Dna footprinting. Medical search

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)

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.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

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.

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.

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.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

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.

Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.

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.

Organic esters of sulfuric acid.

The univalent radical OH. Hydroxyl radical is a potent oxidizing agent.

Two-dimensional separation and analysis of nucleotides.

Nucleic acid sequences involved in regulating the expression of genes.

The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

Oligopeptide antibiotics from Streptomyces distallicus. Their binding to DNA inhibits synthesis of nucleic acids.

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)

A cytotoxic polypeptide quinoxaline antibiotic isolated from Streptomyces echinatus that binds to DNA and inhibits RNA synthesis.

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 found in any species of bacterium.

Inorganic compounds that contain the OH- group.

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.

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.

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.

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.

The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.

Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.

Proteins found in 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.

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.

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.

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.

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.

Deoxyribonucleic acid that makes up the genetic material of bacteria.

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.

Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.

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.

Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.

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)

Polymers where the main polymer chain comprises recurring amide groups. These compounds are generally formed from combinations of diamines, diacids, and amino acids and yield fibers, sheeting, or extruded forms used in textiles, gels, filters, sutures, contact lenses, and other biomaterials.

Azoles of one NITROGEN and two double bonds that have aromatic chemical properties.

Compounds containing 1,3-diazole, a five membered aromatic ring containing two nitrogen atoms separated by one of the carbons. Chemically reduced ones include IMIDAZOLINES and IMIDAZOLIDINES. Distinguish from 1,2-diazole (PYRAZOLES).

The covalent bonding of an alkyl group to an organic compound. It can occur by a simple addition reaction or by substitution of another functional group.

Glycosidic antibiotic from Streptomyces griseus used as a fluorescent stain of DNA and as an antineoplastic agent.

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.

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.

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 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.

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.

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.

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.

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.

A cell line derived from cultured tumor cells.

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)

Site-directed mutagenesis Restriction digest DNA footprinting Kamvysselis, M. (2003). Computational molecular genomics: genes, ... This step often involves extraction of the DNA from the organism it resides in and PCR amplification. Sequence the region. DNA ... Promoter bashing is often done with deletions from either the 5' or 3' end of the DNA strand; this assay is easier to perform ... This is an example procedure for a promoter bashing assay, adapted from Boulin et al.: Clone the region of DNA thought to act ...

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

It is different from the more commonly used DNA footprinting assay. The toeprinting assay has been utilized to examine the ... To do a toeprint assay, one need the mRNA of interest, ribosomes, a DNA primer, free nucleotides, and reverse transcriptase (RT ...

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

"A nanoplasmonic molecular ruler for measuring nuclease activity and DNA footprinting". Nature Nanotechnology. Springer Science ...

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

This method is deployed for DNA sequencing, genome walking, and DNA footprinting. A related technique is amplified fragment ... thus directing DNA synthesis from defined DNA sequences present in the sample. Presence of the target sequence initiates DNA ... "DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA". Proc. ... There are several DNA polymerases that are used in PCR. The Klenow fragment, derived from the original DNA Polymerase I from E ...

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

DMS modification can also be used for DNA, for example in footprinting DNA-protein interactions. Selective 2′-hydroxyl ... Tullius, T. D.; Dombroski, B. A. (1986). "Hydroxyl radical "footprinting": high-resolution information about DNA-protein ... When the RNA is reverse transcribed using a reverse transcriptase into a DNA copy, the DNA generated is truncated at the ... The collection of DNA molecules of various truncated lengths therefore informs the frequency of reaction at every base position ...

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

PAGE gels are widely used in techniques such as DNA foot printing, EMSA and other DNA-protein interaction techniques. The ... DNA damage due to increased cross-linking will also reduce electrophoretic DNA migration in a dose-dependent way. Circular DNA ... The gel sieves the DNA by the size of the DNA molecule whereby smaller molecules travel faster. Double-stranded DNA moves at a ... The ethidium bromide fluoresces reddish-orange in the presence of DNA, since it has intercalated with the DNA. The DNA band can ...

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

"Binding of tachyplesin I to DNA revealed by footprinting analysis: significant contribution of secondary structure to DNA ... It is hypothesized this mode of action is similar to that of tachyplesin I, which binds to the minor groove of DNA. The ...

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

... to non specific DNA sequences whilst having a 20 fold higher affinity for loxP sequences and results of early DNA footprinting ... DNA found between two loxP sites oriented in the same direction will be excised as a circular loop of DNA whilst intervening ... Two separate DNA species both containing loxP sites can undergo fusion as the result of Cre mediated recombination. DNA ... The effect of the two-domain structure is to form a C-shaped clamp that grasps the DNA from opposite sides. The active site of ...

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

... in a PCR assay among a mixture of DNA sequences only the specific target is amplified into millions of copies by a DNA ... DNase footprinting assay Filter binding assay Gel shift assay Bicinchoninic acid assay (BCA assay) Bradford protein assay Lowry ... or phosphorimager Polymerase Chain Reaction Assays that amplify a DNA (or RNA) target rather than the signal Combination ... in solution by Flow cytometry Molecular biology techniques such as DNA microarrays, in situ hybridization, combined to PCR, ...

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

... a somewhat specific DNA cleavage pattern that can be useful for studying DNA recognition by a technique called DNA footprinting ... DNA recognition by the DBD can occur at the major or minor groove of DNA, or at the sugar-phosphate DNA backbone (see the ... For example, the DNA-cutting enzyme DNAse I cuts DNA almost randomly and so must bind to DNA in a non-sequence-specific manner ... DNA-binding domains with functions involving DNA structure have biological roles in DNA replication, repair, storage, and ...

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

Galas DJ, Schmitz A (1978). "DNAse footprinting: a simple method for the detection of protein-DNA binding specificity". Nucleic ... Protein-DNA interactions occur when a protein binds a molecule of DNA, often to regulate the biological function of DNA, ... Also proteins that repair DNA such as uracil-DNA glycosylase interact closely with it. In general, proteins bind to DNA in the ... A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, ...

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

Nuclease digestion and DNA footprinting experiments suggest that the globular domain of histone H1 localizes near the ... It is uncertain whether H1 promotes a solenoid-like chromatin fiber, in which exposed linker DNA is shortened, or whether it ... Xiao B, Freedman BS, Miller KE, Heald R, Marko JF (December 2012). "Histone H1 compacts DNA under force and during chromatin ... In addition to binding to the nucleosome, the H1 protein binds to the "linker DNA" (approximately 20-80 nucleotides in length) ...

https://en.wikipedia.org/wiki/Histone_H1

In DNA footprinting the protein is envisioned to make an imprint (or footprint) at a particular point of interaction. This ... Protein footprinting is a term used to refer to a method of biochemical analysis that investigates protein structure, assembly ... RP-MS/Protein footprinting studies of protein complexes can also employ computational approaches to assist with this modeling. ... This method was the first employed to apply protein footprinting to the study of a protein complex. The exposure of proteins to ...

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

... and then specific region binding can be assessed using the DNA footprinting technique. The DNA footprinting technique can be ... DNA footprinting is a method of investigating the sequence specificity of DNA-binding proteins in vitro. This technique can be ... Techniques like DNA footprinting help elucidate which proteins bind to these associated regions of DNA and unravel the ... DNase footprinting Protein footprinting Toeprinting assay Galas, D; Schmitz, A (1978). "DNAse footprinting: a simple method for ...

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

"Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule ... DNA damage appears to be the primary underlying cause of cancer.[39][40] If accurate DNA repair is deficient, DNA damages tend ... DNA repair genes with hyper/hypo-methylated promoters in cancers[edit]. DNA repair genes are frequently repressed in cancers ... Excess DNA damage can also increase epigenetic alterations due to errors during DNA repair.[41][42] Such mutations and ...

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

A DNase footprinting assay is a DNA footprinting technique from molecular biology/biochemistry that detects DNA-protein ... The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the ... This technique was developed by David Galas and Albert Schmitz at Geneva in 1977 DNA footprinting DNase I Toeprinting assay ... For example, the DNA fragment of interest may be PCR amplified using a 32P 5' labeled primer, with the result being many DNA ...

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

MBD has negligible non-specific affinity for unmethylated DNA. In vitro foot-printing with the chromosomal protein MeCP2 showed ... DNA methylation at CpG dinucleotides, the most common DNA modification in eukaryotes, has been associated with various ... Effects of DNA methylation are mediated through proteins that bind to symmetrically methylated CpGs. Such proteins contain a ... The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, and in cases of MeCP2, MBD1 and MBD2, preferentially to ...

https://en.wikipedia.org/wiki/Methyl-CpG-binding_domain

Cells can integrate BrdU in newly synthesized DNA as a substitute for thymidine. When BrdU is integrated into DNA, it is ... A comparative footprinting study". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 949 (2): 158-68. doi: ... Because Hoechst stains bind to DNA, they interfere with DNA replication during cell division. Consequently, they are ... The dyes bind to the minor groove of double-stranded DNA with a preference for sequences rich in adenine and thymine. Although ...

