DNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Protein Footprinting: A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Deoxyribonuclease I: An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Sulfuric Acid Esters: Organic esters of sulfuric acid.Hydroxyl Radical: The univalent radical OH. Hydroxyl radical is a potent oxidizing agent.Nucleotide Mapping: Two-dimensional separation and analysis of nucleotides.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Distamycins: Oligopeptide antibiotics from Streptomyces distallicus. Their binding to DNA inhibits synthesis of nucleic acids.Potassium Permanganate: Permanganic acid (HMnO4), potassium salt. A highly oxidative, water-soluble compound with purple crystals, and a sweet taste. (From McGraw-Hill Dictionary of Scientific and Technical Information, 4th ed)Echinomycin: A cytotoxic polypeptide quinoxaline antibiotic isolated from Streptomyces echinatus that binds to DNA and inhibits RNA synthesis.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Bacterial Proteins: Proteins found in any species of bacterium.Hydroxides: Inorganic compounds that contain the OH- group.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Sp1 Transcription Factor: Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Operator Regions, Genetic: The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Intercalating Agents: Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.PhenanthrolinesDNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Netropsin: A basic polypeptide isolated from Streptomyces netropsis. It is cytotoxic and its strong, specific binding to A-T areas of DNA is useful to genetics research.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Encyclopedias as Topic: Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)Chromomycin A3: Glycosidic antibiotic from Streptomyces griseus used as a fluorescent stain of DNA and as an antineoplastic agent.Chromomycins: A complex of several closely related glycosidic antibiotics from Streptomyces griseus. The major component, CHROMOMYCIN A3, is used as a fluorescent stain of DNA where it attaches and inhibits RNA synthesis. It is also used as an antineoplastic agent, especially for solid tumors.Olivomycins: A mixture of several closely related glycosidic antibiotics obtained from Actinomyces (or Streptomyces) olivoreticuli. They are used as fluorescent dyes that bind to DNA and prevent both RNA and protein synthesis and are also used as antineoplastic agents.Plicamycin: 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.Genes, Tumor Suppressor: Genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check. When tumor suppressor genes are inactivated or lost, a barrier to normal proliferation is removed and unregulated growth is possible.Tumor Suppressor Proteins: Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.Hepatitis, Infectious Canine: A contagious disease caused by canine adenovirus (ADENOVIRUSES, CANINE) infecting the LIVER, the EYE, the KIDNEY, and other organs in dogs, other canids, and bears. Symptoms include FEVER; EDEMA; VOMITING; and DIARRHEA.Tumor Suppressor Protein p53: Nuclear phosphoprotein encoded by the p53 gene (GENES, P53) whose normal function is to control CELL PROLIFERATION and APOPTOSIS. A mutant or absent p53 protein has been found in LEUKEMIA; OSTEOSARCOMA; LUNG CANCER; and COLORECTAL CANCER.Dog Diseases: Diseases of the domestic dog (Canis familiaris). This term does not include diseases of wild dogs, WOLVES; FOXES; and other Canidae for which the heading CARNIVORA is used.Cell Line, Tumor: A cell line derived from cultured tumor cells.Loss of Heterozygosity: The loss of one allele at a specific locus, caused by a deletion mutation; or loss of a chromosome from a chromosome pair, resulting in abnormal HEMIZYGOSITY. It is detected when heterozygous markers for a locus appear monomorphic because one of the ALLELES was deleted.

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (1/1876)

Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed.  (+info)

Transposition of the autonomous Fot1 element in the filamentous fungus Fusarium oxysporum. (2/1876)

