift assay in agarose gels and immunoblotting analysis. We found that both latent and active p53 forms bound to random sequences of DNA globally modified by cisplatin with a higher affinity than to unmodified DNA. Interestingly, the latent form exhibited a more pronounced selectivity for platinated DNA than the active p53. Consistently with this observation, the preference of the latent form for platinated DNA decreased as a consequence of the activation of latent p53 by ...
The project will start with the design and ordering of CooA (wild type/mutants) and its response element (wild type/mutants) sequences. CooA mutants were reported to have higher affinity for CO. They were included in our order to shorten CO response time if needed. Two promoters, PCOOF and PCOOM, were previously reported as strong and weak promoters of CooA. We will also design several PCOOF promoter mutants (point mutations). These mutants are expected to have changed affinity for CooA. Binding affinity of CooA and mutated promoters will be determined as a part of characterization work package which includes Isothermal Titration Calorimetry (ITC), Electrophoretic Mobility Shift Assay (EMSA) and Intrinsic Tryptophan Fluorescence (ITF). Following this, promoters with different CooA affinities will be coupled and constructs will be prepared for in-vivo cell sensor experiments ...
The project will start with the design and ordering of CooA (wild type/mutants) and its response element (wild type/mutants) sequences. CooA mutants were reported to have higher affinity for CO. They were included in our order to shorten CO response time if needed. Two promoters, PCOOF and PCOOM, were previously reported as strong and weak promoters of CooA. We will also design several PCOOF promoter mutants (point mutations). These mutants are expected to have changed affinity for CooA. Binding affinity of CooA and mutated promoters will be determined as a part of characterization work package which includes Isothermal Titration Calorimetry (ITC), Electrophoretic Mobility Shift Assay (EMSA) and Intrinsic Tryptophan Fluorescence (ITF). Following this, promoters with different CooA affinities will be coupled and constructs will be prepared for in-vivo cell sensor experiments ...
Recent reports claimed that thymoquinone exhibited inhibitory results over the cell proliferation of various cancer cell strains. This research was done to investigate the antitumor and anti-angiogenic results of thymoquinone on osteosarcoma in vitro As well as in vivo. Our outcomes confirmed that thymoquinone induced a higher proportion of expansion inhibition and apoptosis within the human osteosarcoma mobile line SaOS-two in comparison with that of Regulate, and thymoquinone considerably blocked human umbilical vein endothelial mobile (HUVEC) tube development inside a dose-dependent way. To analyze the achievable mechanisms linked to these activities, we executed electrophoretic mobility shift assay (EMSA) and western blot Examination, and located that thymoquinone considerably downregulated NF-κB DNA-binding action, XIAP, survivin and VEGF in SaOS-two cells ...
Fewer girls than boys are referred for ADHD treatment, but they have a similar pattern of impairment and receive similar treatment. Evolution of socio-economic inequalities in mortality in small geographical areas of the two largest cities in Spain (Barcelona and Madrid), 1996-2007. An experimental system for the study of metastasis has been developed using an epithelioid cell line of hepatic origin which had previously been chemically transformed in vitro. Electrophoretic mobility shift assays were carried out to study the ability of IntI1 to bind the integrase primary target sites attI and aadA1 attC.. Sutureless repair of uncomplicated gastroschisis can be performed safely, however, it is associated with a significant increase in time to full feeds and time to discharge. Proper preparation for barium study of the stomach should involve treatment with a mucolytic agent about 15 minutes before the examination. There is a renewed interest in teaching psychotherapy in psychiatry training programs ...
Abramson, Harold Alexander, Furchgott, Robert F., Ponder, Eric (March 1939) The electrophoretic mobility of rabbit erythrocytes and ghosts. J Gen Physiol., 22 (4). pp. 545-553. ...
Maintaining a stable fold for recombinant proteins is challenging, especially when working with highly purified and concentrated samples at temperatures >20 °C. Therefore, it is worthwhile to screen f
The CIVITAS Initiative has produced a toolkit designed to help local, regional, and national authorities to communicate with transport users. It contains materials for the development of a strategic communications plan, the organisation of events, and the development and dissemination of printed and online media materials.. Sustainable mobility indicators for cities. In this report, the WBCSD sets out the results of a piece of work to develop a comprehensive set of sustainable mobility indicators for cities. These will also allow cities to understand the evolution of the system over time, and measure the improvements resulting from the implementation of new mobility practices or policies.. ...
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The methods include the so-called electrophoretic mobility shift assay, charge shift electrophoresis and affinity capillary ... A type of electrophoretic mobility shift assay (AMSA), agarose gel electrophoresis is used to separate protein-bound amino acid ... Ream JA, Lewis LK, Lewis KA (October 2016). "Rapid agarose gel electrophoretic mobility shift assay for quantitating protein: ... Membrane proteins may be identified by a shift in mobility induced by a charged detergent. Nucleic acids or nucleic acid ...
An electrophoretic mobility shift assay can assess whether a structure incorporates all desired strands. Fluorescent labeling ...
By using electrophoretic mobility shift assay (EMSA), the activation profile of transcription factors can be detected. A ...
The study utilized an electrophoretic mobility shift assay (EMSA) by notably not changing the DNA melting temperature. This ... Acridine derivatives are also G4 ligands and through fluorescence resonance energy transfer (FRET) melting assays, ... assay. SWCNTs stabilize i-motif DNA by attracting water molecules from the structure. GQDs intercalate with DNA to aid in the ... which was assessed by a TRAP assay. The binding of ligands can increase and modify i-motif functions. The first known selective ...