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

Minisatellites can be used in DNA footprinting and as regulators of gene control. The success of DNA based markers lead to the ... DNA ligation is the process by which linear DNA pieces are connected to each other via covalent bonds; more specifically, these ... The DNA is digested by a particular restriction enzyme, resulting in DNA pieces of varying molecular masses. One of the ... AFLP markers are run alongside a DNA marker on a gel. A common AFLP DNA marker is 30-330bp long. The fragments of this marker ...

https://en.wikipedia.org/wiki/Molecular-weight_size_marker

... dna footprinting MeSH E05.393.620.311 - ligase chain reaction MeSH E05.393.620.374 - self-sustained sequence replication MeSH ... dna MeSH E05.393.760.700.300 - dna mutational analysis MeSH E05.393.760.705 - sequence analysis, protein MeSH E05.393.760.705. ... dna shuffling MeSH E05.393.420.301 - gene therapy MeSH E05.393.420.451 - genetic enhancement MeSH E05.393.420.601 - protein ... random amplified polymorphic dna technique MeSH E05.393.525.870 - two-hybrid system techniques MeSH E05.393.560.150 - comet ...

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

Historically, the experimental techniques of choice to discover and analyze DNA binding sites have been the DNAse footprinting ... DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from ... DNA binding sites were finally confirmed in both systems with the advent of DNA sequencing techniques. From then on, DNA ... DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for ...

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

Footprinting indicates that gyrase, which forms a 140-base-pair footprint and wraps DNA, introduces negative supercoils, while ... A strand of DNA, called the gate, or G-segment, is bound by a central DNA-binding gate (DNA-gate). A second strand of DNA, ... the ends of the DNA are separated, and a second DNA duplex is passed through the break. Following passage, the cut DNA is re- ... Roca J, Wang JC (May 1994). "DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism". Cell. 77 ...

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

Gene-centered view of evolution Gene regulatory network Intergenic region Intragenomic conflict Phylogenetic footprinting ... Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is ... of coding DNA. Parts of the non-coding DNA were being deleted by the plant and this suggested that non-coding DNA may not be as ... protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented ...

https://en.wikipedia.org/wiki/Non-coding_DNA

Assays are created that combine reporter fusions, electrophoretic mobility shift assays, DNase footprinting, and fluorescence ... DNA-binding domain DNA-binding protein DNA-binding protein from starved cells Transcription factor Drlica K, Rouviere-Yaniv J ( ... In DNA replication at the lagging strand site, DNA polymerase III removes nucleotides individually from the DNA binding protein ... consequently increasing the efficiency of DNA polymerase III to synthesize a new DNA strand. Initially, bacterial DNA binding ...

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

In vivo footprinting experiments obtained on Cdc2 and B-myb promoters demonstrated E2F DNA binding site occupation during G0 ... DHFR DNA repair: BARD1, RAD51, UNG1,2, FANCA, FANCC, FANCJ DNA replication: PCNA, histone H2A, DNA pol α {\displaystyle \alpha ... E2F targets genes that encode proteins involved in DNA replication (for example DNA polymerase, thymidine kinase, dihydrofolate ... Six others act as suppressors: E2F3b, E2F4-8. All of them are involved in the cell cycle regulation and synthesis of DNA in ...

https://en.wikipedia.org/wiki/E2F

DNA gang replication, DNA repair or RNA processing and maturation, as well as pre-mRNA splicing. Although precursors can be ... Gel shift assays are often performed in vitro concurrently with DNase footprinting, primer extension, and promoter-probe ... DNA probe without protein present) will contain a single band corresponding to the unbound DNA or RNA fragment. However, ... This procedure can determine if a protein or mixture of proteins is capable of binding to a given DNA or RNA sequence, and can ...

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

Unlike electrophoretic mobility shift and DNA foot printing, determination of molecular weight of unknown proteins that bind to ... "Southwestern blot mapping" is a time-efficient way of identifying DNA-binding proteins and specific sites on the genomic DNA ... Finally, the specifically-bound DNA is eluted from each individual protein-DNA complex and analyzed by another application of ... A procedure for simultaneous characterization of DNA binding proteins and their specific genomic DNA target sites". Analytical ...

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

Computational footprinting methods can be performed on ATAC-seq to find cell specific binding sites and transcription factors ... The tagged DNA fragments are then purified, PCR-amplified, and sequenced using next-generation sequencing. Sequencing reads can ... This can be achieved by looking at the number of reads around TF motifs or footprinting analysis. Buenrostro JD, Giresi PG, ... Hendrickson DG, Soifer I, Wranik BJ, Botstein D, Scott McIsaac R (2018), Simultaneous Profiling of DNA Accessibility and Gene ...

https://en.wikipedia.org/wiki/ATAC-seq

DNA footprinting is a method aimed at identifying protein-bound DNA. It uses labeling and fragmentation coupled to gel ... In nature, DNA can form three structures, A-, B-, and Z-DNA. A- and B-DNA are very similar, forming right-handed helices, ... Galas, D. J.; Schmitz, A. (1978-09-01). "DNAse footprinting: a simple method for the detection of protein-DNA binding ... Linker DNA is relatively resistant to bending and rotation. This makes the length of linker DNA critical to the stability of ...

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

... it has been used for DNA sequencing, genome walking, and DNA footprinting. Methylation-specific PCR (MSP): developed by Stephen ... a DNA template that contains the DNA target region to amplify a DNA polymerase; an enzyme that polymerizes new DNA strands; ... The two DNA strands then become templates for DNA polymerase to enzymatically assemble a new DNA strand from free nucleotides, ... Digital PCR (dPCR): used to measure the quantity of a target DNA sequence in a DNA sample. The DNA sample is highly diluted so ...

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

... d'un extrem del DNA. Aquest intermediari és seguidament atacat pel grup hidroxil 3' de l'altre extrem de DNA, formant un nou ... From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways». J. Bacteriol., 184, 16, ... A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double-strand breaks». ... Wilkinson A, Day J, Bowater R «Bacterial DNA ligases». Mol. Microbiol., 40, 6, 2001, pàg. 1241-8. DOI: 10.1046/j.1365-2958.2001 ...

https://ca.wikipedia.org/wiki/Nicotinamida_adenina_dinucleòtid

"A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double-strand breaks". ... "From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways". J. Bacteriol. 184 (16): ... Wilkinson A, Day J, Bowater R (2001). "Bacterial DNA ligases". Mol. Microbiol. 40 (6): 1241-8. PMID 11442824. doi:10.1046/j. ... Chambon P, Weill JD, Mandel P (1963). "Nicotinamide mononucleotide activation of new DNA-dependent polyadenylic acid ...

https://gl.wikipedia.org/wiki/NADH

... it has been used for DNA sequencing, genome walking, and DNA footprinting.[53] ... including a DNA template that contains the DNA target region to amplify; a DNA polymerase; an enzyme that polymerizes new DNA ... Digital PCR (dPCR): used to measure the quantity of a target DNA sequence in a DNA sample. The DNA sample is highly diluted so ... The two DNA strands then become templates for DNA polymerase to enzymatically assemble a new DNA strand from free nucleotides, ...

https://en.m.wikipedia.org/wiki/Polymerase_chain_reaction

DNA Patterns analysis. References[edit]. *^ Darling A.E.; Miklós I.; Ragan M.A. (2008). "Dynamics of Genome Rearrangement in ... "Finding functional features in Saccharomyces genomes by phylogenetic footprinting". Science. 301 (5629): 71-76. Bibcode:2003Sci ... As DNA sequencing technology has become more accessible, the number of sequenced genomes has grown. With the increasing ... It was built to visualize the results of comparative analysis based on DNA alignments. The presentation of comparative data ...

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

Main article: DNA-binding domain. The portion (domain) of the transcription factor that binds DNA is called its DNA-binding ... DNA-binding domainEdit. Domain architecture example: Lactose Repressor (LacI). The N-terminal DNA binding domain (labeled) of ... DNA-binding domain (DBD), which attaches to specific sequences of DNA (enhancer or promoter. Necessary component for all ... Accessibility of DNA-binding siteEdit. In eukaryotes, DNA is organized with the help of histones into compact particles called ...

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

Other NAD-dependent enzymes include bacterial DNA ligases, which join two DNA ends by using NAD+ as a substrate to donate an ... "From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways". J. Bacteriol. 184 (16): ... "A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double-strand breaks". ... This contrasts with eukaryotic DNA ligases, which use ATP to form the DNA-AMP intermediate.[67] ...

https://en.m.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide

... dan juga sebagai substrat bagi enzim DNA ligase bakteri dan enzim sirtuin yang menggunakan NAD+ untuk melepaskan gugus asetil ... "From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways". J. Bacteriol. 184 (16): ...

https://id.wikipedia.org/wiki/Nikotinamida_adenina_dinukleotida

"DNA Res. 16 (2): 115-29. doi:10.1093/dnares/dsp003. PMC 2673734. PMID 19261625.. ... "Finding functional features in Saccharomyces genomes by phylogenetic footprinting". Science. 301 (5629): 71-6. Bibcode:2003Sci ...

