Electrophoretic mobility shift assay. Medical search

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.

The expected function of a member of a particular profession.

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.

A plant genus of the LAMIACEAE family. It is known as a spice and medicinal plant.

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 collection of watery fluid in the pleural cavity. (Dorland, 27th ed)

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)

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 ...

https://en.wikipedia.org/wiki/Affinity_electrophoresis

An electrophoretic mobility shift assay can assess whether a structure incorporates all desired strands. Fluorescent labeling ...

https://en.wikipedia.org/wiki/DNA_nanotechnology

By using electrophoretic mobility shift assay (EMSA), the activation profile of transcription factors can be detected. A ...

https://en.wikipedia.org/wiki/Transcription_factor

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 ...

https://en.wikipedia.org/wiki/I-motif_DNA

... when tested in an electrophoretic mobility shift assay, its affinity for ssDNA is significantly higher than for dsDNA. FANCA ...

https://en.wikipedia.org/wiki/FANCA

A further mutation, rs208747, was shown by electrophoretic mobility shift assays to create or destroy a promoter transcription ...

https://en.wikipedia.org/wiki/DISC1

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 ...

https://en.wikipedia.org/wiki/Bromopyrogallol_red

... 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. ...

https://en.wikipedia.org/wiki/DNA_binding_site

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. ...

https://en.wikipedia.org/wiki/DNA-binding_protein

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". ...

https://en.wikipedia.org/wiki/RNA_immunoprecipitation_chip

Electrophoretic mobility shift assay (DNA:protein). *Far-western blot (protein:protein). *Far-eastern blot (lipid:post ... Analysis of gene expression can be done by several different methods including RT-PCR, RNase protection assays, microarrays, ...

https://en.wikipedia.org/wiki/Northern_blot

Where the traditional Electrophoretic Mobility Shift Assay (EMSA) method can be used, BLI can act as a suitable substitute if ... Assay configuration in BLI can, in stable conditions, allow for recovery of samples. Assay configuration in SPR allows for ... Since the wavelength shift is direct measure of the change in thickness of the biological layer and the biological layer ... The wavelength shift (Δλ) between these two reflection patterns creates an interference pattern (Figure 3) from which all ...

https://en.wikipedia.org/wiki/Bio-layer_interferometry

... 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 ...

https://en.wikipedia.org/wiki/Donald_Crothers

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 ...

https://en.wikipedia.org/wiki/Promoter_bashing

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: ...

https://en.wikipedia.org/wiki/History_of_electrophoresis

Assays are created that combine reporter fusions, electrophoretic mobility shift assays, DNase footprinting, and fluorescence ...

https://en.wikipedia.org/wiki/Bacterial_DNA_binding_protein

History of electrophoresis Electrophoretic mobility shift assay Gel extraction Isoelectric focusing Pulsed field gel ... 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 ...

https://en.wikipedia.org/wiki/Gel_electrophoresis

... 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 ...

https://en.wikipedia.org/wiki/List_of_MeSH_codes_(E05)

Electron Microscopy Society of America former name of the Microscopy Society of America Electrophoretic mobility shift assay ...

https://en.wikipedia.org/wiki/EMSA

... microscopy Molecular dynamics Mass spectrometry Isotopic labeling Coimmunoprecipitation Electrophoretic mobility shift assay ...

https://en.wikipedia.org/wiki/Outline_of_biochemistry

... 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. ...

https://en.wikipedia.org/wiki/Electrophoretic_mobility_shift_assay

... 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 ...

https://en.wikipedia.org/wiki/Selection_and_amplification_binding_assay

By using electrophoretic mobility shift assay (EMSA),[87] the activation profile of transcription factors can be detected. A ...

https://en.wikipedia.org/wiki/Transcription_factors

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". DNA-Protein Interactions. Methods in ...

https://en.wikipedia.org/wiki/Southwestern_blot

It uses no charged dye so the electrophoretic mobility of proteins in CN-PAGE (in contrast to the charge shift technique BN- ... in subsequent western blot detection or activity assays) or fluorescence of proteins with prosthetic groups (e.g. heme or ... 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.[ ...

https://en.wikipedia.org/wiki/Gel_electrophoresis_of_proteins

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 ...

https://en.wikipedia.org/wiki/Spot_42_RNA

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 ...