... when tested in an electrophoretic mobility shift assay, its affinity for ssDNA is significantly higher than for dsDNA. FANCA ...
A further mutation, rs208747, was shown by electrophoretic mobility shift assays to create or destroy a promoter transcription ...
It has been used in the electrophoretic mobility shift assay and p50 and title comp preincubated in assay buffer, pH 7.5 (room ... In the presence of ammonia salts, the bathochromic shifts increase. The hydrophilic group on the ammonia salts also change the ...
... to discover and analyze DNA binding sites have been the DNAse footprinting assay and the Electrophoretic Mobility Shift Assay ( ... 2010). "Protein-binding assays in biological liquids using microscale thermophoresis". Nature Communications. 1 (7): 100. ...
The following lists some methods currently in use: Electrophoretic mobility shift assay (EMSA) is a widespread qualitative ... Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or ... DNA-Protein-Interaction - Enzyme-Linked ImmunoSorbant Assay (DPI-ELISA) allows the qualitative and quantitative analysis of DNA ... DNase footprinting assay can be used to identify the specific sites of binding of a protein to DNA at basepair resolution. ...
Previous techniques aiming to understand protein-RNA interactions included RNA Electrophoretic Mobility Shift Assays and UV- ... "Optimized RNA Gel-Shift and UV Cross-Linking Assays for Characterization of Cytoplasmic RNA-Protein Interactions". ...
... the most frequently cited papers from the Crothers lab is a method for the widely used electrophoretic mobility shift assay, ... better known as a "gel shift" assay, which is used to detect and estimate the affinity of protein-nucleic acid complexes. He ...
Proteins which associate with the promoter can be identified using an electrophoretic mobility shift assay (EMSA), and the ... The gene products are assayed and the rates of reporter transcription are measured. From the data received from assaying the ... However, it is possible that there may not be enough data present and the assay must be re-run with a different promoter region ... Promoter bashing is often done with deletions from either the 5' or 3' end of the DNA strand; this assay is easier to perform ...
Electrophoretic mobility shift assay, Isotachophoresis, Pulsed-field gel electrophoresis, and Preparative electrophoresis. ... 4-5 Vesterberg, p. 5 Vesterberg, Olof (1989). "History of Electrophoretic Methods", Journal of Chromatography, volume 480, pp. ... "A New Apparatus for Electrophoretic Analysis of Colloidal Mixtures". The method spread slowly until the advent of effective ... "A new apparatus for electrophoretic analysis of colloidal mixtures". Transactions of the Faraday Society. 33: 524-531. doi: ...
Assays are created that combine reporter fusions, electrophoretic mobility shift assays, DNase footprinting, and fluorescence ...
2D gel analysis software History of electrophoresis Electrophoretic mobility shift assay Gel extraction Isoelectric focusing ... RNA is able to form more intramolecular interactions than DNA which may result in change of its electrophoretic mobility. Urea ... Characterization through ligand interaction of nucleic acids or fragments may be performed by mobility shift affinity ... which leads to a sieving effect that now determines the electrophoretic mobility of the proteins. After the electrophoresis is ...
... electrophoretic mobility shift assay MeSH E05.196.401.568 - immunoelectrophoresis MeSH E05.196.401.568.250 - ... colony-forming units assay MeSH E05.200.500.383.910 - tumor stem cell assay MeSH E05.200.500.385 - cytogenetic analysis MeSH ... drug screening assays, antitumor MeSH E05.337.550.200.800 - tumor stem cell assay MeSH E05.337.550.200.900 - xenograft model ... drug screening assays, antitumor MeSH E05.200.500.388.930 - tumor stem cell assay MeSH E05.200.500.410 - electroporation MeSH ...
Electron Microscopy Society of America former name of the Microscopy Society of America Electrophoretic mobility shift assay ...
... microscopy Molecular dynamics Mass spectrometry Isotopic labeling Coimmunoprecipitation Electrophoretic mobility shift assay ...
... or mobility shift electrophoresis, also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel ... A mobility shift assay is electrophoretic separation of a protein-DNA or protein-RNA mixture on a polyacrylamide or agarose gel ... Hellman, Lance M; Fried, Michael G (2007). "Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid ... Fried MG (1989). "Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay". Electrophoresis. ...
... is isolated by autoradiography as per an Electrophoretic mobility shift assay (EMSA) protocol. Amplify the bound template by ... Selection and amplification binding assay (SAAB) is a molecular biology technique typically used to find the DNA binding site ... By combining the power of random-sequence selection with pooled sequencing, the SAAB imprint assay makes possible simultaneous ...
Electrophoretic mobility shift assay. *Gel electrophoresis. *Immunoelectrophoresis. *Iontophoresis. *Isotachophoresis. *Moving- ... this also allows the elimination of electrophoretic motion of particles due to inherent particle charge. ...
Electrophoretic mobility shift assay. *Gel electrophoresis. *Immunoelectrophoresis. *Iontophoresis. *Isotachophoresis. *Moving- ... Harris, Neil S.; Winter, William E. (2012). Multiple Myeloma and Related Serum Protein Disorders: An Electrophoretic Guide. ... IgA has the most anodal mobility and typically migrates in the region between the beta and gamma zones also causing a beta/ ... Alpha-1 antitrypsin has an SG group and thiol compounds may be bound to the protein altering their mobility. A decreased band ...