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

ParM is an actin homologue that is coded in a plasmid and it is involved in the regulation of plasmid DNA.[4][198] ParMs from ... "Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprinting". Proceedings of the National Academy ... Giant nemaline rods produced by the transfection of a DNA sequence of ACTA1, which is the carrier of a mutation responsible for ... It also has two different DNA promoters.[183] It has been noted that the sequences translated from this locus and from that of ...

https://en.m.wikipedia.org/wiki/Actin

It is used for DNA labelling (5' and 3'), leaving the nucleic acids intact. ... footprinting experiments, and detection of low-abundance phosphorylated species. Phosphorus-32 is also relatively inexpensive. ...

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

When bound to DNA, Chromomycin A3 has a maximum excitation wavelength of 445 nm (blue), and a maximum emission wavelength of ... Footprinting with (methidiumpropyl-EDTA)iron(II)". Biochemistry. 22 (10): 2373-2377. doi:10.1021/bi00279a011. ISSN 0006-2960. ... Evaluation of male fertility: Chromomycin A3 and protamines compete for the same binding sites in the DNA, so CMA3 positivity ... 7). In the presence of Mg2+ ions, Chromomycin A3 binds reversibly to DNA, preferentially to contiguous G/C base pairs. ...

https://en.wikipedia.org/wiki/Chromomycin_A3

Tijian and coworkers went on to show that by footprinting a partially purified polymerase 1 preparation could bind to the human ... "Recruitment of TATA-binding protein-TAFI complex SL1 to the human ribosomal DNA promoter is mediated by the carboxy-terminal ...

https://en.wikipedia.org/wiki/Selective_factor_1

... fragmented DNA including the left and right transposon and 16 base pair of surrounding genomic DNA is produced. The 16 base ... "Functional analysis of the genes of yeast chromosome V by genetic footprinting". Science. 274 (5295): 2069-74. Bibcode:1996Sci ... use a DNA shearing[clarification needed] technique that produce a range of PCR product sizes that could cause shorter DNA ... After transduction, the DNA is cleaved[clarification needed] and the inserted sequence amplified through PCR. The recognition ...

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

Nucleosomes or the DNA-protein complexes can be purified from the sample and the bound DNA can be subsequently purified via gel ... "Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome". Cell Reports. 13 ... DNA bound to histones or other chromatin-bound proteins (e.g. transcription factors) may remain undigested. The uncut DNA is ... This ultimately elucidated that ~146bp of DNA wrap around the nucleosome core, ~50bp linker DNA connect each nucleosome, and ...

https://en.wikipedia.org/wiki/MNase-seq

The portion (domain) of the transcription factor that binds DNA is called its DNA-binding domain. Below is a partial list of ... a class of ligand activated transcription factors Phylogenetic footprinting TRANSFAC database Latchman DS (December 1997). " ... Methylation of cytosine in DNA primarily occurs where cytosine is followed by guanine in the 5' to 3' DNA sequence, a CpG site ... Some transcription factors, so-called pioneer factors are still able to bind their DNA binding sites on the nucleosomal DNA. ...

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

Before phylogenetic footprinting, DNase footprinting was used, where protein would be bound to DNA transcription factor binding ... One such technique is Phylogenetic Footprinting. Phylogenetic footprinting relies upon two major concepts: The function and DNA ... Unlike DNase footprinting, phylogenetic footprinting relies on evolutionary constraints within the genome, with the "important ... Phylogenetic footprinting is a technique used to identify transcription factor binding sites (TFBS) within a non-coding region ...

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

MEME takes as input a group of DNA or protein sequences (the training set) and outputs as many motifs as requested. It uses ... An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data. ... A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences and is often associated ... Multiple Expectation maximizations for Motif Elicitation (MEME) is a tool for discovering motifs in a group of related DNA or ...

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

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

In situ detection of protein-DNA interactions in filamentous fungi by in vivo footprinting.. Wolschek MF1, Narendja F, ... The method described here allows the detection of protein-DNA interactions in vivo in filamentous fungi. We outline culture ...

https://www.ncbi.nlm.nih.gov/pubmed/?term=9685506%5BPMID%5D

DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. ... "DNA Footprinting" by people in this website by year, and whether "DNA Footprinting" was a major or minor topic of these ... "DNA Footprinting" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, ...

https://profiles.umassmed.edu/display/109568

Quantitative DNase I footprinting is used to determine equilibrium association constants (K_a) for polyamide-DNA complexes at ... Trauger, John W. and Dervan, Peter B. (2001) Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes. In ... John W Trauger, Peter B Dvan, Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes, Methods in ... This chapter describes three complementary footprinting methods and the protocols used for analysis of polyamide : DNA ...

https://authors.library.caltech.edu/66824/

The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by in silico footprinting. ... In Silico Footprinting of Ligands Binding to the Minor Groove of DNA ... Silico Footprinting, Ligands Binding, Minor Groove, DNA, energy minimization, noncovalent binding modes, X-ray crystallography ... In Silico Footprinting of Ligands Binding to the Minor Groove of DNA. Journal of Chemical Information and Modeling, 45 (6). pp ...

https://strathprints.strath.ac.uk/816/

Radiolytic footprinting - beta-rays, gamma-photons, and fast-neutrons probe DNA-protein interactions ... Detection of minor adducts in cisplatin-modified DNA by transcription footprinting. * Detection of polymorphisms in the ... Detection of minor adducts in cisplatin-modified DNA by transcription footprinting. Febs Letters 323 (1-2) 55-58 ... Radioprotection of DNA by a DNA-binding protein - mc1 chromosomal protein from the archaebacterium methanosarcina sp chti55 ...

http://cbm.cnrs-orleans.fr/spip.php?article3899

FeBABE DNA Footprinting.. Core RNAP was incubated with 5-fold molar excess of each FeBABE-σ70 on ice for 30 min to form ... Plasmids and DNA.. Templates for in vitro transcription and footprinting were obtained from pM650 (for λ pR′) and ppM416 (for ... Cleavage of DNA in phage 82 complexes by a panel of FeBABE conjugates to regions 2, 3, and 4 of σ70, and to Q82. DNA was ... Cleavage of DNA in phage λ complexes by a panel of FeBABE conjugates to regions 2, 3, and 4 of σ70. DNA was labeled at the 5′ ...

https://www.pnas.org/content/98/16/8972?ijkey=174f4ff93e11a0eeeb17eb7a1980660a224db612&keytype2=tf_ipsecsha

Quantitative Footprinting Analysis of the Chromomycin A3-DNA Interaction. Allison Stankus, Jerry Goodisman, James C. Dabrowiak ... Quantitative Footprinting Analysis of the Chromomycin A3-DNA Interaction. / Stankus, Allison; Goodisman, Jerry; Dabrowiak, ... title = "Quantitative Footprinting Analysis of the Chromomycin A3-DNA Interaction",. abstract = "Chromomycin A3 (CHR) binding ... Stankus, A, Goodisman, J & Dabrowiak, JC 1992, Quantitative Footprinting Analysis of the Chromomycin A3-DNA Interaction, ...

https://experts.syr.edu/en/publications/quantitative-footprinting-analysis-of-the-chromomycin-asub3sub-dn

Quantitative footprinting analysis of the chromomycin A3-DNA interaction. Allison Stankus, Jerry Goodisman, James C. Dabrowiak ... title = "Quantitative footprinting analysis of the chromomycin A3-DNA interaction",. abstract = "Chromomycin A3 (CHR) binding ... Quantitative footprinting analysis of the chromomycin A3-DNA interaction. / Stankus, Allison; Goodisman, Jerry; Dabrowiak, ... Quantitative footprinting analysis of the chromomycin A3-DNA interaction. Biochemistry. 1992;31(38):9310-9318. ...

https://experts.syr.edu/en/publications/quantitative-footprinting-analysis-of-the-chromomycin-a3-dna-inte

Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. Odell, M. and Shuman, S. 1999. Footprinting of ... Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. ... To delineate the ligase-DNA interface, we have footprinted the enzyme binding site on DNA and the DNA binding site on ligase. ... westminsterresearch.westminster.ac.uk/item/94537/footprinting-of-chlorella-virus-dna-ligase-bound-at-a-nick-in-duplex-dna ...

https://westminsterresearch.westminster.ac.uk/item/94537/footprinting-of-chlorella-virus-dna-ligase-bound-at-a-nick-in-duplex-dna