Autonomous mobility of different copies of the Fot1 element was determined for several strains of the fungal plant pathogen Fusarium oxysporum to develop a transposon tagging system. Two Fot1 copies inserted into the third intron of the nitrate reductase structural gene (niaD) were separately introduced into two genetic backgrounds devoid of endogenous Fot1 elements. Mobility of these copies was observed through a phenotypic assay for excision based on the restoration of nitrate reductase activity. Inactivation of the Fot1 transposase open reading frame (frameshift, deletion, or disruption) prevented excision in strains free of Fot1 elements. Molecular analysis of the Nia+ revertant strains showed that the Fot1 element reintegrated frequently into new genomic sites after excision and that it can transpose from the introduced niaD gene into a different chromosome. Sequence analysis of several Fot1 excision sites revealed the so-called footprint left by this transposable element. Three reinserted Fot1 elements were cloned and the DNA sequences flanking the transposon were determined using inverse polymerase chain reaction. In all cases, the transposon was inserted into a TA dinucleotide and created the characteristic TA target site duplication. The availability of autonomous Fot1 copies will now permit the development of an efficient two-component transposon tagging system comprising a trans-activator element supplying transposase and a cis-responsive marked element.  (+info)

P1 ParA interacts with the P1 partition complex at parS and an ATP-ADP switch controls ParA activities. (3/1876)

The partition system of P1 plasmids is composed of two proteins, ParA and ParB, and a cis-acting site parS. parS is wrapped around ParB and Escherichia coli IHF protein in a higher order nucleoprotein complex called the partition complex. ParA is an ATPase that autoregulates the expression of the par operon and has an essential but unknown function in the partition process. In this study we demonstrate a direct interaction between ParA and the P1 partition complex. The interaction was strictly dependent on ParB and ATP. The consequence of this interaction depended on the ParB concentration. At high ParB levels, ParA was recruited to the partition complex via a ParA-ParB interaction, but at low ParB levels, ParA removed or disassembled ParB from the partition complex. ADP could not support these interactions, but could promote the site-specific DNA binding activity of ParA to parOP, the operator of the par operon. Conversely, ATP could not support a stable interaction of ParA with parOP in this assay. Our data suggest that ParA-ADP is the repressor of the par operon, and ParA-ATP, by interacting with the partition complex, plays a direct role in partition. Therefore, one role of adenine nucleotide binding and hydrolysis by ParA is that of a molecular switch controlling entry into two separate pathways in which ParA plays different roles.  (+info)

Hepatocyte nuclear factor-4 regulates intestinal expression of the guanylin/heat-stable toxin receptor. (4/1876)

We have investigated the regulation of gene transcription in the intestine using the guanylyl cyclase C (GCC) gene as a model. GCC is expressed in crypts and villi in the small intestine and in crypts and surface epithelium of the colon. DNase I footprint, electrophoretic mobility shift assay (EMSA), transient transfection assays, and mutagenesis experiments demonstrated that GCC transcription is regulated by a critical hepatocyte nuclear factor-4 (HNF-4) binding site between bp -46 and -29 and that bp -38 to -36 were essential for binding. Binding of HNF-4 to the GCC promoter was confirmed by competition EMSA and by supershift EMSA. In Caco-2 and T84 cells, which express both GCC and HNF-4, the activity of GCC promoter and/or luciferase reporter plasmids containing 128 or 1973 bp of 5'-flanking sequence was dependent on the HNF-4 binding site in the proximal promoter. In COLO-DM cells, which express neither GCC nor HNF-4, cotransfection of GCC promoter/luciferase reporter plasmids with an HNF-4 expression vector resulted in 23-fold stimulation of the GCC promoter. Mutation of the HNF-4 binding site abolished this transactivation. Transfection of COLO-DM cells with the HNF-4 expression vector stimulated transcription of the endogenous GCC gene as well. These results indicate that HNF-4 is a key regulator of GCC expression in the intestine.  (+info)

Specific binding of the E2 subunit of pyruvate dehydrogenase to the upstream region of Bacillus thuringiensis protoxin genes. (5/1876)

During sporulation, Bacillus thuringiensis produces inclusions comprised of different amounts of several related protoxins, each with a unique specificity profile for insect larvae. A major class of these genes designated cry1 have virtually identical dual overlapping promoters, but the upstream sequences differ. A gel retardation assay was used to purify a potential regulatory protein which bound with different affinities to these sequences in three cry1 genes. It was identified as the E2 subunit of pyruvate dehydrogenase. There was specific competition for binding by homologous gene sequences but not by pUC nor Bacillus subtilis DNA; calf thymus DNA competed at higher concentrations. The B. thuringiensis gene encoding E2 was cloned, and the purified glutathione S-transferase-E2 fusion protein footprinted to a consensus binding sequence within an inverted repeat and to a potential bend region, both sites 200-300 base pairs upstream of the promoters. Mutations of these sites in the cry1A gene resulted in decreased binding of the E2 protein and altered kinetics of expression of a fusion of this regulatory region with the lacZ gene. Recruitment of the E2 subunit as a transcription factor could couple the change in post exponential catabolism to the initiation of protoxin synthesis.  (+info)