Electrophoretic mobility shift assay. *Gel electrophoresis. *Immunoelectrophoresis. *Iontophoresis. *Isotachophoresis. *Moving- ... according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation and charge of ... The electrophoretic mobilities of these proteins is a linear function of the logarithms of their molecular weights. Without SDS ... The choice of buffer also affects the electrophoretic mobility of the buffer counterions and thereby the resolution of the gel ...
It uses no charged dye so the electrophoretic mobility of proteins in CN-PAGE (in contrast to the charge shift technique BN- ... Minde DP (2012). "Determining biophysical protein stability in lysates by a fast proteolysis assay, FASTpp". PLOS ONE. 7 (10): ... Thus, the electrophoretic mobility depends not only on the charge-to-mass ratio, but also on the physical shape and size of the ... The electrophoretic mobilities of these proteins will be a linear function of the logarithms of their molecular weights. Native ...
Unlike electrophoretic mobility shift and DNA foot printing, determination of molecular weight of unknown proteins that bind to ... A rapid dimethylsulphate (DMS) protection assay can be used to identify non-specific binding vs. specific binding on blots. ... Fourth, shifting to probe creation, particular restriction enzymes are chosen and used on the region of DNA under study to ... Jia, Yinshan; Nagore, Linda; Jarrett, Harry (2015). "Southwestern Blotting Assay". Methods in Molecular Biology (Clifton, N.J ...
In these experiments the electrophoretic mobility of Spot42 was similar to that of 5S rRNA. In 1979 Spot42 was found to ... resulted in impaired growth and lowered ability to adapt to shifts to richer media. Further, shift from glucose to succinate as ... Using a filter binding assay and other methods showed that Spot 42 is not an mRNA. In this approach the affinity between Spot42 ...
Post-translational modifications of proteins can lead to a different relative mobility (i.e. a band shift) or to a change in ... For electrophoretic separation of larger protein complexes, agarose gel electrophoresis can be used, e.g. the SDD-AGE. Some ... Single proteins can be isolated from a mixture by affinity chromatography or by a pull-down assay. Some historically early and ... The relative mobility (called Rf value or Rm value) is the quotient of the distance of the band of the protein and the distance ...
... and having little to no assay preparation, in comparison to the Ninhydrin chemical assay which requires assay preparation such ... The binding of the dye to a protein causes a shift in the absorbance maximum of the dye from 465 to 595 nm. The increase of ... Two years later in 1965 Meyer and Lambert used Coomassie Brilliant Blue R-250 to stain protein samples after electrophoretic ... The mobility of the complex in the polyacrylamide gel will depend on both the size of the protein complex (i.e. the molecular ...
Through the use of immunofluorescence studies, live cell imaging, gel mobility shift assays, and bimolecular fluorescence ... This larger group was named this for their high electrophoretic mobility in polyacrylamide gels and is differentiated into 3 ... High mobility group González-Romero R, Eirín-López JM, Ausió J (January 2015). "Evolution of high mobility group nucleosome- ... HMGN (High Mobility Group Nucleosome-binding) proteins are members of the broader class of high mobility group (HMG) ...
Before an electrophoretic run is started the prepared 4% T (total polymer content (T)), 2.67% C (cross-linker concentration (C ... agarose gel electrophoresis). Proteins migrate in it more or less on the basis of their free mobility. For these reasons ... A shifting peak in the respective electropherogram may indicate that the standardized time of gel polymerization (69 hr, RT) is ... conjugation of extracellular matrix proteins to characterized polyacrylamide substrates for cell mechanotransduction assays". ...
In some very specific cases, the detection of the phosphorylation as a shift in the protein's electrophoretic mobility is ... "A cell-based immunocytockemical assay for monitoring kinase signaling pathways and drug efficacy" (PDF). Anal. Biochem. 338 (1 ... Most of the phosphorylation sites for which such a mobility shift has been described fall in the category of SP and TP sites (i ... mobility shift, bead-based detection, and cell-based formats.[48][49] ATP[edit]. ATP, the "high-energy" exchange medium in the ...
By using electrophoretic mobility shift assay (EMSA),[80] the activation profile of transcription factors can be detected. A ...
Guide for Measurement of Electrophoretic Mobility and Zeta Potential of Nanosized Biological Materials E2866 - 12(2016) Test ... 17a Test Methods for Assay of Organic Peroxides E299 - 17a Test Method for Trace Amounts of Peroxides In Organic Solvents E299- ... Guide for Raman Shift Standards for Spectrometer Calibration E1841 - 04(2012) Guide for Conducting Renewal Phytotoxicity Tests ... Mobility: Maneuvering Tasks: Sustained Speed E2830 - 11(2020) Test Method for Evaluating the Mobility Capabilities of Emergency ...
In some very specific cases, the detection of the phosphorylation as a shift in the protein's electrophoretic mobility is ... March 2005). "A cell-based immunocytockemical assay for monitoring kinase signaling pathways and drug efficacy" (PDF). Anal. ... Most of the phosphorylation sites for which such a mobility shift has been described fall in the category of SP and TP sites (i ... mobility shift, bead-based detection, and cell-based formats. Protein phosphorylation is common among all clades of life, ...
... or mobility shift electrophoresis, also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel ... A mobility shift assay is electrophoretic separation of a protein-DNA or protein-RNA mixture on a polyacrylamide or agarose gel ... Hellman, Lance M; Fried, Michael G (2007). "Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid ... Fried MG (1989). "Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay". Electrophoresis. ...