... Academic Article ... The fluorescence footprinting of the oligonucleotide was followed using steady-state and time-resolved fluorescence methods. ... This report examines the interaction of TyrR with a 42 bp DNA oligonucleotide containing a centrally located binding site for ... one reflecting the motion of the probe at its point of attachment to the DNA (220-290 ps), the other reflecting the global ...

https://vivo.scripps.edu/display/endnote90710

DNA Footprinting. Ricci, M. Stacey (et al.). Pages 117-127 Preview Buy Chapter $49.95 ... Electrophoretic Mobility Shift Analysis of the DNA Binding of Tumor Suppressor Gene Products ...

http://www.springer.com/us/book/9780896039872

In Drug-DNA Interactions, expert researchers describe powerful molecular techniques designed to illuminate and explore the ... interaction of drugs and ligands with DNA, often perfected in their own labor ... Footprinting Studies with Nucleosome-Bound DNA Philip M. Brown, Keith R. Fox ... A Gel Mobility Shift Assay for Probing the Effect of Drug-DNA Adducts on DNA-Binding Proteins ...

https://link.springer.com/book/10.1385/089603447X

A modest increase in Cas9-dependent and -independent DNA off-target editing, and in transcriptome-wide RNA off-target editing ... Functional footprinting of regulatory DNA. Nat. Methods 12, 927-930 (2015).. CAS PubMed PubMed Central Google Scholar ... a, DNA editing comparing SaABE7.10, SaABE8e, and SaABE8e(TadA-8e V106W) at four genomic sites in HEK293T cells. b, DNA editing ... Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551, 464-471 (2017). ...

https://www.nature.com/articles/s41587-020-0453-z?proof=t&error=cookies_not_supported&code=63f50573-ec82-4a08-964d-2a06c35128b4

The ruler was further developed into a new DNA footprinting platform. We showed the specific binding of a protein to DNA and ... which can perform label-free and real-time monitoring of DNA length changes and perform DNA footprinting. The ruler was created ... The scattering spectra of Au-DNA nanoconjugates showed red-shifted peak plasmon resonance wavelength dependent on DNA length, ... The spectra of individual Au-DNA nanoconjugates in the presence of nuclease showed a time-resolved dependence on the reaction ...

https://digital.library.unt.edu/search/?q5=%22Plasmons%22&t5=dc_subject&searchType=advanced

The ruler was further developed into a new DNA footprinting platform. We showed the specific binding of a protein to DNA and ... which can perform label-free and real-time monitoring of DNA length changes and perform DNA footprinting. The ruler was created ... Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable ... Entry of DNA follows irreversible binding. The entry step, in which donor DNA is converted to single strands, requires action ...

https://digital.library.unt.edu/search/?q5=%22Nucleases%22&t5=dc_subject&searchType=advanced

... at origins of DNA replication. ORC recognizes specific origin DNA sequences in an ATP-dependent manner. Here we demonstrate ... DNA / genetics * DNA / metabolism* * DNA Footprinting * DNA Primers * Electrophoretic Mobility Shift Assay ... at origins of DNA replication. ORC recognizes specific origin DNA sequences in an ATP-dependent manner. Here we demonstrate ... ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA Nat Struct Mol Biol. 2005 Nov;12(11):965-71. doi: 10.1038/ ...

https://pubmed.ncbi.nlm.nih.gov/16228006/

Functional footprinting of regulatory DNA.. Vierstra J, Reik A, Chang KH, Stehling-Sun S, Zhou Y, Hinkley SJ, Paschon DE, Zhang ...

https://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Stamatoyannopoulos+G%5Bau%5D&dispmax=50

The archaeal MCM helicase can load in multiple orientations on DNA but translocation proceeds with a leading N-terminal domain ... DNaseI footprinting. Request a detailed protocol DNaseI footprinting experiments were performed in stoichiometric MCM6:DNA ... Using multiple site-specific DNA footprinting techniques, the orientation population distribution of the DNA fork bound ... There is an increase in total DNA unwound with -WH compared to WT (grey arrow). (C) DNA unwinding of 3-long arm fork DNA ...

https://elifesciences.org/articles/46096

... centromeric nucleosome complex where CENP-C clamps down a stable nucleosome conformation and CENP-N fastens CENP-A to the DNA. ... nucleosome complex wherein CENP-C confers a stable CENP-A nucleosome conformation and CENP-N fastens CENP-A to the DNA. ... N-terminal domain of CENP-N that becomes rigidified 1,000-fold upon crossbridging CENP-A and its adjacent nucleosomal DNA. ... Hydroxyl radical footprinting. CENP-A nucleosomes assembled with HEX-labelled 147 bp α-satellite DNA20 were reconstituted and ...

https://www.nature.com/articles/ncomms15775?error=cookies_not_supported&code=bb6557c6-f094-4d46-814c-df4434a4261b

T4 DNA replication accessory proteins), and gp 32 (T4 helix destabilizing protein) by DNA footprinting. ... Analysis of T4 DNA polymerase (gp 43) and gp 44/62, gp 45 ( ... DNA footprinting studies of the complex formed by the T4 DNA ... We have used DNA footprinting techniques to analyze the interactions ... We have used DNA footprinting techniques to analyze ... T4 DNA replication accessory proteins), and gp 32 (T4 helix destabilizing protein) by DNA footprinting. ...

https://polbase.neb.com/references/14

DNA, DNA Footprinting, Kinetics, Protein Binding, Proteins, Time Factors. Abstract. Transcription is often regulated at the ... Time-resolved footprinting for the study of the structural dynamics of DNA-protein interactions.. ... Time-resolved footprinting for the study of the structural dynamics of DNA-protein interactions.. ... and DNase I footprinting results in a strong signal-to-noise ratio from DNA protection at the binding site and hypersensitivity ...

http://www.lcqb.upmc.fr/content/time-resolved-footprinting-study-structural-dynamics-dna-protein-interactions

... as well as for interactions of minor groove DNA bending proteins with DNA which may be masked in hydroxyl radical footprinting ... as well as for interactions of minor groove DNA bending proteins with DNA which may be masked in hydroxyl radical footprinting ... as well as for interactions of minor groove DNA bending proteins with DNA which may be masked in hydroxyl radical footprinting ... as well as for interactions of minor groove DNA bending proteins with DNA which may be masked in hydroxyl radical footprinting ...

https://arizona.pure.elsevier.com/en/publications/cc-1065-as-a-structural-probe-of-mu-transposase-induced-bending-o-2

During DNA foot-printing, what is the purpose of radioactively labeling only one end of the DNA fragment?. Ask Question ... In DNA-footprinting we are not concerned with identifying the bases: the DNA has probably already been sequenced or we can do ... The Strategy of DNA Footprinting. In DNA sequencing there are two conceptual pieces of information one is trying to discover: ... I read that during DNA foot-printing analysis, DNA is radioactively labeled on one end before being cleaved by DNase 1. I ...

https://biology.stackexchange.com/questions/87987/during-dna-foot-printing-what-is-the-purpose-of-radioactively-labeling-only-one

DNA Footprinting * DNA, Bacterial / genetics * DNA, Bacterial / metabolism * Electrophoretic Mobility Shift Assay ... CodY was found to bind with high affinity to a DNA fragment containing the promoter region of the tcdR gene, which encodes a ...

https://pubmed.ncbi.nlm.nih.gov/17725558/?dopt=Abstract

Aids; Bioterrorism; Botulinum Toxin; Cell Biology; Cell Growth Regulation; Complementary DNA; DNA Footprinting; Gene Expression ...

https://www.jefferson.edu/university/jmc/departments/pathology/faculty/strayer.html

Phylogenetic Footprinting to Find Functional DNA Elements. Pages 367-379. Ganley, Austen R.D. (et al.) ...

https://www.springer.com/us/book/9781588296931?wt_mc=ThirdParty.SpringerLink.3.EPR653.About_eBook

DNA Footprinting. DNA, Viral / genetics. DNA-Binding Proteins / genetics, metabolism. Dependovirus / genetics*. Gene Expression ... 0/Cross-Linking Reagents; 0/DNA, Viral; 0/DNA-Binding Proteins; 0/Macromolecular Substances; 0/Sp1 Transcription Factor; 0/ ... In vitro DNA binding experiments confirmed that the Sp1-50 and GGT-70 sites were bound by Sp1 or Sp1-like proteins. Two other ... Mutation of these elements resulted in a modest decrease in p40 transcription, but DNA binding experiments did not clearly ...

http://www.biomedsearch.com/nih/adeno-associated-virus-type-2/9151818.html

b. Binding of TBP distorts DNA at TATA box. c. binding creates an 80 degree bend in the DNA. d. Bending introduces 5 kinks in ... a technique used to identify where proteins bind to DNA DNA footprinting ... T/F) in Xeroderma Pigmentosum, DNA damage can be reversed by DNA repair mechanisms ... that distort DNA structure and disrupt the passage of both DNA and RNA polymerases; induced by UV light ...