Genes for the human mitochondrial trifunctional protein alpha- and beta-subunits are divergently transcribed from a common promoter region. (6/1876)

Human HADHA and HADHB genes encode the subunits of an enzyme complex, the trifunctional protein, involved in mitochondrial beta-oxidation of fatty acids. Both genes are located in the same region of chromosome 2p23. We isolated genomic clones, including 5' flanking regions, for HADHA and HADHB. Sequencing revealed that both of these genes are linked in a head-to-head arrangement on opposite strands and have in common a 350-bp 5' flanking region. The 5' flanking region has bidirectional promoter activity within this region; two cis elements proved critical for the activity. Transcription factor Sp1 functions as an activator for the bidirectional promoter by binding to both elements. Therefore, expression of trifunctional protein subunits are probably coordinately regulated by a common promoter and by Sp1.  (+info)

Hoxa5 gene regulation: A gradient of binding activity to a brachial spinal cord element. (7/1876)

The Hox genes cooperate in providing positional information needed for spatial and temporal patterning of the vertebrate body axis. However, the biological mechanisms behind spatial Hox expression are largely unknown. In transgenic mice, gene fusions between Hoxa5 (previously called Hox-1.3) 5' flanking regions and the lacZ reporter gene show tissue- and time-specific expression in the brachial spinal cord in day 11-13 embryos. A 604-bp regulatory region with enhancer properties directs this spatially specific expression. Fine-detail mapping of the enhancer has identified several elements involved in region-specific expression, including an element required for expression in the brachial spinal cord. Factors in embryonic day 12.5 nuclear extracts bind this element in electrophoretic mobility shift assays (EMSA) and protect three regions from DNase digestion. All three sites contain an AAATAA sequence and mutations at these sites reduce or abolish binding. Furthermore, this element binds specific individual embryonic proteins on a protein blot. The binding activity appears as a gradient along the anterior-posterior axis with two- to threefold higher levels observed in extracts from anterior regions than from posterior regions. In parallel with the EMSA, the proteins on the protein blot also show reduced binding to probes with mutations at the AAATAA sites. Most importantly, transgenic mice carrying Hoxa5/lacZ fusions with the three AAATAA sites mutated either do not express the transgene or have altered transgene expression. The brachial spinal cord element and its binding proteins are likely to be involved in spatial expression of Hoxa5 during development.  (+info)

The GATA factor AreA is essential for chromatin remodelling in a eukaryotic bidirectional promoter. (8/1876)

The linked niiA and niaD genes of Aspergillus nidulans are transcribed divergently. The expression of these genes is subject to a dual control system. They are induced by nitrate and repressed by ammonium. AreA mediates derepression in the absence of ammonium and NirA supposedly mediates nitrate induction. Out of 10 GATA sites, a central cluster (sites 5-8) is responsible for approximately 80% of the transcriptional activity of the promoter on both genes. We show occupancy in vivo of site 5 by the AreA protein, even under conditions of repression. Sites 5-8 are situated in a pre-set nucleosome-free region. Under conditions of expression, a drastic nucleosomal rearrangement takes place and the positioning of at least five nucleosomes flanking the central region is lost. Remodelling is strictly dependent on the presence of an active areA gene product, and independent from the NirA-specific and essential transcription factor. Thus, nucleosome remodelling is independent from the transcriptional activation of the niiA-niaD promoter. The results presented cast doubts on the role of NirA as the unique transducer of the nitrate induction signal. We demonstrate, for the first time in vivo, that a GATA factor is involved directly in chromatin remodelling.  (+info)