I want to ask some question regarding protein-DNA binding interaction assay. I am so new in this field. For my project, I have ... Electrophoretic Mobility Band Shift Assay (EMSA) - posted in Electrophoresis: Hello everyone, ... Electrophoretic Mobility Band Shift Assay (EMSA). Started by Nurhikmah Mohd Sharif, Jun 08 2015 12:55 AM ... EMSA Shifted band in Free probe only lane Started by rob_toxi, 06 Mar 2014 EMSA, Free probe, bad shift and 1 more... * 1 reply ...
Die elektrophoretische Mobilität Shift-Assay (EMSA) ist eine biochemische Verfahren zur Bindung zwischen Proteinen und ... Electrophoretic Mobility Shift Assay (EMSA) für das Studium von RNA-Protein-Wechselwirkungen: Die IRE / IRP Beispiel Carine ... Elektrophoretische Mobilität Shift Assay (EMSA). USE JoVE IN YOUR CLASSROOM CREATE A JoVE TEST ... EMSA, elektrophoretische Mobilität-Shift-Test, auch bekannt als das Gel Schicht Assay, ist ein vielseitiger und sensible ...
This fluorescence-based Electrophoretic Mobility Shift Assay (EMSA) Kit provides a fast, easy and quantitative method to detect ... This fluorescence-based Electrophoretic Mobility Shift Assay (EMSA) Kit provides a fast, easy and quantitative method to detect ... Electrophoretic Mobility-Shift Assay (EMSA) Kit, with SYBR™ Green & SYPRO™ Ruby EMSA stains ... Electrophoretic Mobility-Shift Assay (EMSA) Kit, with SYBR™ Green & SYPRO™ Ruby EMSA stains. ...
For both electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genetic variants, ... Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity ... Precipitation Assay (DAPA).. Miller DE1, Patel ZH2, Lu X3, Lynch AT1, Weirauch MT4, Kottyan LC5. ...
A Proteomics Approach for the Identification of DNA Binding Activities Observed in the Electrophoretic Mobility Shift Assay. ... We present here a novel method for the identification of DNA-binding proteins seen in electrophoretic mobility shift assay ( ... DNase I footprinting and electrophoretic mobility shift assays (EMSA)1 are generally employed for the rapid characterization of ... A Proteomics Approach for the Identification of DNA Binding Activities Observed in the Electrophoretic Mobility Shift Assay ...
This assay is for example used for the identification of sequency-specific DNA-binding proteins as well as transcription ... electrophoretic mobility shift assay. Synonyms: *EMSA. *gel mobility shift assay. *gel retardation assay ... German: Electrophoretic mobility shift assay Japanese: 電気泳動移動度シフト解析 ...
A sensitive two-color electrophoretic mobility shift assay for detecting both nucleic acids and protein in gels. Proteomics. ... The utility of a two-color fluorescence electrophoretic mobility shift assay procedure for the analysis of DNA replication ... Retrieved from "https://openwetware.org/mediawiki/index.php?title=Knight:Electrophoretic_mobility_shift_assay&oldid=70953" ...
Inhibition of recombinant human PI3Ka using fluorescein-labeled peptide as substrate by fluorescence-electrophoretic mobility ... shift assay. ...
Inhibition of recombinant human c-Raf using fluorescein-labeled peptide as substrate by fluorescence-electrophoretic mobility ... shift assay. ...
The Gelshift Chemiluminescent EMSA Assay Kit simplifies the process of identifying protein:DNA binding interactions by ... providing an easy-to-use, non-radioactive assay with proven reagents. ... Electrophoretic mobility shift assays (EMSA), also known as gel shifts, gel retardation assays or mobility assays can be used ... non-radioactive assay to identify protein-DNA binding with proven reagents. In this electrophoretic mobility shift assay (EMSA ...
Hellman, L. M., Fried, M. G. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat ... Fillebeen, C., Wilkinson, N., Pantopoulos, K. Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein ... Ryder, S. P., Recht, M. I., Williamson, J. R. Quantitative analysis of protein-RNA interactions by gel mobility shift. Methods ... A functional assay for translational repression and direct demonstration of the iron switch. Eur. J. Biochem. 218, 657-667 ( ...
... and templates for the chromatography step were chosen according to the results of an electrophoretic mobility shift assay ... From: From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach ...
Profacgen offers professional Electrophoretic Mobility Shift Assay (EMSA) service to help your study on DNA-protein interaction ... Electrophoretic Mobility Shift Assay (EMSA) Service • Transcription Factor Analysis , Electrophoretic Mobility Shift Assay ( ... Electrophoretic mobility shift assay (EMSA, also called gel retardation assay or gel shift assay) is an in vitro method to ... Electrophoretic Mobility Shift Assay (EMSA) DNase I Footprinting Assay Chromatin Immunoprecipitation Assay (ChIP) ...
Validation of miRNA-mRNA interactions by electrophoretic mobility shift assays. Author: Solé Ferré, Anna. Mencía Trinchant, ... CONCLUSIONS: In this study, we explored a new application for the electrophoretic mobility shift assay and we demonstrated that ... incubated together and their interaction studied under different binding conditions using electrophoretic mobility shift assays ...