https://www.brainscape.com/flashcards/finals-gene-expression-4548148/packs/6223664

In vivo footprinting approaches to searching for unusual DNA structures in living mammalian cells. Nicole Becker received her ... triple-helical DNA, Z-form DNA, G-quadruplex DNA) but the in vivo biology of such putative structures remains obscure at best. ... These structures share the property of having unpaired DNA bases within or adjacent to their location if embedded in B-form DNA ... Nicole traveled to the City of Hope National Medical Center to learn from Gerd Pfeiffer techniques for in vivo footprinting by ...

https://www.mayo.edu/research/labs/nucleic-acid-structure-recognition/education-training/about-student-research/nicole-becker

Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. (nature.com)
Analysis of CpG methylation and genomic footprinting at the tyrosine aminotransferase gene. (uni-muenchen.de)
Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors. (ncl.edu.tw)
Cyclic AMP treatment of hepatoma cells leads to increased protein binding at the cyclic AMP response element (CRE) of the tyrosine aminotransferase (TAT) gene in vivo, as revealed by genomic footprinting, whereas no increase is observed at the CRE of the phosphoenolpyruvate carboxykinase (PEPCK) gene. (uni-muenchen.de)
Genomic footprinting analysis shows that the glucocorticoid receptor uses local DNA demethylation as one of several steps to recruit transcription factors in hepatoma cells. (embopress.org)

Add a cleavage agent to both portions of DNA template. (wikipedia.org)
A protein that specifically binds a region within the DNA template will protect the DNA it is bound to from the cleavage agent. (wikipedia.org)
The DNA template with the protein will result in ladder distribution with a break in it, the "footprint", where the DNA has been protected from the cleavage agent. (wikipedia.org)
It is a good cleavage agent for footprinting because its size makes it easily physically hindered. (wikipedia.org)
DNA cleavage is inhibited where the ligand binds to DNA. (umassmed.edu)
This chapter describes three complementary footprinting methods and the protocols used for analysis of polyamide : DNA complexes: (1) MPE-Fe(II) footprinting, (2) affinity cleavage, and (3) quantitative DNase I footprint titration. (caltech.edu)
Affinity cleavage is used to determine the orientation of the bound polyamide in the minor groove of DNA. (caltech.edu)
The structure of an intermediate in the initiation to elongation transition of Escherichia coli RNA polymerase has been visualized through region-specific DNA cleavage by the hydroxyl radical reagent FeBABE. (pnas.org)
Apparently, any drug-induced alteration in DNA structure does not affect cleavage by DMS enough to be observed by these experiments. (syr.edu)
Protease cleavage of the native enzyme prior to DNA addition results in loss of DNA binding. (westminster.ac.uk)
As expected, the DNA polymerase binds near the 3' end of this molecule (at the primer-template junction) and protects the adjacent double-stranded region from cleavage. (neb.com)
Moser et al, "Sequence-specific cleavage of double helical DNA by triple helix formation", Science 238: 645 (1987). (patentgenius.com)
Topoisomerase I-mediated DNA cleavage studies reveal that the OH→NH 2 substitution does not affect the capacity of the drug to stabilize enzyme-DNA covalent complexes. (aspetjournals.org)
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)
Restriction-modification (R-M) systems recognise self from non-self DNA by modification (methylation) of their own DNA at specific sequences, protecting their DNA from cleavage by the cognate endonuclease. (port.ac.uk)
They are molecular motors, hydrolysing ATP to translocate along DNA prior to cleavage. (port.ac.uk)

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)
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)
Physical separation, in turn, has enabled us to probe the protein composition of the complex by "supershift" assays and the region of the substrate in contact with the proteins by DNase I footprinting. (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)
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)
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)
Using DNA footprinting and gel retardation assays (EMSA), we identified the binding sites for the C protein at the promoters controlling the R-M genes. (port.ac.uk)

Footprinting and fluorescence data indicate that the dimerization constant for the drug in solution is ~ 10 5 M −1 . (syr.edu)
The fluorescence footprinting of the oligonucleotide was followed using steady-state and time-resolved fluorescence methods. (scripps.edu)
The drug-DNA interactions were studied by thermal denaturation, fluorescence, and footprinting experiments. (aspetjournals.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)

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)

Due to their small size, the resulting DNA footprint has high resolution. (wikipedia.org)
The size of the exonuclease III footprint of ligase bound a single nick in duplex DNA is 19-21 nucleotides. (westminster.ac.uk)
We showed the specific binding of a protein to DNA and the accurate mapping of its footprint. (unt.edu)
When the gene 32 protein binds to the single-stranded tail, it reduces the concentration of the DNA polymerase required to observe the polymerase footprint by 10-30-fold. (neb.com)
Footprinting experiments demonstrate the formation of a weak complex between the DNA polymerase and the gene 45 protein, but there is no effect of the 44/62 protein or ATP on this enlarged footprint. (neb.com)
The excision nuclease makes an assymmetric DNase I footprint of ≈30 bp around the damage and increases the DNase I sensitivity of the DNA on both sides of the footprint. (pnas.org)

This technique can be used to study protein-DNA interactions both outside and within cells. (wikipedia.org)
Photoreactions can include: single strand breaks, interactions between or within DNA strands, reactions with solvents, or crosslinks with proteins. (wikipedia.org)
Drug-DNA Interactions will be highly useful to all investigators needing the kind of detailed experimental and technical information often omitted from scientific papers. (springer.com)
This work promises a very fast and convenient platform for mapping DNA-protein interactions, for nuclease activity monitoring, and for other DNA size-based methods. (unt.edu)
We have used DNA footprinting techniques to analyze the interactions of five DNA replication proteins at a primer-template junction: the bacteriophage T4 DNA polymerase (the gene 43 protein), its three accessory proteins (the gene 44/62 and 45 proteins), and the gene 32 protein, which is the T4 helix-destabilizing (or single-stranded DNA-binding) protein. (neb.com)
Time-resolved footprinting for the study of the structural dynamics of DNA-protein interactions. (upmc.fr)
This study illustrates the utility of (+)-CC-1065 as a probe for protein-induced bending of DNA, as well as for interactions of minor groove DNA bending proteins with DNA which may be masked in hydroxyl radical footprinting experiments. (elsevier.com)
However, there are no reports on the interactions of these proteins with DNA fragments containing a single lesion. (pnas.org)
The divalent cations Ca2+ and Mg2+ play specific roles in stabilizing histone-DNA interactions within nucleosomes that are partially redundant with the core histone tail domains. (rochester.edu)
DNA footprinting analysis will be used to test suspected protein-promoter interactions. (epa.gov)
The DNA-protein register is fixed by sequence-specific interactions. (cancer.gov)
Although no one technical approach can be said to have brought the filed to its current level of sophistication, the ability to map the interactions of trans-acting factors with their DNA recognition sequences to a high level of precision has certainly been one of the more important advances. (worldcat.org)
Efficient conversion of closed promoter complexes (generically called CC) to open complexes (generically OC) requires interactions of RNA polymerase (RNAP) with upstream and downstream DNA as well as with the central recognition region from the −35 element to the transcription start site (+1). (pubmedcentralcanada.ca)
3 - 5 Interactions of RNAP with 40-50 bp of DNA upstream of the −35 element, including the region of the UP element and far-upstream DNA, are necessary for rapid isomerization of the CC to the OC. (pubmedcentralcanada.ca)
Formation of the initial CC (often called RP c or RP c1 ) in which the promoter DNA is presumed to be linear and interactions with RNAP extend downstream only to the discriminator region (−7 to −2) 9 - 11 sets in motion a series of conformational changes in RNAP and promoter DNA. (pubmedcentralcanada.ca)

The simplest application of this technique is to assess whether a given protein binds to a region of interest within a DNA molecule. (wikipedia.org)
It binds the minor groove of DNA and cleaves the phosphodiester backbone. (wikipedia.org)
In the holoenzyme complex with core enzyme, σ 70 binds the −35 and −10 elements of the predominant class of bacterial promoters: region 4 of σ 70 recognizes the −35 element ( 1 , 2 ) as double-stranded (ds)DNA, and region 2 of σ 70 recognizes the −10 element as both dsDNA and single-stranded (ss)DNA ( 2 - 6 ). (pnas.org)
Like some activators, Q binds to DNA just upstream or overlapping the upstream portion of RNAP ( 13 ), positioning Q and RNAP for contact. (pnas.org)
The protein binds to six att sites, three at each end of Mu DNA. (elsevier.com)
1) In the study of DNA, footprinting is the method used to identify the nucleic acid sequence that binds with proteins. (techtarget.com)
Interestingly, similar mutations at the equivalent position in CRP result in a transcriptionally active, CRP* mutant form which binds with high affinity to target DNA in the absence of the activating cofactor, cAMP. (asm.org)
The structure also reveals how the GABPα ETS domain binds to its core GGA DNA-recognition motif. (sciencemag.org)
The GABPα/β heterodimer binds to DNA sequences containing a core GGA motif with greater affinity than the GABPα subunit alone ( 17 , 18 ). (sciencemag.org)
Two GABPα/β heterodimers associate via the COOH-terminal residues of GABPβ, resulting in a heterotetramer that binds to DNA sequences containing two tandem repeats of the GGA motif ( 19 ). (sciencemag.org)