  • However, as radioactive labeling has safety concern and is not as convenient as fluorescence labeling, Profacgen uses fluorescence labeling in combination with sequencer (e.g. supplied by Applied Biosystem), enabling our DNase I footprinting assay safer, faster and more sensitive. (profacgen.com)
  • Reference: DNA footprinting studies of the complex formed by the T4 DNA polymerase holoenzyme at a primer-template junction. (neb.com)
  • Note: Maxam-Gilbert chemical DNA sequencing can be run alongside the samples on the polyacrylamide gel to allow the prediction of the exact location of ligand binding site. (wikipedia.org)
  • The DNA template labeled at the 3' or 5' end, depending on the location of the binding site(s). (wikipedia.org)
  • Radioactivity has been traditionally used to label DNA fragments for footprinting analysis, as the method was originally developed from the Maxam-Gilbert chemical sequencing technique. (wikipedia.org)
  • In 1978, David Galas and Albert Schmitz developed the DNA footprinting technique to study the binding specificity of the lac repressor protein. (wikipedia.org)
  • Ultraviolet irradiation can be used to excite nucleic acids and create photoreactions, which results in damaged bases in the DNA strand. (wikipedia.org)
  • In situ detection of protein-DNA interactions in filamentous fungi by in vivo footprinting. (nih.gov)
  • The method described here allows the detection of protein-DNA interactions in vivo in filamentous fungi. (nih.gov)
  • Carey MF, Peterson CL, Smale ST. In vivo dimethyl sulfate (DMS) footprinting via ligation-mediated polymerase chain reaction (LM-PCR). (umassmed.edu)
  • A number of interesting variations to conventional double-helical DNA structure have been detected in vitro (e.g. triple-helical DNA, Z-form DNA, G-quadruplex DNA) but the in vivo biology of such putative structures remains obscure at best. (mayo.edu)
  • Nicole traveled to the City of Hope National Medical Center to learn from Gerd Pfeiffer techniques for in vivo footprinting by ligation-mediated PCR for application to monitoring DNA structure in vivo. (mayo.edu)
  • Her work detected no unusual DNA structures in vivo at these sites, raising important questions about the prevalence of unusual DNA structures in vivo. (mayo.edu)
  • DNA methylation alone is not sufficient to prevent protein binding in vivo. (uni-muenchen.de)
  • An in vivo phosphorylation-dependent change in binding of CREB increases the occupancy of weak binding sites used for transactivation, such as the TATCRE, while high affinity sites may have constitutive binding of transcriptionally active and inactive CREB dimers, as demonstrated by in vivo footprinting at the PEPCK CRE. (uni-muenchen.de)
  • FUSE is melted in vivo when c-myc is expressed, and the solution structure of the FBP-FUSE complex demonstrates that single-stranded DNA is slotted into the grooves of FBP's KH-domains. (cancer.gov)
  • The revolution in biological research initiated by the demonstration that particular DNA molecules could be isolated, recombined in novel ways, and conveniently replicated to high copy number in vivo for further study, that is, the recombinant DNA era, has spawned many additional advances, both methodological and intellectual, that have enhanced our understanding of cellular processes to an astonishing degree. (worldcat.org)
  • Put more simply, that an interaction can be demonstrated to occur between purified factors and a particular piece of DNA in a test tube does not, of course, say anything regarding whether such interactions are occurring in vivo. (worldcat.org)
  • The ability to probe for such interactions as they occur inside cells, with due attention paid to the relevant developmental stage, or to the tissue specificity of the interaction being probed, has made in vivo footprinting approach an invaluable adjunct to the "gene jockey's" arsenal of weapons. (worldcat.org)
  • A Perspective on In Vivo Footprinting (M. Nenoi and I.L. Cartwright). (worldcat.org)
  • Dr. Kouzine focuses on the understanding of how mechanical forces generated by genetic processes modify DNA and chromatin structure to regulate genes in health and disease. (cancer.gov)
  • Dr. Kouzine's research interests currently focus on the coupling and interdependence of DNA topology, DNA structure, chromatin architecture and transcription from a genome-wide perspective. (cancer.gov)