https://en.wikipedia.org/wiki/SDS-PAGE

... allows the Bradford assay to be used for fingerprint analysis. The assay was successfully used to identify the biological sex ... The mobility of the complex in the polyacrylamide gel will depend on both the size of the protein complex (i.e., the molecular ... 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 ...

https://en.wikipedia.org/wiki/Coomassie_brilliant_blue

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) ...

https://en.wikipedia.org/wiki/HMGN

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". ...

https://en.wikipedia.org/wiki/QPNC-PAGE

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, ...

https://en.wikipedia.org/wiki/Protein_phosphorylation

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 ...

https://www.activemotif.com/catalog/648/gelshift-chemiluminescent-emsa

Inhibition of recombinant human CK1delta using fluorescein-labeled peptide as substrate by fluorescence-electrophoretic ... mobility shift assay. ...

https://pubchem.ncbi.nlm.nih.gov/bioassay/1260247

Electrophoretic mobility shift assay (EMSA). Nuclear extracts were prepared, and EMSA was performed as described previously53 ... κB was evaluated by the formation of a distinct and specific complex in electrophoretic mobility shift assay (EMSA), the ... Chromatin immunoprecipitation (ChIP) assay. Recruitment of NF-κB to α-syn gene promoters was determined by ChIP assay as ... Luciferase assay. BV-2 cells plated at 50-60% confluence in 12-well plates were transfected with 0.25 µg pNF-κB-Luc construct ...

https://www.nature.com/articles/s41467-021-25767-1?error=cookies_not_supported&code=7d4ded0d-cfe9-413f-bb8a-0ceed9278edb

Electrophoretic mobility shift assay (EMSA). Single-stranded DNA oligonucleotides were labeled with DIG-11-ddUTP by terminal ... transferase using a Dig Gel Shift kit (Roche). The gel shift assays were performed using 1 μg of TcRPA-1 or increased ... for 5 minutes for replication assays or treated with 20 mM of hydroxyurea or UV radiation for DNA damage assays. The cells were ... Infection assay. LLC-MK2 cells (Rhesus Monkey Kidney Epithelial Cells) (2x104 cells/well) were cultured in a 6-well culture ...

https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0005181

Electrophoretic Mobility Shift Assays. For analysis, 8% non-denaturing native-PAGE (37.5:1) was used in the presence of 89 mM ... This may affect the mobility of labeled RNAs and drastically alter their function. In turn, the split GFP system, in which two ...

https://www.mdpi.com/1420-3049/23/12/3178

... by means of electrophoretic mobility shift assays (EMSAs). The results of these assays for the -409/-388 Actin302promoter ... Electrophoretic mobility shift assays. Nuclear extracts from Artemia franciscana cysts and nauplii,obtained after 20 h of cyst ... 388 of the Actin302 promoter was used as a probe in an electrophoretic mobility shift assay. Either cyst nuclear extracts (10μg ... 388 of the Actin302 promoter was used as a probe in an electrophoretic mobility shift assay. Either cyst nuclear extracts (10μg ...

https://journals.biologists.com/jeb/article/206/9/1565/14684/Regulation-of-promoter-occupancy-during-activation

Electrophoretic Mobility Shift Assay * Lysine / genetics * Lysine / metabolism* * Models, Molecular * Mutagenesis, Site- ... gel mobility shift assay, and kinetic assay of the methyl transfer reaction. Based on these biochemical studies and the crystal ... To confirm this idea, we carried out the kinetic studies, a gel mobility shift assay with a mutant protein disrupted in the ...

https://pubmed.ncbi.nlm.nih.gov/16963456/

... electrophoretic mobility shift assay; functional genomics; gene regulation; genetic; histone; isocyanate; luciferase assay; ... Electrophoretic mobility shift assays detected allele-dependent nuclear protein binding in A549 cells for 8 of 21 variants. In ... and IMR-90 lung cell lines by using electrophoretic mobility shift assays. DNA constructs were cloned into a pGL3 promoter ... and functional assays. Methods: NGS was performed in 91 workers with DA. Fourteen loci with known DA-associated single ...

http://www2a.cdc.gov/nioshtic-2/BuildQyr.asp?s1=asthma+OR+%27allerg%2A%27+OR+%27immune%2A%27&f1=%2A&Startyear=&Adv=0&terms=1&EndYear=&Limit=10000&sort=&D1=10&PageNo=53&RecNo=522&View=f&