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)
Combined with a careful quantitative analysis of the evolution of the signals, this approach allows for the identification and kinetic and structural characterization of the intermediates in the pathway of DNA sequence recognition by a protein, such as a transcription factor or RNA polymerase. (upmc.fr)
Mutation of these elements resulted in a modest decrease in p40 transcription, but DNA binding experiments did not clearly demonstrate binding of transcription factors to these sites. (biomedsearch.com)
Promoter bashing is a technique used in molecular biology to identify how certain regions of a DNA strand, commonly promoters, affect the transcription of downstream genes. (wikipedia.org)
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)
Finally, testing of specific point mutations in the α subunit of RNAP revealed that a number of RNAP-DNA contacts play a key role in transcription of the icd gene. (asm.org)
Although they contain salt, digestion of DNA in Ambion's MAXIscript™, MEGAscript™ and other transcription buffers works well since the total number of units of DNase I added to degrade the DNA template is in large excess. (thermofisher.com)
RNA polymerase II transcribes the majority of protein-coding genes in higher eukaryotes, where transcription is directed by DNA elements including the core promoter, a regulatory promoter, and linked enhancer sequences ( 7 , 26 ). (asm.org)
DNA Complexed Structure of the Key Transcription Factor Initiating Development in Sporulating Bacteria Structure (London, England : 1993). (jove.com)
The protein:protein and protein:DNA interfaces revealed in the crystal provide a basis for interpreting the transcription activation process and for the design of drugs to counter infections by these bacteria. (jove.com)
We demonstrate that protein binding footprints resulting from transcription factor binding can be revealed by combining the DH site data sets with known protein binding sites or known cis -regulatory DNA elements. (plantcell.org)
Nucleosome footprinting in circulating tumor DNA can identify active tumor-specific transcription factors. (sciencemag.org)
TEs are DNA sequences often occurring tens to hundreds of kilobases away from their cognate gene, which activate gene transcription by recruitment of transcription factors (TFs) to the gene locus. (frontiersin.org)
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)
We have discovered that in addition to conventional transcription factors (including AP1, octamer, and the RFX, as described in our early investigations), several proteins that bind sequence specifically with single stranded DNA (ssDNA) interact with particular elements in the c-myc promoter and its upstream regulatory region. (cancer.gov)
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)
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)
In the nucleus, G4 formation can occur in double‐stranded G‐rich regions when DNA becomes transiently single‐stranded, during (a) transcription and (c) replication and (b) at the single‐stranded telomeric G‐rich overhangs. (els.net)
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)
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)

CodY was found to bind with high affinity to a DNA fragment containing the promoter region of the tcdR gene, which encodes a sigma factor that permits RNA polymerase to recognize promoters of the two major toxin genes as well as its own promoter. (nih.gov)
DNA Sequencing is necessary to identify differences in mutated promoters from the wild-type promoter, and to correlate those differences with differences in gene expression. (wikipedia.org)
The start points relative to these promoter sites were mapped by primer extension analysis, and then the precise contacts between RNA polymerase (RNAP) and its promoters and between Cra and its DNA operator were analyzed by the base removal method and the DNase I footprinting technique, respectively. (asm.org)
Gene expression and regulation in eukaryotes is controlled by orchestrated binding of regulatory proteins, including both activators and repressors, to promoters and other cis -regulatory DNA elements. (plantcell.org)
The function of each gene is controlled by binding of regulatory proteins to promoters and other regulatory DNA elements. (plantcell.org)
This can be accomplished because different gene features, such as exons, introns, promoters, polyadenylation signal etc are associated with unique patterns in the DNA sequence. (tripod.com)
2005) Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. (els.net)

CENP-A nucleosome retention at centromeres requires a core centromeric nucleosome complex where CENP-C clamps down a stable nucleosome conformation and CENP-N fastens CENP-A to the DNA. (nature.com)
Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays. (rochester.edu)
Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. (rochester.edu)
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)

Carey MF, Peterson CL, Smale ST. Experimental strategies for cloning or identifying genes encoding DNA-binding proteins. (umassmed.edu)
Such mechanisms could include repression of E2F and Myc activities, which transactivate various genes required for mitotic stimulation, cell-cycle progression, and DNA replication ( 1- 3 ). (sciencemag.org)
Most recently he is exploring the genome-wide utilization of supercoiled driven changes in DNA to regulate genes in health and disease. (cancer.gov)
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)
Many carcinogens in cigarette smoke are known to cause DNA lesions called DNA adducts and many carcinogens are known to leave unique signatures on cancer-related genes in the form of specific mutations at specific locations, noted Dr. Ahmad Besaratinia and Dr. Gerd Pfeifer, of the Beckman Research Institute of the City of Hope National Medical Center in Duarte, Calif. (drugs.com)
GA-binding protein (GABP) is a cellular heteromeric DNA-binding protein involved in the activation of nuclear genes encoding mitochondrial proteins ( 12 ), adenovirus early genes ( 13 ), and herpes simplex virus immediate-early genes ( 14 ). (sciencemag.org)

We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting. (strath.ac.uk)
ORC recognizes specific origin DNA sequences in an ATP-dependent manner. (nih.gov)
Identification of protein binding sequences on DNA (DNase I footprinting), 4. (thermofisher.com)
Creation of a fragmented library of DNA sequences for in vitro recombination reactions. (thermofisher.com)
These results illustrate the value of DH , the signature of open chromatin, in mapping and characterizing regulatory DNA sequences in plants. (plantcell.org)
Wells et al, "The chemistry and biology of unusual DNA structures adopted by oligopurione-oligopyrimidine sequences", FASEB Journal 2: 2939 (1988). (patentgenius.com)
Phylogenetic footprinting is a method that identifies putative regulatory elements in DNA sequences. (washington.edu)
It identifies regions of DNA that are unusually well conserved across a set of orthologous sequences. (washington.edu)

However, it has been more difficult to optimize because it is not always sensitive enough to detect the low concentrations of the target DNA strands used in DNA footprinting experiments. (wikipedia.org)
The domain structure of Chlorella virus ligase inferred from the solution experiments is consistent with the structure of T7 DNA ligase determined by x-ray crystallography. (westminster.ac.uk)
cross-linking experiments report on the formation of specific amino acid-DNA contacts, and DNase I footprinting results in a strong signal-to-noise ratio from DNA protection at the binding site and hypersensitivity at curved or kinked DNA sites. (upmc.fr)
Using this drug in experiments in which either gel retardation or DNA strand breakage are used to monitor the stability of the A-protein - DNA complex or the (+)-CC-1065 alkylation sites on DNA (att site L3), we have demonstrated that of the three minor grooves implicated in the interaction with A-protein, the peripheral two are 'open' or accessible to drug bonding following protein binding. (elsevier.com)
In vitro DNA binding experiments confirmed that the Sp1-50 and GGT-70 sites were bound by Sp1 or Sp1-like proteins. (biomedsearch.com)
Furthermore, electron microscopy experiments demonstrated that when Rep is bound to an upstream Rep binding element, it can interact with a proximal Sp1 site by protein contacts and create a loop in the intervening DNA. (biomedsearch.com)