... and templates for the chromatography step were chosen according to the results of an electrophoretic mobility shift assay ... Mach-Aigner, A.R., Grosstessner-Hain, K., Poças-Fonseca, M.J. et al. From an electrophoretic mobility shift assay to isolated ... From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach. *Astrid R ... Electrophoretic mobility shift assay (EMSA). Radioactive EMSA synthetic oligonucleotides (VBC, Vienna, Austria) (Table 1) were ...
Electrophoretic mobility shift assay. DNA-ParB binding was assayed using purified protein and double-stranded DNA fragments of ... 43 HE Cy 3 shift free (EX BP 550/25, BS FT 570, and EM BP 605/70), and 49 DAPI shift free (EX G 365, BS FT 395, and EM BP 445/ ... Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J. 4, ... We further assayed chromosomal SMC-loading sites by making use of a well-characterized SMC ATP-hydrolysis mutant E1084Q32,53,54 ...
Electrophoretic mobility shift assays showing the effect of oleic acid on DNA binding of ToxTENV256 wild-type (a) and K231A (b ... c Electrophoretic mobility shift assay of wild-type and K158E ToxTENV256 binding to the tcpA promoter. All lanes contain 9 nM ... Electrophoretic mobility shift assay. A 5-digoxigenin (DIG) labeled 84-bp dsDNA fragment containing the ToxT-binding sequence ... To confirm that dimerization at the helix α3 interface is necessary for DNA-binding, electrophoretic mobility shift assays were ...
Electrophoretic Mobility Shift Assay.. Nuclear proteins were extracted and incubated with biotin-labeled DNA probes, gel- ... we documented STAT3 binding in the gel electromobility shift assay (EMSA) (Fig. 4C). The specificity of binding of both probes ... as shown in the gel electromobility shift and chromatin immunoprecipitation assays, and is required for the PD-L1 gene ... siRNA Assay.. A mixture of four STAT3- or STAT5B-specific siRNA or nontargeting siRNA (all purchased from Dharmacon) was ...
A) Electrophoretic mobility shift assay of CcaR. Purified CcaR [0 ng (lane 1), 100 ng (lane 2), 200 ng (lane 3), or 300 ng ( ... Electrophoretic Mobility Shift Assay.. For probes, the promoter region of cpeC was amplified with the primer set NpccaRD-3/ ... The results of an electrophoretic mobility shift assay suggest that CcaR binds to the promoter region of cpeC-cpcG2-cpeR1, ... examined the ability of CcaR to bind to the promoter region of cpeC-cpcG2-cpeR1 using the electrophoretic mobility shift assay ...
Electrophoretic mobility shift assay. Nuclei from rat muscle were prepared with a modified version of previously described ... The final concentrations in the assay were: carbonyl cyanide m-chlorophenyl hydrazone (CCCP; 5 μmol/l); antimycin A (AA; 1 μg/ ... The major findings of this study are that: (1) hyperinsulinaemia in the high physiological range causes a shift towards a more ... Glutathione is the major buffering system for scavenging ROS, and a shift towards its oxidised form reflects a more oxidised ...
Electrophoretic mobility shift assay:. Probes for the electrophoretic mobility shift assay (EMSA) were prepared by annealing ... Using an electrophoresis mobility shift assay, we show that the 26-bp region contains a cis-regulatory element. Finally, we ... Through molecular characterization of the mutant locus using luciferase and gel shift assays, genetic analysis of recombining ... Cell culture and dual-luciferase reporter assay:. Cell culture and dual-luciferase reporter assay were processed as described ( ...
Electrophoretic mobility shift assay. The preparation of nuclear extracts from treated and untreated cells was prepared ... Cells were treated with CNTF every 24 hr for time points that were ,1 d. Electrophoretic mobility shift assay (EMSA) was also ... EMSA assays were performed to determine the extent of activation of STAT proteins as described in Materials and Methods and the ... EMSA assays were then performed to determine the extent of activation of the STAT proteins in these extracts. The complexes ...
The electrophoretic mobility shift assay (EMSA), also known as "gel shift assay", is used to examine the binding parameters and ... 8. Confirm protein purity on SDS-PAGE gel, and protein quantity using Bradford assay and Western blot analysis. ...
Electrophoretic Mobility Shift Assays (EMSA). EMSA were carried out using purified proteins and fluorescently Cy5-labelled attL ... Electrophoretic mobility shift assay (EMSA) experiments were performed using the KplE1 attL recombination region that contains ... Electrophoretic mobility shift assay (EMSA) experiments were performed using the KplE1 attL recombination region that contains ... Electrophoretic mobility shift assay (EMSA) were performed essentially as described [30], except that two different ...
Electrophoretic mobility shift assay Is the Subject Area "Electrophoretic mobility shift assay" applicable to this article? Yes ... Electrophoretic mobility-shift assay (EMSA). ARs binding to double-stranded oligos was assessed in LNCaP cell nuclear extracts ... 6C). Only probe 1 showed a mobility shift (Fig. 6D). To confirm that this mobility shift is specific to AR, we added anti-AR ... probe 1 showed a further mobility shift (Fig. 6D). Although unlabeled wild-type probe 1 was able to compete with labeled probe ...
Electrophoretic mobility shift assay Is the Subject Area "Electrophoretic mobility shift assay" applicable to this article? Yes ... Electrophoretic mobility shift assays (EMSA) showed decreased NF-κB binding at 2.5 µM of Bay-11-7082 treatment for 72 hrs in ... Electrophoretic mobility shift assay (EMSA). A double stranded DNA probe with the sequence 5′-GATCCGGCAGGGGAATCTCCCTCTC-3′ was ... Electrophoretic mobility shift assays (EMSA) were performed to determine the ability of NF-κB to bind to DNA following ...