... promoter deletion constructs and electrophoretic mobility shift assays. Symptomatic -10T allele carriers suffered from stroke, ... Electrophoretic mobility shift assay (EMSA). Nuclear protein extracts of EA.hy926 cells were prepared by a modified protocol [ ... promoter deletion constructs and electrophoretic mobility shift assays. Symptomatic -10T allele carriers suffered from stroke, ... Exon trapping assay. The influence of intronic GLA variants on splice events was analyzed by use of the exon trapping vector ...

https://ojrd.biomedcentral.com/articles/10.1186/s13023-014-0178-5

Evidence that ZRE sequences identified by RSAT are functional Zap1 binding sites. A) Electrophoretic mobility shift assay of ... Electrophoretic mobility shift assays. The Zap1 DNA binding domain (Zap1DBD, residues 687-880) was expressed in E. coli as a ... we performed electrophoretic mobility shift assays (EMSA) (Fig. 3A). The Zap1 DNA binding domain (Zap1DBD, residues 687-880) ... Electrophoretic mobility shift assays were performed as previously described using purified Zap1DBD protein and radiolabeled ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-370

Electrophoretic mobility shift assay reveals a total inhibition of LPS-induced formation of nuclear factor κB.DNA binding ...

https://www.cdc.gov/niosh/awards/hamilton/aliceabs03.html

Electrophoretic mobility shift assay The following primer and its complementary primer were used as a HSE probe: 5′- ... Abbreviations used in this paper: DBD, DNA binding domain; EMSA, electrophoretic mobility shift assay; GFP, green fluorescent ... Abbreviations used in this paper: DBD, DNA binding domain; EMSA, electrophoretic mobility shift assay; GFP, green fluorescent ... investigated the possibility that pHuR98 repeats were the DNA target of HSF1 granules by electrophoretic mobility shift assay ( ...

https://rupress.org/jcb/article/156/5/775/32361/In-vivo-binding-of-active-heat-shock-transcription

Electrophoretic mobility shift assay. Electrophoretic mobility shift assay (EMSA) experiments were performed as described ... All data from Western blot analysis, PCR, luciferase assays, gel shift assays, and cell growth assays were expressed as mean ± ... Transient transfection, gel mobility shift assays, and chromatin immunoprecipitation experiments showed that PGE2 induced ILK ... in the presence or absence of dmPGE2 for an additional 24 h for Western blot and cell growth and gel mobility shift assays. ...

https://aacrjournals.org/cancerres/article/69/3/896/552883/Prostaglandin-E2-Stimulates-Human-Lung-Carcinoma

ELISA = Enzyme-linked Immunosorbent Assay;. *EMSA = Electrophoretic Mobility Shift Assay. *FC = Flow Cytometry; ... DNA Methylation ELISAs & Other Assays * DNA Methyltransferases (DNMT) * DNMT Activity / Inhibition Assay ... Chromatin IP Assays. This antibody has been validated for use in ChIP and/or ChIP-Seq, and can be used with Active Motifs ChIP ... WEBINAR] Improved Chromatin Analysis with CUT&Tag Assays. * [WEBINAR] Utilizing Single-cell Workflows for Clinical Multiomics ...

https://www.activemotif.com/catalog/details/61467/dnmt1-antibody-mab-clone-2c1

Electrophoretic Mobility Shift Assay (EMSA) 18. Experimental Mouse Metastasis Model 19. Colony Formation Assay 20. Statistical ... Wound Healing Migration Assay, Trans-Well Migration, and Invasion Assay 13. Plasmid Construction 14. Lentivirus Production and ... Generation of the Reporter Construct and Luciferase Assay 17. Chromatin Immunoprecipitation Assay (ChIP) 18. ...

https://ndltd.ncl.edu.tw/cgi-bin/gs32/gsweb.cgi/login?o=dnclcdr&s=id=%22103YM005380008%22.&searchmode=basic

Extracts have been quality control tested by Western blot and the Electrophoretic Mobility Shift Assay (EMSA). ... Extracts have been quality control tested by Western blot and the Electrophoretic Mobility Shift Assay (EMSA). ... Multiplex miRNA assays. Multiplex Assays. By research area. Cancer. Cardiovascular. Cell Biology. Epigenetics. Metabolism. ... Cellular and biochemical assays. Proteins and Peptides. By product type. Proteomics tools. Agonists, activators, antagonists ...

https://www.abcam.com/lncap-nuclear-extract-lysate-ab14857.html

Practicals provide hands-on experience of currently used laboratory techniques such as electrophoretic mobility shift assay, ...