Carey MF, Peterson CL, Smale ST. DNase I footprinting. (umassmed.edu)
Quantitative DNase I footprinting is used to determine equilibrium association constants (K_a) for polyamide-DNA complexes at previously identified match and mismatch sites. (caltech.edu)
I read that during DNA foot-printing analysis, DNA is radioactively labeled on one end before being cleaved by DNase 1. (stackexchange.com)
The frame on the extreme left addresses the question of labelling and visualization by showing the fragmentation of uniformed-labelled DNA by DNase. (stackexchange.com)
The DNA is labelled at one end and treated with DNase at a concentration that will generate a range of fragment sizes. (stackexchange.com)
The assembly and composition of human excision nuclease were investigated by electrophoretic mobility shift assay and DNase I footprinting. (pnas.org)
DNase I is a versatile enzyme that nonspecifically cleaves DNA to release 5'-phosphorylated di-, tri-, and oligonucleotide products (1). (thermofisher.com)
A powerful research tool for DNA manipulations, DNase I is used in a range of molecular biology applications. (thermofisher.com)
Will DNase I degrade DNA in DNA:RNA hybrids? (thermofisher.com)
Can DNase I remove 100% of DNA contamination from RNA preparations? (thermofisher.com)
The specific activity of a given DNase I preparation reflects the potency of the enzyme per unit mass in degrading double-stranded DNA (dsDNA). (thermofisher.com)
Historically, this activity has been expressed in Kunitz units (2), where 1 Kunitz unit is the amount of DNase I added to 1 mg/ml salmon sperm DNA that causes an increase of 0.001 absorbance units per min when assayed in a 0.1 M NaOAc (pH 5.0) buffer. (thermofisher.com)
Consequently, Ambion offers DNase I with a unit designation that better reflects how well the enzyme will degrade DNA under standard conditions. (thermofisher.com)
Although DNase I is commonly perceived to cleave DNA nonspecifically, in practice it does show some sequence preference. (thermofisher.com)
Ambion's Technical Service Department is frequently asked whether DNase I cleaves only dsDNA or whether it can also degrade single-stranded DNA (ssDNA) and the DNA in RNA-DNA hybrids. (thermofisher.com)
Binding to nucleic acids was examined by spectroscopic, chiroptical, and DNase I footprinting techniques as a function of ionic strength and base composition. (aspetjournals.org)

In EBV-associated cancers such as nasopharyngeal cancer (NPC), the viral encoded oncogene product, latent membrane protein 1 (LMP1) can activate DNA methyltransferases (Dnmt1, 3a and 3b), strongly implying the role of LMP1 in manipulating the cellular DNA methylation machinery. (ncl.edu.tw)
DNA methylation is an important epigenetic modification, which regulates gene expression. (ncl.edu.tw)
Improper DNA methylation has been demonstrated to be associated with increasing risk of cancers. (ncl.edu.tw)
Thus, LMP1-mediated DNA methylation may play a role in the tumorigenesis of NPC. (ncl.edu.tw)
Alterations in DNA methylation: a fundamental aspect of neoplasia. (ncl.edu.tw)
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)
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)

Footprinting with methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] is used to identify high-affinity polyamide-binding sites to near nucleotide resolution. (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)
In this study, we have identified the minimum set of repair factors required for formation of a high affinity and specificity DNA-protein complex and physically have separated this complex from the free DNA and proteins in the reaction mixture by electrophoresis on nondenaturing polyacrylamide gels. (pnas.org)
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)
In this study we show that the DNA-binding affinity and sequence selectivity of a rebeccamycin derivative can be enhanced by replacing the glucose residue with a 2′-aminoglucose moiety. (aspetjournals.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)

The 177-nucleotide-long DNA substrate consisted of a perfect 52-base pair hairpin helix with a protruding single-stranded 5' tail. (neb.com)
The rat poly Pyrimidine Tract binding protein (PTB) interacts with a single-stranded DNA motif in a liverspecific enhancer. (uni-muenchen.de)
The method comprises:contacting a recombination protein with a double-stranded DNA molecule and with a single-stranded DNA molecule sufficiently complementary to one strand of the double-stranded DNA molecule to hybridize therewith, which contacting is effected under conditions such that the single-stranded DNA molecule hybridizes to the double-stranded molecule so that the three stranded DNA molecule is formed. (patentgenius.com)
Single-stranded DNA-binding proteins play a key role in DNA replication. (port.ac.uk)
The gene 5 protein (g5p) of filamentous bacteriophage fd is responsible for the switch from double-stranded to single-stranded viral DNA replication, following infection of the bacterial cell. (port.ac.uk)

Techniques like DNA footprinting help elucidate which proteins bind to these associated regions of DNA and unravel the complexities of transcriptional control. (wikipedia.org)
Transcriptional regulation of the human DNA Methyltransferase (dnmt1) gene. (ncl.edu.tw)
Transcriptional activator C protein-mediated unwinding of DNA as a possible mechanism for mom gene activation. (semanticscholar.org)
DNA-footprinting analyses revealed new transcriptional regulators associated with regenerative ability. (ibecbarcelona.eu)
We have long-standing interests in the molecular mechanisms that control gene expression, and how transcriptional regulator proteins (both activators and repressors) recognize their cognate DNA binding sites with varying degrees of specificity. (port.ac.uk)

This can limit the precision of predicting a protein's binding site on the DNA molecule.Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. (wikipedia.org)
These hydroxyl molecules react with the DNA backbone, resulting in a break. (wikipedia.org)
The negative aspect of using hydroxyl radicals is that they are more time consuming to use, due to a slower reaction and digestion time.Ultraviolet irradiation can be used to excite nucleic acids and create photoreactions, which results in damaged bases in the DNA strand. (wikipedia.org)
Ding, ZM, Harshey, RM & Hurley, L 1993, ' (+)-CC-1065 as a structural probe of Mu transposase-induced bending of DNA: Overcoming limitations of hydroxyl-radical footprinting ', Nucleic Acids Research , vol. 21, no. 18, pp. 4281-4287. (elsevier.com)

Binding of Cdc6 to the origin recognition complex (ORC) is a key step in the assembly of a pre-replication complex (pre-RC) at origins of DNA replication. (nih.gov)
The hexameric MCM complex is conserved throughout archaea and eukaryotic species as the DNA helicase that unwinds the duplex genome providing leading and lagging strand templates for replication. (elifesciences.org)
Analysis of T4 DNA polymerase (gp 43) and gp 44/62, gp 45 (T4 DNA replication accessory proteins), and gp 32 (T4 helix destabilizing protein) by DNA footprinting. (neb.com)
D. thesis project on control of DNA replication in bacteria. (frankwu.com)
Rao, "A three-stranded DNA complex remains afer strand exchange mediated by rec A protein", in Molecular Mechanisms in DNA Replication, 1990, Alan R. Liss, Inc., pp. 387-398. (patentgenius.com)
our philosophy is that by combining structural and biophysical analysis with biochemical and functional studies, we will be able to build up a complete picture of the mechanism of action of the relevant macromolecules and their role in fundamental biological processes, particularly those related to gene expression and DNA replication. (port.ac.uk)
They are therefore central to the regulation of multiple cellular processes, such as chromatin remodeling and DNA replication. (port.ac.uk)

The recent discovery that short hybrid RNA:DNA molecules (siHybrids) induce long-term silencing of gene expression in mammalian cells conflicts with the currently hypothesized mechanisms explaining the action of small, interfering RNA (siRNA). (unt.edu)
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)
Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. (biomedcentral.com)
These unusual DNA structures then bind by specialized factors to feedback regulate gene expression. (cancer.gov)
Gene expression in eukaryotes is frequently mediated by multiprotein complexes that bind DNA in a sequence-specific manner. (sciencemag.org)
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)

DNA footprinting is a method of investigating the sequence specificity of DNA-binding proteins in vitro. (wikipedia.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)

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)

These can influence the kinetic properties and/or structures of the intermediate RNA polymerase-DNA complexes in the pathway. (upmc.fr)
Individual repair factors or any combination of up to four repair factors failed to form DNA-protein complexes of high specificity and stability. (pnas.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)

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)
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)

Methods used in this approach include: iTRAQ analysis, RT-PCR, DNA microarray hybridization, DNA footprinting analysis, recombinant protein expression and allelic exchange to create a gene knockout mutation. (usda.gov)
Dapple is a program for quantitating spots on a two-color DNA microarray image. (washington.edu)

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)

Glucocorticoid hormones were found to regulate DNA demethylation within a key enhancer of the rat liver‐specific tyrosine aminotransferase ( Tat ) gene. (embopress.org)

Results: We developed a computational protocol based on molecular and structural criteria to perform biologically meaningful and accurate phylogenetic footprinting analyses. (mendeley.com)
In our protocol, the abovementioned criteria were used to analyze a profile of consensus motifs generated from canonical Phylogenetic Footprinting Analyses using a set of analysis windows of incremental sizes. (mendeley.com)

DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. (umassmed.edu)
The spectra of individual Au-DNA nanoconjugates in the presence of nuclease showed a time-resolved dependence on the reaction dynamics, allowing quantitative, kinetic and real-time measurement of nuclease activity. (unt.edu)
Fusion of the C gene to the efficient translation initiation region of the Escherichia coli atpE gene allowed significant overproduction of C protein, which was subsequently purified and assayed for DNA binding by gel retardation and nuclease footprinting techniques. (semanticscholar.org)

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)
Biochemical Techniques for the Characterization of G-Quadruplex Structures: EMSA, DMS Footprinting, and DNA Polymerase Stop Assay. (alfa.com)

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 the latter case, a single Cra-binding site was detected by electrophoretic mobility shift analysis (EMSA) in the DNA fragment encompassing the regulatory region of the icd gene ( 28 ). (asm.org)
GeneMapper® Software is a flexible fragment analysis software package that provides quality DNA sizing and allele calls for all Applied Biosystems Genetic Analyzers. (thermofisher.com)
They noted that a technique called DNA-lesion footprinting, in conjunction with mutagenicity analysis, is currently used to find carcinogen signatures. (drugs.com)
Sequence-specific DNA binding of the phage Mu C protein: footprinting analysis reveals altered DNA conformation upon protein binding. (semanticscholar.org)