  • They are therefore central to the regulation of multiple cellular processes, such as chromatin remodeling and DNA replication. (port.ac.uk)
  • Additionally, we found that based on a genome-wide profiling of ∼100 recombinant yeast strains, the location of open chromatin borders tends to vary mostly within 150 bp upon genetic perturbation whereas this positional variation increases in proportion to the sequence preferences of the underlying DNA for nucleosome formation. (prolekare.cz)
  • Open chromatin provides access to a wide spectrum of DNA binding proteins for genetic regulation processes such as transcription, repair, recombination, and replication. (prolekare.cz)
  • We have systematically measured the effect of normal genetic variation present in a human population on the binding of a specific chromatin protein (CTCF) to DNA by measuring its binding in 51 human cell lines. (prolekare.cz)
  • Interestingly, methylation interference and DNA footprinting analyses show almost indistinguishable patterns between ternary and bromocomplexes, suggesting that CBP-(1100-1286) interacts via Elk-1 and does not require specific DNA contacts. (cnrs.fr)
  • His research focuses on the genetic and epigenetic mechanisms of carcinogenesis with a special emphasis on DNA damage and repair, mutagenesis, DNA methylation, and histone modifications. (usc.edu)
  • A Versatile Assay for Detection of Aberrant DNA Methylation in Bladder Cancer Methods Mol Biol. (usc.edu)
  • Epigenetic alterations, such as deoxyribonucleic acid (DNA) methylation, play a role in carcinogenesis. (els.net)
  • Some tumours have a very large number of genetic alterations (chromosomal rearrangements, point mutations and DNA methylation), and others have many fewer alterations. (els.net)
  • Type I enzymes are the most complex, being multi-subunit enzymes with both DNA methylation (MTase) and endonuclease (ENase) activity. (port.ac.uk)
  • The generality of the repressive nature of cytosine methylation is widely admitted now, but the role of this DNA modification is still controversial. (embopress.org)
  • Biochemical Techniques for the Characterization of G-Quadruplex Structures: EMSA, DMS Footprinting, and DNA Polymerase Stop Assay. (alfa.com)
  • Preferred assay conditions are also provided for recognition of homopurine-homopyrimidine double-helical tracts within large DNA by triple helix formation under physiological conditions. (google.com)
  • An integrated encyclopedia of DNA elements in the human genome. (umassmed.edu)
  • The complex structure and repetitive nature of eukaryotic ribosomal DNA (rDNA) is a challenge for genome assembly, thus the consequences of sequence variation in rDNA remain unexplored. (genetics.org)
  • Thus, genome-wide DH site mapping will be an important tool for systematic identification of all cis -regulatory DNA elements in plants. (plantcell.org)
  • The Arabidopsis DH sites were significantly associated with various cis -regulatory DNA elements previously characterized in the Arabidopsis genome. (plantcell.org)
  • Junk DNA: A Journey Through the Dark Matter of the Genome , by Nessa Carey, ISBN:9780231539418, Columbia University Press, Apr 2015. (panspermia.org)
  • His work showed that in living cells torque generated during transcription modifies DNA structure dynamically at particular supercoil-sensitive spots in the genome. (cancer.gov)
  • Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. (cancer.gov)
  • M. Blanchette , M. Tompa , 'Discovery of regulatory elements by a computational method for phylogenetic footprinting' , Genome Res. (washington.edu)
  • By using randomly damaged DNA as substrate and a variety of methods including filter binding and gel retardation assays for detecting DNA-protein complexes, it has been shown that RPA ( 9 , 10 ), XPA ( 11 , 12 ), the combination of XPA and RPA ( 13 , 14 ), and XPC ( 15 ) bind with moderately higher affinity to damaged DNA compared with undamaged DNA. (pnas.org)
  • Gel retardation assays performed with a DNA fragment carrying the PrfA binding site of the plcA promoter demonstrated that the PrfA* mutant form is much more efficient than wild-type PrfA at forming specific DNA-protein complexes. (asm.org)
  • Stasiak et al, "Visualization of RecA-DNA complexes involved in consecutive stages of an in vitro strand exchange reaction", Cold Spring Harbor Symposia on Quantitative Biology 49: 561 (1984). (patentgenius.com)