Electrophoretic mobility shift assay (EMSA). EMSA experiments were performed as previously described (Valsecchi et al., 2011). ... For LDH assay, cells were plated in 24 well plates at a density of 1 × 106 cells/well; for luciferase assay, they were plated ... for LDH assay) and 15 μg for 100 mm plates (for Western blot analysis) of the above mentioned constructs. For luciferase assay ... Re-ChIP assay revealed that Sp3, REST, HDAC1, and HDAC2 (Fig. 6e,g,h, lanes 4), and Sp1, HIF-1, and p300 (Fig. 6f,i, lanes 5) ...
Electrophoretic Mobility Shift Assay. NF-κB binding activity was performed as previously reported.6 The binding bands were ... Figure 1. Electrophoretic mobility shift assay of NF-κB in rat liver. Rats underwent hemorrhagic shock (Hem) or sham shock ( ... because the integrated intensity of group samples from different electrophoretic mobility shift assay batches would be affected ...
Electrophoretic mobility shift assay.. The activation of NF-κB was assayed by a gel mobility shift assay using nuclear extracts ... as demonstrated by electrophoretic mobility shift assay (EMSA) and luciferase reporter assay, respectively (Fig. 5A and B). ... NF-κB luciferase assay.. Cells were seeded on 24-well culture plates at 2 × 104 cells/well and adapted for 12 h. Cells were ... 3B). Results were similar to those of MTT assay.. Effect of SIRT1 overexpression on IL-1β-and IFN-γ-induced iNOS expression and ...
  • 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)
  • The nucleic acids and proteins are stained sequentially in the gel after electrophoresis, so there is no possibility that labeling will interfere with the protein binding being assayed. (thermofisher.com)
  • We present here a novel method for the identification of DNA-binding proteins seen in electrophoretic mobility shift assay (EMSA) using the power of two-dimensional electrophoresis coupled with mass spectrometry. (mcponline.org)
  • Using an electrophoresis mobility shift assay, we show that the 26-bp region contains a cis -regulatory element. (genetics.org)
  • The methods include the so-called electrophoretic mobility shift assay, charge shift electrophoresis and affinity capillary electrophoresis. (wikipedia.org)
  • A type of electrophoretic mobility shift assay (AMSA), agarose gel electrophoresis is used to separate protein-bound amino acid complexes from free amino acids. (wikipedia.org)
  • Electrophoretic mobility shift assays (EMSA), also known as gel shifts, gel retardation assays or mobility assays can be used to study DNA-protein interactions 1-3 . (activemotif.com)
  • Electrophoretic mobility shift assay ( EMSA , also called gel retardation assay or gel shift assay ) is an in vitro method to detect the interaction between proteins and nucleotides. (profacgen.com)
  • STAT3 binds to the CD274 gene promoter in vitro and in vivo , as shown in the gel electromobility shift and chromatin immunoprecipitation assays, and is required for the PD-L1 gene expression, as demonstrated by siRNA-mediated STAT3 depletion. (pnas.org)
  • Northern blot analysis revealed a decrease in MMP-9 mRNA expression following treatment with PPARγ which resulted from the inhibition of NF-κB activation in these cells, as determined by transient transfection assays and electromobility shift assays. (bmj.com)
  • Nuclear translocation of the pro-inflammatory transcription factors nuclear factor-κB (NF-κB) and activator protein 1 (AP-1) were also measured by electromobility shift assay in BAL fluid leucocytes and lung biopsy samples. (bmj.com)
  • monocyte chemotactic protein-1 (MCP-1) by ELISA and NF-κB by electromobility gel shift assay. (onlinejacc.org)
  • We showed that CR1 activity is modulated by the transcription factors NF-κB and AP-1 via electrophoretic mobility shift assays (EMSA), EMSA supershift, and chromatin immunoprecipitation (ChIP) assays. (plos.org)
  • Chromatin immunoprecipitation assay demonstrated occupation of the PU.1 sites by PU.1 in vivo in HL-60 cells. (bloodjournal.org)
  • This method is referred to as a supershift assay, and is used to unambiguously identify a protein present in the protein - nucleic acid complex. (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)
  • For those that wish to make their own Gel shift / Supershift Assay , we offer specialized binding buffers with differing properties to best fit the transcription factor you are interested in. (activemotif.com)
  • A supershift assay revealed that both c-Fos and c-Jun bind to this AP-1 site. (ahajournals.org)
  • The involvement of the aryl hydrocarbon receptor (AHR) and aryl hydrocarbon nuclear translocator (ARNT) in mediating the effects of oltipraz on the XRE is supported by electrophoretic mobility supershift data and AHR/ARNT overexpression studies. (aspetjournals.org)
  • Gel shift assays are often performed in vitro concurrently with DNase footprinting, primer extension, and promoter-probe experiments when studying transcription initiation, DNA gang replication, DNA repair or RNA processing and maturation, as well as pre-mRNA splicing. (wikipedia.org)
  • Furthermore, the inhibition activities against RSS-siRNA complex in vitro and in vivo of the chemicals screened by SPR were also confirmed by EMSA and protoplast-based assay, respectively. (rsc.org)
  • In the present study, we used in vitro assays and in vivo xenograft models to examine the effects of SO on the pancreatic CSC population. (aacrjournals.org)
  • Mutation of this region abolishes LFY binding in vitro and in yeast one hybrid assays, but has no obvious effect on AP3 expression in planta. (biologists.org)