https://www.ed.ac.uk/global/study-abroad/course?year=22-23&vcf-period=semester_1&vcf-college=SCE&vcf-subject=Biology&course=70562

An electrophoretic mobility shift assay like the one exemplified here confirmed that Cas9/cgRNA stably bound to target DNA in ... Exemplary depiction of an electrophoretic mobility shift assay. Lane 1 = DNA; Lane 2 = DNA plus irrelevant (control) protein; ... After uncaging with light for incremental periods of time between 1 second to 30 minutes, this assay showed asymptotically ... Lane 3 = DNA plus specific DNA-binding protein causing band "shift" by slower eluting (higher molecular weight) DNA-protein ...

https://www.trilinkbiotech.com/blog/very-fast-crispr-vfcrispr-on-demand/

... kB DNA consensus sequences were examined using an electrophoretic mobility shift assay. The localization of p65 in the cells ...

http://www2.cdc.gov/nioshtic-2/BuildQyr.asp?s1=asbestos%2A&f1=TI&Startyear=&t1=1&s2=asbestos%2A&B1=Search&terms=3&Adv=1&f2=KW&Limit=500&Sort=DP%2BDESC&D1=75&EndYear=&PageNo=5&RecNo=371&View=f&

Electrophoretic Mobility Shift Assay 45% * Gels 33% * Gene Expression 24% * Genes 16% ...

https://mayoclinic.pure.elsevier.com/en/publications/the-schizosaccharomyces-pombe-mbf-complex-requires-heterodimeriza/fingerprints/?sortBy=alphabetically

For Electrophoretic Mobility Shift Assay (EMSA) Mt-4-Mt-1-Mt-7 ... Dead cytotoxicity assay kit was obtained from Molecular probes ... Luciferase assay kit (Promega#1500), Gateway cloning kit, DMEM, FBS, RPMI, Opti-MEM medium,Met-/Cys-DMEM, dialyzed FBS,trypsin- ... Kitfor TUNEL assay kit wasobtained from Invitrogen(Carlsbad, CA, USA). PCR reagents (PCR buffer, dNTPs, MgCl2, Taq DNA ...

https://hypothes.is/search?q=tag%3Amt-1

The cell viability assay and immunofluorescence study to know the status of kDNA were performed. Macrophages were infected with ... Tryparedoxin(TXN)-tryparedoxin peroxidase(TXNPx) assay as well as co-overexpression of cytochrome-b5 reductase-like protein ( ... Electrophoretic mobility shift assay (EMSA). The binding affinity of LdUMSBP with UMS in vitro was analysed by EMSA [28]. ... MTT assay to check the cell viability. The MTT assay is a quantitative colorimetric assay for measurement of metabolically ...

https://cellandbioscience.biomedcentral.com/articles/10.1186/s13578-016-0072-z

This element specifically binds HNF-4α in electrophoretic mobility shift assays. A luciferase-linked hOAT2 promoter fragment ...

https://molpharm.aspetjournals.org/content/67/5/1629

Electrophoretic mobility shift assay showing the binding complex of ELK1 protein and indicated probes, as indicated by red and ...

https://www.jci.org/articles/view/161308/figure/3

Electrophoretic mobility shift assays and reporter assays were used to assess activation of ETS1, ELK1, and ETV4 in response to ... Electrophoretic mobility shift assays and reporter assays were used to assess activation of ETS1, ELK1, and ETV4 in response to ... Electrophoretic mobility shift assays and reporter assays were used to assess activation of ETS1, ELK1, and ETV4 in response to ... A-C) Representative examples of electrophoretic mobility shift assays and mean values of probe binding intensity (expressed as ...

https://www.frontiersin.org/articles/10.3389/fphys.2021.683651/full

... as shown by electrophoretic-mobility-shift assays. ...

https://www.cell.com/ajhg/issue?pii=S0002-9297

Embryonic fibroblasts from IP patients demonstrated lack of NF-kappa-B activation upon electrophoretic mobility shift assay. ...

http://mips.helmholtz-muenchen.de/phenodis/disease/show/5666

In an electrophoretic mobility shift assay, each domain alone showed, however, nucleosome-binding activity. The binding of the ... Using two different in vitro assays, we found that the bromodomain/PHD finger region of the transcriptional cofactor p300 can ... In a nucleosome retention assay, both domains were required for binding. Replacement of the p300 PHD finger with other PHD ...