ETS domains bind DNA as monomers and recognize a consensus sequence that contains a core GGA motif. (sciencemag.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)
A method for determining the sequence specificity of DNA-binding proteins. (umassmed.edu)
The enzyme has intrinsic specificity for binding to nicked duplex DNA. (westminster.ac.uk)
The XPF⋅ERCC1 heterodimer changes the electrophoretic mobility of the DNA-protein complex formed with the other five repair factors, but it does not confer additional specificity. (pnas.org)
Our data show that XPA, RPA, TFIIH, XPC⋅HHR23B, and XPG are required for high specificity DNA-protein complex formation and that XPC⋅HHR23B is a molecular matchmaker that is not present in the ultimate dual incision complex that covers an ≈30-bp region of DNA around the lesion. (pnas.org)
In many cases, greater DNA target specificity is achieved by the cooperative binding of ETS family members with partner proteins ( 5 ). (sciencemag.org)

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)

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)

M. Blanchette , M. Tompa , 'FootPrinter: A program designed for phylogenetic footprinting' , Nucleic Acids Res. (washington.edu)
MicroFootPrinter is a front end to the FootPrinter phylogenetic footprinting program, but with specific focus on prokaryotic genomes. (washington.edu)
S. Neph , M. Tompa , 'MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes' , Nucleic Acids Res. (washington.edu)

Common genetic variants associated with human traits and disease susceptibility are enriched within lineage-specific regulatory DNA. (harvard.edu)
Regulatory DNA elements are made accessible upon histone depletion. (prolekare.cz)

A very remarkable sequence preference pattern dramatically favors GC steps in double-helical DNA, whereas the carbocyclic reference compounds show a substantially lower selectivity for GC. (aspetjournals.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)
We have shown that DNA binding triggers a large contraction of the open form of the enzyme to a compact form. (port.ac.uk)

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)

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)
The thermodynamic parameters indicate that the newly introduced amino group on the glycoside residue significantly enhanced binding to DNA by increasing the contribution of the polyelectrolyte effect to the binding free energy, but does not appear to participate in any specific molecular contacts. (aspetjournals.org)

Register et al, "Electron microscopic visualization of the RecA protein-mediated pairing and branch migration phases of DNA strand exchange", J. Biol. (patentgenius.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)
Carey MF, Peterson CL, Smale ST. Experimental strategies for the identification of DNA-binding proteins. (umassmed.edu)
Chromomycin A 3 (CHR) binding to the duplex d(CAAGTCTGGCCATCAGTC)· d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. (syr.edu)
The 5'-phosphate moiety is essential for the binding of Chlorella virus ligase to nicked DNA. (westminster.ac.uk)
These results suggest a bipartite domain structure in which the interdomain segment either comprises part of the DNA binding site or undergoes a conformational change upon DNA binding. (westminster.ac.uk)
This report examines the interaction of TyrR with a 42 bp DNA oligonucleotide containing a centrally located binding site for TyrR (TyrR box). (scripps.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)
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)
Helicases are composed of two domains, an N- terminal DNA binding domain (NTD) and a C- terminal motor domain (CTD). (elifesciences.org)
Wounding and methyl jasmonate treatments induced differently these DNA-binding activities. (plantphysiol.org)
Footprinting of DNA-binding proteins in intact cells. (uni-muenchen.de)
In the crystal lattice, two molecules form a tandem dimer upon binding to adjacent sites on DNA. (jove.com)
The α subunit contains a DNA-binding domain that is a member of the ETS family, whereas the β subunit contains a series of ankyrin repeats. (sciencemag.org)
and behind the pipetters are two 'footprinting' gels which show a protein binding to DNA. (frankwu.com)
and iv) isolating said three-stranded DNA molecule bound to said second member of said binding pair. (patentgenius.com)
The physicochemical and DNA-binding properties of anticancer 9-aza-anthrapyrazoles (9-aza-APs) were investigated and compared with the carbocyclic analogs losoxantrone (LX) and mitoxantrone (MX). (aspetjournals.org)

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)
Expanded encyclopedias of DNA elements in the human and mouse genomes. (washington.edu)

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)

d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. (syr.edu)

Recombinant DNA. (uni-muenchen.de)

A defect in c-myc regulation may compound the DNA repair deficit of the afflicted and contribute to their several thousand-fold increased risk for cutaneous malignancies. (cancer.gov)

Thus FBP-FIR action is obligatorily coupled with factors, processes or conditions that destabilize duplex DNA. (cancer.gov)
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)

The combination of different probing agents is especially powerful in revealing different aspects of the conformational changes taking place at the protein-DNA interface. (upmc.fr)
Recent developments in protein footprinting allow for the direct characterization of conformational changes of the proteins in the complex. (upmc.fr)
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)

MYC is regulated by a bewildering array of intracellular and extra cellular signals and conditions operating through a host of DNA-bound transfactors. (cancer.gov)

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)
In each case, the glycoside residue plays a significant role in the interaction of the drug with the DNA double helix. (aspetjournals.org)

Electrophoretic sequencing gels or capillary electrophoresis have been successful in analyzing footprinting of fluorescent tagged fragments. (wikipedia.org)
Two DNA restriction fragments containing either a d(GC)5 or a d(TTGCTTGATTAGTTGTGTT) insert were subjected to reaction with cis-diamminedichloroplatinum(II) and were then used as templates for RNA synthesis by T7 RNA polymerase. (cnrs-orleans.fr)
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)

In the presence of cyanide ions, the adducts are much less stable at the d(GpA) sites than at the d(GpCpG) sites, in double-stranded DNA. (cnrs-orleans.fr)

During DNA foot-printing, what is the purpose of radioactively labeling only one end of the DNA fragment? (stackexchange.com)

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)

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)
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)

Protease accessible sites are clustered within a short segment from amino acids 210-225 located distal to conserved motif V. The ligase is protected from proteolysis by nicked DNA. (westminster.ac.uk)
Such processing could account for the very small deletions often found at DNA double-strand break repair sites. (unt.edu)
By using substrates with single lesions at predetermined sites and either purified repair factors ( 6 ) or cell extracts from wild-type and mutant cell lines ( 7 ), it was found that the dual incision event is preceded by unwinding of DNA by 20-25 bp by the bidirectional helicase activity of the TFIIH subunit. (pnas.org)
CpG sites or CG sites are regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length. (wikiversity.org)

Preparation of nucleosomes containing a specific H2A-H2A cross-link forming a DNA-constraining loop structure. (rochester.edu)
2) In computers, footprinting is the process of accumulating data regarding a specific network environment, usually for the purpose of finding ways to intrude into the environment. (techtarget.com)

Hsieh et al, "Recombinases can form DNA joint molecules in the absence of strand displacement", Cold Spring Harbor, Sep. (patentgenius.com)

Anatomy1

Organisms1

Diseases2

Chemicals and Drugs29

Analytical, Diagnostic and Therapeutic Techniques and Equipment5

Phenomena and Processes17

Technology, Industry, Agriculture1

Information Science3

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)

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

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

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

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

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

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

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

DNA Footprinting

Protein Footprinting

Base Sequence

Promoter Regions, Genetic

Molecular Sequence Data

DNA-Binding Proteins

Binding Sites

DNA

Transcription, Genetic

Transcription Factors

Deoxyribonuclease I

Gene Expression Regulation, Bacterial

Protein Binding

Sulfuric Acid Esters

Hydroxyl Radical

Nucleotide Mapping

Regulatory Sequences, Nucleic Acid

Nucleic Acid Conformation

Distamycins

Potassium Permanganate

Echinomycin

Enhancer Elements, Genetic

Bacterial Proteins

Hydroxides

Escherichia coli

Sp1 Transcription Factor

Electrophoretic Mobility Shift Assay

Oligodeoxyribonucleotides

Operator Regions, Genetic

Repressor Proteins

Nuclear Proteins

Plasmids

Gene Expression Regulation

Intercalating Agents

Operon

Phenanthrolines

DNA, Bacterial

Netropsin

Restriction Mapping

Consensus Sequence

Trans-Activators

Encyclopedias as Topic

Nylons

Pyrroles

Imidazoles

Alkylation

Chromomycin A3

Chromomycins

Olivomycins

Plicamycin

Genes, Tumor Suppressor

Tumor Suppressor Proteins

Hepatitis, Infectious Canine

Tumor Suppressor Protein p53

Dog Diseases

Cell Line, Tumor

Loss of Heterozygosity

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)

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

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

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

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

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

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

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

DNA footprinting - Wikipedia

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DNase footprinting assay - Wikipedia

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