  • NO. 4, as assessed by in vitro competitive binding assay. (freepatentsonline.com)
  • The Gelshift Chemiluminescent EMSA Assay Kit provides a simple, non-radioactive assay to identify protein-DNA binding with proven reagents. (activemotif.com)
  • The Gelshift Chemiluminescent EMSA Assay Kit includes all the reagents needed to study protein-DNA binding for your sample system. (activemotif.com)
  • These buffers are not used in the Gelshift Chemiluminescent EMSA Assay Kit. (activemotif.com)
  • The non-radioactive format of the Gelshift Chemiluminescent EMSA Assay Kit does not sacrifice sensitivity when compared to 32 P or digoxigenin methods. (activemotif.com)
  • Further studies found that oridonin inhibited nuclear factor-κB (NF-κB) DNA-binding activity in these cells as measured by luciferase reporter gene, ELISA-based, and electrophoretic mobility shift assays. (aacrjournals.org)
  • Functional effects were tested in luciferase reporter assays in HEK293T cells and allele-specific TF binding was investigated by electrophoretic mobility gel shift assays. (bmj.com)
  • In transient expression assays, NtmybA1 and A2 activated the MSA-containing promoters, whereas NtmybB repressed them. (plantcell.org)
  • Using yeast three-hybrid, electrophoretic mobility shift, RNA immunoprecipitation, and protoplast transient assays, we found that AtBRNs bind to the 3′ UTR of SOC1 RNA and participate in mRNA decay, which was mediated by the distal region of the SOC1 3′ UTR. (wiley.com)
  • In vivo Arf pull down assay demonstrated that IQ-ArfGEF/BRAG1 activated Arf6 more potently than Arf1. (nih.gov)
  • Functional genomics analysis demonstrated that the promoter SNP rs11191612 was associated with altered luciferase activation in reporter assays and altered DNA-protein binding in gel shift assays. (aspetjournals.org)
  • Osteopontin and β 3 integrin ligation rapidly increased NF-κB activity as measured by gel shift and reporter activity. (rupress.org)
  • Then, to identify transcription factors involved in UTP-induced OPN transcription, we located a promoter element activated by UTP within the rat OPN promoter using a gene reporter assay strategy. (ahajournals.org)
  • This assay is for example used for the identification of sequency-specific DNA -binding proteins as well as transcription factors . (emf-portal.org)
  • Expression of cytokines and proteins was measured by ELISA assay and Western blot analysis, respectively. (biomedcentral.com)
  • Membrane proteins may be identified by a shift in mobility induced by a charged detergent. (wikipedia.org)
  • Protein-deoxyribonucleic acid interactions linked to gene expression: electrophoretic mobility shift assay. (unab.cl)
  • The principle of EMSA is based on the electrophoretic mobility discrepancy between biomolecules with different molecular masses. (profacgen.com)
  • Through molecular characterization of the mutant locus using luciferase and gel shift assays, genetic analysis of recombining populations, and in vivo rescue experiments, we provide evidence that a 26-bp deletion within the Bm-ASH2 promoter is closely linked to the sl locus and leads to loss of Bm-ASH2 expression and the scaleless-wings phenotype. (genetics.org)
  • Molecular Probes fluorescent nucleic acid gel stains-SYBR Gold, SYBR Green I, SYBR Green II and SYBR Safe dyes-are high-sensitivity reagents for staining DNA and RNA in electrophoretic gels. (thermofisher.com)
  • Yeast one-hybrid assays revealed that the msh-like homeodomain protein, MSX1, bound specifically to the Hx sequence of MFCS1. (g3journal.org)
  • 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)
  • The results of an electrophoretic mobility shift assay suggest that CcaR binds to the promoter region of cpeC - cpcG2 - cpeR1 , which contains a conserved direct-repeat motif. (pnas.org)
  • Mutation or deletion of each PU.1 site decreased promoter activity, and the level of activity mediated by each site correlated with its binding avidity for PU.1, as determined by gel shift competition assays. (bloodjournal.org)
  • Electrophoretic mobility shift assays, using a probe containing the STAT element of the perforin promoter, indicated that this element can bind STAT3 from YT cells. (jimmunol.org)
  • Mobility shift assay and siRNA knock-down were used to prove hypoxia responsive elements (HRE) and HIF binding within the S100A4 promoter. (springer.com)
  • Putative HREs could be identified in the promoter region of the human S100A4 gene and their functionality was confirmed by mobility shift assay. (springer.com)
  • Western blot analysis and gel mobility shift assay showed that fish oil significantly induced AP-2α protein expression and AP-2 DNA-binding activity in the ILK gene promoter and that this was dependent on PPARγ activation. (aacrjournals.org)
  • Although precursors can be found in earlier literature, most current assays are based on methods described by Garner and Revzin and Fried and Crothers. (wikipedia.org)
  • The methods are based on changes in the electrophoretic pattern of molecules (mainly macromolecules) through biospecific interaction or complex formation. (wikipedia.org)
  • I want to ask some question regarding protein-DNA binding interaction assay. (protocol-online.org)
  • FINDINGS: RNA molecules corresponding to miR-224 and to the 3[prime]-UTR of SLC4A4 were incubated together and their interaction studied under different binding conditions using electrophoretic mobility shift assays. (ub.edu)
  • The interaction or binding of a molecule, charged or uncharged, will normally change the electrophoretic properties of a molecule. (wikipedia.org)