https://smart.embl.de/smart/do_annotation.pl?DOMAIN=PHD&START=1074&END=1120&E_VALUE=2.94e-2&TYPE=SMART&BLAST=KCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMFFKDKTMLCPMHK

Optix binding to the rpr-4S3 Dfd-HRE was additionally confirmed by electrophoretic mobility shift assay (EMSA) experiments. ... A cell-culture assay using the well-established Dfd responsive module responsible for rpr expression in a few anterior- ... In contrast, the MH-associated motor unit of Dfd3 animals shifted to the restrictive temperature during larval stages was ... Concomitantly, the morphology of synaptic boutons on this muscle was also changed in late-shifted Dfd3 third-instar larvae: ...

https://www.sdbonline.org/sites/FLY/segment/deformd1.htm

EMSA Chromatin Enzyme-linke Immunofluorescence Reporter Exon Protein ELISA Extracts Electrophoresis Chromatography Functional Gene Expression Mutant Absence Cell Bound Western Study Formation Properties Element Role

The Gelshift Chemiluminescent EMSA Assay Kit provides a simple, non-radioactive assay to identify protein-DNA binding with proven reagents. (activemotif.com)
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)
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)
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)
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)
Extracts have been quality control tested by Western blot and the Electrophoretic Mobility Shift Assay (EMSA). (abcam.com)
Electrophoretic mobility shift assay (EMSA) revealed intact binding ability in both control and arsenic-exposed offspring to a synthetic GRE. (unm.edu)
Another transcription factor BmILF regulates BmPOUM2 expression by binding to its i-motif structure, as demonstrated by electrophoretic mobility shift assay (EMSA) and DNA chromatin immunoprecipitation (DNA ChIP). (biomedcentral.com)

Transient transfection, gel mobility shift assays, and chromatin immunoprecipitation experiments showed that PGE 2 induced ILK promoter activity and increased Sp1, although it had no effect on nuclear factor-κB and AP-2 DNA-binding activity. (aacrjournals.org)
Electrophoretic mobility shift assay and chromatin immunoprecipitation assays confirmed NFκB binding to BMP-2 promoter upon IL-1β stimulation in beta cells. (ku.dk)
For example, the assay for transposase accessible chromatin with sequencing (ATAC-seq) maps regions of 'open' chromatin, which have the potential to regulate gene expression through binding of transcription factors. (bl.uk)
Using the electrophoretic mobility shift assay, I further show that two single nucleotide polymorphisms associated with Alzheimer's disease, and within regions of open chromatin in adult microglia, alter binding of protein from microglial nuclei. (bl.uk)

IMSEAR at SEARO: HIV-1 subtyping using gag/env heteroduplex mobility assay and peptide enzyme-linked immunosorbent assay. (who.int)
Simparak W, Kositanont U, Sutthent R, Wasinrapee P, Chaowanachan T, Wasi C. HIV-1 subtyping using gag/env heteroduplex mobility assay and peptide enzyme-linked immunosorbent assay. (who.int)
The blood samples were subtyped by heteroduplex mobility assay (HMA) and peptide enzyme-linked immunosorbent assay (PEIA). (who.int)

The cell viability assay and immunofluorescence study to know the status of kDNA were performed. (biomedcentral.com)

DNA constructs were cloned into a pGL3 promoter vector for luciferase gene reporter assays. (cdc.gov)
Electrophoretic mobility shift assays and reporter assays were used to assess activation of ETS1, ELK1, and ETV4 in response to Ang-1 exposure. (frontiersin.org)
Deoxyribonucleic acid fragments (approximately 1 kb in length) containing these regions were amplified and tested in reporter gene assays for steroid responsiveness. (unboundmedicine.com)
Nuclear factor kappa B- (NFκB) binding sites were identified in the rat BMP-2 promoter, and reporter assays verified the role of NFκB in cytokine-induced BMP-2 expression. (ku.dk)

Functional impact of the haplotype was determined by molecular genetic methods including real-time PCR, exon trapping, promoter deletion constructs and electrophoretic mobility shift assays. (biomedcentral.com)
Lastly, we knockdown candidate splice factors to determine their effect on MAPT exon 3 using a novel allele-specific qPCR assay. (ox.ac.uk)