  • Footprinting with methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] is used to identify high-affinity polyamide-binding sites to near nucleotide resolution. (caltech.edu)
  • Affinity cleavage is used to determine the orientation of the bound polyamide in the minor groove of DNA. (caltech.edu)
  • In the design phase, it is often the case that the sequence preference, as well as the energetics of any new molecule binding at each potential site, is not perfectly understood and it is crucial to scan "libraries" of many potential DNA-binding sites in order to identify true high-affinity binding sites. (caltech.edu)
  • To investigate how the structurally dissimilar GABP α and β subunits form a tight heterodimer with enhanced DNA-binding affinity, we determined the crystal structure of the GABPα/β ETS domain-ankyrin repeat heterodimer bound to DNA. (sciencemag.org)
  • The 9-aza-APs exhibit prominent affinity for DNA, with an important electrostatic contribution to the binding free energy. (aspetjournals.org)
  • Hence, bioisosteric substitution and ring-hydroxy deletion play an important role in defining the physicochemical properties and in modulating the affinity of anthrapyrazoles for the nucleic acid, the geometry of the intercalation complex, and the sequence specific contacts along the DNA chain. (aspetjournals.org)
  • Our results show that both the DNA substrate and the C-terminal winged-helix (WH) domain influence the orientation but that translocation on DNA proceeds N-first. (elifesciences.org)
  • The MCM proteins themselves are bilobal with a N-terminal domain (NTD) that acts to stabilize binding to single-strand DNA (ssDNA), a C-terminal domain (CTD) that contains the conserved AAA + (ATPases associated with diverse cellular activities) motor domain that provide energy for translocation and DNA unwinding, and a winged-helix (WH) domain for DNA binding ( Trakselis, 2016 ). (elifesciences.org)
  • These proteins have in common a conserved DNA-binding domain whose structure, as determined for the ETS proteins Fli-1, Ets-1, and PU.1, has an overall topology similar to that of the "winged helix-turn-helix" family of proteins ( 6-9 ). (sciencemag.org)
  • Techniques like DNA footprinting help elucidate which proteins bind to these associated regions of DNA and unravel the complexities of transcriptional control. (wikipedia.org)
  • Any of various techniques used to determine the sites at which proteins bind to DNA or RNA, employed especially in the study of gene expression and regulation. (oxforddictionaries.com)
  • Thus, information on what proteins bind to cis -regulatory DNA elements and when and where these proteins bind is important to understand the regulation and thus function of each gene. (plantcell.org)
  • To delineate the ligase-DNA interface, we have footprinted the enzyme binding site on DNA and the DNA binding site on ligase. (westminster.ac.uk)
  • Protease cleavage of the native enzyme prior to DNA addition results in loss of DNA binding. (westminster.ac.uk)
  • Drug stimulation of topoisomerase II-mediated DNA cleavage is remarkably attenuated in the aza-bioisosteric derivatives, suggesting that other non-enzyme-mediated cytotoxic mechanism(s), possibly connected with free radical production, are responsible for efficient cell killing. (aspetjournals.org)
  • We have shown that DNA binding triggers a large contraction of the open form of the enzyme to a compact form. (port.ac.uk)
  • DNA Modifying Enzymes: Cytosine-C5-specific DNA methyltransferases, in particular the monospecific enzyme, M. (sheffield.ac.uk)
  • These can influence the kinetic properties and/or structures of the intermediate RNA polymerase-DNA complexes in the pathway. (upmc.fr)
  • Nicole Becker received her BS degree in biotechnology from St. Cloud State University and came to Mayo Graduate School to study the potential for monitoring the formation of unusual DNA structures within living cells. (mayo.edu)
  • These structures share the property of having unpaired DNA bases within or adjacent to their location if embedded in B-form DNA. (mayo.edu)
  • These unusual DNA structures then bind by specialized factors to feedback regulate gene expression. (cancer.gov)
  • Finally, in the paused complexes, the Q DNA-binding element is in a position analogous to binding sites of transcription activators that contact σ 70 region 4 in open complex ( 19 ). (pnas.org)