  • This difference in electrophoretic separation of DNA-protein complexes can be visualized as a 'shift' in migration of the labeled DNA band. (activemotif.com)
  • Because the original mixture of analyte and receptor molecule were bound together in an equilibrium, the slow dissociation of these two bound molecules during the electrophoretic experiment will result in their separation and a subsequent shift in equilibrium towards further dissociation. (wikipedia.org)
  • However, assuming that the protein is capable of binding to the fragment, the lane with a protein that binds 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)
  • This fluorescence-based Electrophoretic Mobility Shift Assay (EMSA) Kit provides a fast, easy and quantitative method to detect both nucleic acid and protein in the same gel. (thermofisher.com)
  • Then the inhibition activities of these inhibitors on the association between P19 and siRNA were also affirmed by electrophoretic mobility shift assay. (rsc.org)
  • The electrophoretic mobility shift assay (EMSA), also known as "gel shift assay", is used to examine the binding parameters and relative affinities of protein and DNA interactions. (scienceexchange.com)
  • DNase I footprinting and electrophoretic mobility shift assays (EMSA) 1 are generally employed for the rapid characterization of such regions including the definition of cis -acting elements ( 1 ). (mcponline.org)
  • 3 MMP-9 is increased in bronchoalveolar lavage fluid 4 and bronchial tissue in patients with bronchial asthma, 5, 6 while the expression of TIMP-1 is increased to a lesser extent, thus shifting the balance towards matrix degradation in the airway wall. (bmj.com)
  • EMSA , Free probe , bad shift and 1 more. (protocol-online.org)
  • In this electrophoretic mobility shift assay (EMSA), cell extracts or purified factors are incubated with biotin end-labeled probe containing the consensus binding site of interest. (activemotif.com)
  • Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA). (nih.gov)
  • For both electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genetic variants, a synthetic DNA oligonucleotide (oligo) is used to identify factors in the nuclear lysate of disease or phenotype-relevant cells. (nih.gov)
  • Samples in which the protein of interest bound the target DNA will migrate slower than DNA alone resulting in a 'shift' of the labeled DNA band. (activemotif.com)
  • Caspase activity assays and Western blot analysis showed that H9c2 cells treated with Dox for 16 h had marked increase in the levels of caspases-2, -3, -8, -9, -12, Fas, and cleaved poly(ADP ribose) polymerase (PARP). (physiology.org)
  • Electrophoretic mobility shift assay (EMSA), DNA binding activity, immunofluorescence, and gene transfection were used to delineate the mechanism. (aacrjournals.org)
  • DNA-binding activity was assayed by the gel-shift analysis. (biomedcentral.com)
  • In infected cells, attenuated binding activity of IRP-iron responsive elements (IREs) is observed using the electrophoretic mobility-shift assay. (hindawi.com)
  • Human umbilical vein endothelial cells (ECV 304) and human monocytoid cells (THP-1) were studied in a functional binding assay. (onlinejacc.org)
  • GATA DNA binding complex containing GATA-3 was elevated in Th2 cells as determined by electrophorectic mobility shift assay. (ersjournals.com)
  • 8. Confirm protein purity on SDS-PAGE gel, and protein quantity using Bradford assay and Western blot analysis. (scienceexchange.com)
  • MG132 dose-dependently inhibited vascular smooth muscle cell proliferation with 50% inhibition at 10 μmol/L. TNFα-induced degradation of IκBα and β was blocked, and activation of nuclear factor kappa B was suppressed in a concentration-dependent manner in bandshift assays. (ahajournals.org)
  • Binding constants are generally derived from this technique based upon the peak migration shift of the receptor which is dependent upon the concentration of the analyte in the sample. (wikipedia.org)
  • CONCLUSIONS: In this study, we explored a new application for the electrophoretic mobility shift assay and we demonstrated that it is a useful alternative method to assess, in a direct and specific manner, whether a miRNA binds to a specific predicted target mRNA. (ub.edu)
  • The optimal conditions and templates for the chromatography step were chosen according to the results of an electrophoretic mobility shift assay performed under repressing conditions, which yielded a DNA-protein complex specific to the AGAA-box (the previously identified, tetranucleotide cis -acting element). (biomedcentral.com)
  • The prophage is passively replicated as part of the host chromosome as long as conditions are not threatening to the host, in which case the prophage shifts to a lytic development [ 3 , 4 , 5 ]. (mdpi.com)
  • Specifically, 14-3-3 binds to p90 RSK -phosphorylated Ser 173 of capicúa thereby modulating DNA binding to its HMG (high-mobility group) box, whereas ERK phosphorylations prevent binding of a C-terminal NLS (nuclear localization sequence) to importin α4 (KPNA3). (biochemj.org)
  • According to gelatin zymography and casein zymography assays, VYE inhibited the activities of matrix metalloproteinases (MMPs) and urokinase-type plasminogen activator (u-PA). (medsci.org)
  • Variants of the competition assay are useful for measuring the specificity of binding and for measurement of association and dissociation kinetics. (wikipedia.org)
  • The p65 and p50 subunits were present in the shifted complex. (rupress.org)
  • We quantified β-hydroxybutyrate (BHB) levels with a colorimetric assay. (springer.com)