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)
This difference in electrophoretic separation of DNA-protein complexes can be visualized as a 'shift' in migration of the labeled DNA band. (activemotif.com)
These regions were shown to specifically bind protein factors from nuclear extracts of A. franciscana nauplii by means of electrophoretic mobility shift assays. (biologists.com)
To confirm this idea, we carried out the kinetic studies, a gel mobility shift assay with a mutant protein disrupted in the catalytic center, and the analytical gel-filtration chromatography. (nih.gov)
Electrophoretic mobility shift assays detected allele-dependent nuclear protein binding in A549 cells for 8 of 21 variants. (cdc.gov)
The effects on nuclear protein binding to NF- kB DNA consensus sequences were examined using an electrophoretic mobility shift assay. (cdc.gov)
Tryparedoxin(TXN)-tryparedoxin peroxidase(TXNPx) assay as well as co-overexpression of cytochrome-b5 reductase-like protein (CBRL) and tryparedoxin in L. donovani were done to know the regulation of DNA binding activity of UMSBP. (biomedcentral.com)
J ) Electrophoretic mobility shift assay showing the binding complex of ELK1 protein and indicated probes, as indicated by red and black arrows, respectively ( top ). (jci.org)
To identify whether the protein is binding specifically to the probe, include a mutant probe and see if the shift occurs. (teamstudy.com)
We further investigated the functionality of this region using RNA-electrophoretic mobility shift assays to show differential RNA-protein complex formation at the H1 and H2 sequence variants of SNP rs17651213 and rs1800547 and subsequently identified candidate trans-acting splicing factors interacting with these functional SNPs sequences by RNA-protein pull-down experiment and mass spectrometry. (ox.ac.uk)

ZIKV Biotinylated-EDIII antigen capture ELISA in study of novel assay to measure ZIKV seroprevalence in the Philippines. (cdc.gov)

Risk and nonrisk oligonucleotides were tested for binding of nuclear extracts from A549, BEAS-2B, and IMR-90 lung cell lines by using electrophoretic mobility shift assays. (cdc.gov)
NF-κB in nuclear extracts was determined by electrophoretic mobility shift assay. (elsevier.com)

Electrophoretic gel shift analysis was performed in sodium dodecyl sulphate-polyacrylamide gel electrophoresis with biotinylated EDIII antigen in the presence and absence of streptavidin. (cdc.gov)
Typically one compound is labeled to follow its mobility during electrophoresis. (bvsalud.org)

We analyzed the mutant proteins by S-adenosyl-L-homocysteine affinity column chromatography, gel mobility shift assay, and kinetic assay of the methyl transfer reaction. (nih.gov)

Objective: The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. (cdc.gov)
Electrophoretic mobility shift assays demonstrated that both E-boxes are functional and that transcription factors are capable of binding to the E-box that contains the tri-allelic SNP. (medscape.com)

In the luciferase assay 4 of the 21 SNPs exhibited allele-dependent changes in gene expression. (cdc.gov)

Adherence assays revealed significantly reduced binding of the Δ rga mutant to epithelial HEp-2 cells and to immobilized human keratin 4, respectively. (microbiologyresearch.org)

Further dissection of the NF-kB complex in supershift assays demonstrated complete absence of p65 in the NF-kB complex, which is formed by homodimerization of the p50 component in pregnant FHF patients. (biomedcentral.com)

Cell death was determined by the MTT assay, and apoptosis by Annexin V-FITC staining and caspase-3 activity. (greenmedinfo.com)

Electrophoretic mobility shift assays demonstrated that progesterone receptors (PR) bound to the HRE in pIE1, whereas both PR and glucocorticoid receptors interacted with the HRE in pIE2. (unboundmedicine.com)
If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded. (bvsalud.org)

NF-κB signaling was examined by real-time RT-PCR for interleukin (IL)-8, by Western blotting for IκB phosphorylation/degradation, and by the electrophoretic mobility shift assay. (greenmedinfo.com)

We used electrophoretic mobility shift assays, immunoblotting, and immunohistochemical analysis to study the expression and DNA binding activity of NF-kB p50 and NF-kB p65 in pregnant fulminant hepatic failure (FHF) patients and compared them with their nonpregnant counterparts. (biomedcentral.com)

Electrophoretic mobility shift assay reveals a total inhibition of LPS-induced formation of nuclear factor κB.DNA binding complexes by phenolic antioxidants. (cdc.gov)
TIC self-renewal was examined by oncosphere formation and tumor initiation assay. (biomedcentral.com)

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)