  • Gene expression in eukaryotes is frequently mediated by multiprotein complexes that bind DNA in a sequence-specific manner. (sciencemag.org)
  • The path followed by DNA through the complexes is revealed by EM, using an anti-restriction protein that acts as a DNA mimic. (port.ac.uk)
  • Following biophysical analysis of the relevant DNA-protein complexes underpinning the switch, we have determined the 3D molecular structure of each of the complexes by X-ray crystallography, thereby elucidating the mechanism of R-M gene regulation and paving the way to understanding the principles of differential DNA sequence recognition. (port.ac.uk)
  • We have constructed a nanoplasmonic molecular ruler, which can perform label-free and real-time monitoring of DNA length changes and perform DNA footprinting. (unt.edu)
  • We suggest that Cdc6 and origin DNA activate a molecular switch in ORC that contributes to pre-RC assembly. (nih.gov)
  • Results: We developed a computational protocol based on molecular and structural criteria to perform biologically meaningful and accurate phylogenetic footprinting analyses. (mendeley.com)
  • The Levens Lab has shown that torque generated during transcription of MYC modifies DNA structure dynamically at the FUSE element, that together with FUSE Binding Protein and FBP Interacting Repressor is molecular cruise control for MYC. (cancer.gov)
  • They are molecular motors, hydrolysing ATP to translocate along DNA prior to cleavage. (port.ac.uk)
  • RNA and DNA Polymerases present opportunities for developing a range of molecular biology methods and are in themselves key enzymes in cellular physiology. (sheffield.ac.uk)
  • DNA Complexed Structure of the Key Transcription Factor Initiating Development in Sporulating Bacteria Structure (London, England : 1993). (jove.com)
  • Since it has been suggested that CHR binding alters DNA to the A configuration, quantitative footprinting studies using dimethyl sulfate, which alkylates at N-7 of guanine in the major groove, were also carried out. (syr.edu)
  • AlgR, which belongs to a novel family of response regulators with an unusual LytTR DNA binding domain ( 27 ), plays an important role in the regulation of gene expression in P. aeruginosa ( 19 ). (asm.org)
  • Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. (biomedcentral.com)
  • ETS domain proteins make up a large family of DNA-binding proteins found in organisms ranging from fruit flies to humans that play a role in a variety of developmental pathways, in oncogenesis, and in viral gene expression ( 5 ). (sciencemag.org)
  • Footprinting and fluorescence data indicate that the dimerization constant for the drug in solution is ∼ 10 5 M -1 . (syr.edu)
  • Using a combination of site-specific DNA footprinting, single-turnover unwinding assays, and unique fluorescence translocation monitoring, we have been able to quantify the binding distribution and the translocation orientation of Saccharolobus (formally Sulfolobus ) solfataricus MCM on DNA. (elifesciences.org)
  • To test the proposed bent-wrapped model of duplex DNA in an advanced RNAP- λ P R CC and compare wrapping in the CC and OC, we use fluorescence resonance energy transfer (FRET) between cyanine dyes at far-upstream (−100) and downstream (+14) positions of promoter DNA. (pubmedcentralcanada.ca)
  • This allows the use of promoter bashing to not only discover the location on the DNA strand which affects transcription, but also the proteins which affect that strand. (wikipedia.org)
  • Clone the region of DNA thought to act as a promoter. (wikipedia.org)
  • Allowing activators and repressors to influence sequentially the rate of nucleotide addition between initiation and promoter escape provides a means to sample and integrate the array of DNA-bound transfactors for the genesis of a single transcript. (cancer.gov)
  • Initial recognition of promoter DNA by RNA polymerase (RNAP) is proposed to trigger a series of conformational changes beginning with bending and wrapping of the 40-50 bp of DNA immediately upstream of the −35 region. (pubmedcentralcanada.ca)
  • Wrapping of upstream DNA around RNAP brings it near the α NTD (which act as hinges at the base of the active site cleft) and also near the downstream cleft, triggering conformational changes in the cleft and in downstream mobile elements (DMEs) of RNAP at the λ P R promoter. (pubmedcentralcanada.ca)
  • 1 , 4 , 12 These conformational changes facilitate bending of the downstream duplex into the cleft to form the most advanced CC prior to opening, in which more than 100 bp of promoter DNA (−82 to +20) interacts with RNAP. (pubmedcentralcanada.ca)
  • This selectivity is partially determined by conformational flexibility of the DNA sequence, and the covalent adduct has a bent DNA structure in which narrowing of the minor groove has occurred. (elsevier.com)
  • Significantly, the locus of bending at these sites is spaced approximately two helical turns apart, and the bending is proposed to occur by narrowing of the minor groove of DNA. (elsevier.com)
  • Guanine‐rich regions of nucleic acids can fold into G‐quadruplex, a secondary structure formed by four strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). (els.net)
  • Chromomycin A 3 (CHR) binding to the duplex d(CAAGTCTGGCCATCAGTC)· d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. (syr.edu)
  • These easily reproducible methods involve sequence recognition properties, as well as physical approaches to measuring both the strength of interaction and the mode of drug binding to DNA. (springer.com)
  • Elsewhere on SE Biology I have summarized the strategy of different DNA sequencing methods, so I shall use that as a starting point for this answer. (stackexchange.com)
  • Both DNA and RNA G‐quadruplexes are found in biological systems: They have been computationally predicted and experimentally demonstrated by several methods in the genomes of several organisms, including humans, other eukaryotes, bacteria and viruses. (els.net)
  • Time-resolved footprinting techniques combine the high temporal resolution of a stopped-flow apparatus with the specific structural information obtained by the probing agent. (upmc.fr)
  • J. Buhler , T. Ideker , D. Haynor , 'Dapple: Improved Techniques for Finding Spots on DNA Microarrays' , University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-2000-08-05 , (2000) Supplement . (washington.edu)
  • An Alu element is a short stretch [2-8 nucleotides] of DNA originally characterized by the action of the Alu ( Arthrobacter luteus ) restriction endonuclease. (wikiversity.org)
  • Ultraviolet irradiation can be used to excite nucleic acids and create photoreactions, which results in damaged bases in the DNA strand. (wikipedia.org)
  • Gel mobility shift assays revealed the wound-inducible DNA-binding activity to the −242/−223 region in both stem and leaf nuclear extracts. (plantphysiol.org)
  • Here we demonstrate cooperative binding of Saccharomyces cerevisiae Cdc6 to ORC on DNA in an ATP-dependent manner, which induces a change in the pattern of origin binding that requires the Orc1 ATPase. (nih.gov)
  • DNA binding and glutathione S-transferase pull-down assays demonstrate that binding requires Elk-1(1-212) but not the C-terminal transactivation domain. (cnrs.fr)
  • Thus FBP-FIR action is obligatorily coupled with factors, processes or conditions that destabilize duplex DNA. (cancer.gov)
  • Kinetic studies demonstrated that the presence of upstream DNA facilitates bending and entry of the downstream duplex (to +20) into the active site cleft to form an advanced closed complex (CC), prior to melting of ~13 bp (−11 to +2), including the transcription start site (+1). (pubmedcentralcanada.ca)
  • Electrophoretic sequencing gels or capillary electrophoresis have been successful in analyzing footprinting of fluorescent tagged fragments. (wikipedia.org)
  • End-labelling of one end of the original DNA allowed fragments containing the reference point to be visualized, distinguishing them from others that were unlabelled and hence generated elsewhere. (stackexchange.com)
  • bacterial artificial chromosome (BAC) Artificial chromosome vector derived from bacteria used for cloning relatively large DNA fragments. (kumc.edu)
  • This is a covalent bond between atoms, stable and permanent as opposed to the three hydrogen bonds established after base-pairing of C and G in opposite strands of DNA. (wikiversity.org)
  • The reaction is blocked by specific origin mutations that do not interfere with the interaction between ORC and DNA. (nih.gov)
  • We investigated the interaction of PrfA and PrfA* (Gly145Ser) with target DNA. (asm.org)