DNA Footprinting
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Protein Footprinting
A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.
Base Sequence
Promoter Regions, Genetic
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
DNA-Binding Proteins
Binding Sites
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Transcription, Genetic
Transcription Factors
Deoxyribonuclease I
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Gene Expression Regulation, Bacterial
Protein Binding
Regulatory Sequences, Nucleic Acid
Nucleic Acid Conformation
Distamycins
Potassium Permanganate
Echinomycin
Enhancer Elements, Genetic
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Sp1 Transcription Factor
Electrophoretic Mobility Shift Assay
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Oligodeoxyribonucleotides
Operator Regions, Genetic
Repressor Proteins
Nuclear Proteins
Plasmids
Gene Expression Regulation
Intercalating Agents
Operon
Netropsin
Restriction Mapping
Consensus Sequence
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
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)
DNA 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 ...
Promoter bashing
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 ...
Toeprinting assay
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 needs the mRNA of interest, ribosomes, a DNA primer, free nucleotides, and reverse transcriptase ( ...
Luke Pyungse Lee
"A nanoplasmonic molecular ruler for measuring nuclease activity and DNA footprinting". Nature Nanotechnology. Springer Science ...
Variants of PCR
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 ...
Protein footprinting
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 ...
Nucleic acid structure determination
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 ...
Gel electrophoresis of nucleic acids
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 ...
Arenicin
"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 ...
DNase footprinting assay
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 ...
DNA-binding domain
... 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 ...
Cre recombinase
... 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 ...
Assay
... 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, ...
DNA-binding protein
Galas DJ, Schmitz A (1978). "DNAse footprinting: a simple method for the detection of protein-DNA binding specificity". Nucleic ... was also shown to non-specifically bind to DNA which helps in DNA repair. A distinct group of DNA-binding proteins are the DNA- ... 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 ...
Histone H1
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) ...
Methyl-CpG-binding domain
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 ...
Hoechst stain
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 ...
Molecular-weight size marker
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 ...
List of MeSH codes (E05)
... 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 ...
DNA binding site
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 ...
Type II topoisomerase
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, ... Roca J, Wang JC (May 1994). "DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism". Cell. 77 ... The structures formed a novel beta barrel, which bends DNA by wrapping the nucleic acid around itself. The bending of DNA by ...
Non-coding DNA
Gene-centered view of evolution Gene regulatory network Intergenic region Intragenomic conflict Phylogenetic footprinting ... "nonfunctional DNA." Junk DNA is often confused with non-coding DNA[citation needed]. The Encyclopedia of DNA Elements (ENCODE) ... Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA ... These are regions of the genome where the DNA replication machinery is assembled and the DNA is unwound to begin DNA synthesis ...
Bacterial DNA binding protein
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 ...
E2F
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 ...
Electrophoretic mobility shift assay
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 ...
Southwestern blot
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 ...
ATAC-seq
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, ... Spektor R, Tippens ND, Mimoso CA, Soloway PD (June 2019). "methyl-ATAC-seq measures DNA methylation at accessible chromatin". ...
Chromatin
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 ...
Polymerase chain reaction
... 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 ...
Mathieu Blanchette (computational biologist)
His research focuses on developing new algorithms for the detection of functional regions in DNA sequences. Blanchette studied ... His thesis, titled Algorithms for phylogenetic footprinting, presented the first reasonable algorithm for gene order phylogeny ... His research focuses on developing computational methods for detecting functional regions in DNA sequences. His postdoctoral ... Blanchette, M; Tompa, M (2002). "Discovery of regulatory elements by a computational method for phylogenetic footprinting". ...
Chromomycin A3
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. ...
Selective factor 1
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 ...
Transposon sequencing
... 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 ...
MNase-seq
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 ...
Transcription factor
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 Open Regulatory Annotation Database Phylogenetic footprinting TRANSFAC ... 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. ...
Phylogenetic footprinting
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 ...
DNase-Seq
DNase I footprinting analysis of DNase-seq data in R/Bioconductor HINT : Tutorial for detection of DNAse footprints with HINT. ... DNase-seq requires some downstream bioinformatics analyses in order to provide genome-wide DNA footprints. The computational ... Mar 2011). "High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells". Genome Research ... Mar 2011). "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data". Genome ...
Multiple EM for Motif Elicitation
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 (All ... 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 ...
NFE2
Hung HL, Kim AY, Hong W, Rakowski C, Blobel GA (Apr 2001). "Stimulation of NF-E2 DNA binding by CREB-binding protein (CBP)- ... Strauss EC, Andrews NC, Higgs DR, Orkin SH (1992). "In vivo footprinting of the human alpha-globin locus upstream regulatory ... Hung HL, Kim AY, Hong W, Rakowski C, Blobel GA (2001). "Stimulation of NF-E2 DNA binding by CREB-binding protein (CBP)-mediated ...
Micropeptide
The second predicted micropeptide, MRI-2, may be important in non-homologous end joining (NHEJ) of DNA double strand breaks. In ... "Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation". The EMBO Journal. 33 (9 ... encoded polypeptide that stimulates DNA end joining". The Journal of Biological Chemistry. 289 (16): 10950-7. doi:10.1074/jbc. ...
Go to Relief of cyclin A gene transcriptional inhibition during activation of human primary T lymphocytes via CD2 and CD28...
DNA Footprinting; Receptors, Interleukin-2/genetics/metabolism; T-Lymphocytes/metabolism/*physiology ... To understand the mechanisms underlined in this regulation in normal human cells, we have analysed in vivo protein-DNA ... In vivo genomic DMS footprinting revealed upstream of the major transcription initiation sites, the presence of at least three ... DNA-Binding Proteins/metabolism; Activating Transcription Factor 1; Antibodies, Monoclonal; Antigens, CD2/*physiology; Antigens ...
Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements |...
Ganley A, Kobayashi T: Phylogenetic footprinting to find functional DNA elements. Methods Mol Biol 2007, 395: 367-80. ... Voss R: Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. Phys Rev Lett 1992, 68: 3805-3808. ... Its known that theres a three bases periodicity in the coding DNA signal and the power spectrum at frequency of 1/3 is a ... Phylogenetic footprinting is a powerful tool for such purpose as evolutionary conservation is a significant hallmark of protein ...
MH DELETED MN ADDED MN
DNA Footprinting E5.393.600.300 DNA Tumor Viruses B4.909.204.210 B4.280.210 B4.909.574.204 B4.613.204 DNA Viruses B4.909.204 ... DNA, A-Form G2.111.570.790.486.128 G2.111.570.820.486.128 DNA, B-Form G2.111.570.790.486.142 G2.111.570.820.486.142 DNA, C-Form ... DNA, Circular G2.111.570.790.486.212 G2.111.570.820.486.212 DNA, Concatenated G2.111.570.790.486.268 G2.111.570.820.486.268 DNA ... DNA, Superhelical G2.111.570.790.486.212.250 G2.111.570.820.486.212.250 DNA, Z-Form G2.111.570.790.486.493 G2.111.570.820. ...
DeCS
DNA Footprint. DNA Footprintings. DNA Footprints. Footprint, DNA. Footprinting, DNA. Footprintings, DNA. Footprints, DNA. ... DNA Footprintings Footprinting, DNA Footprintings, DNA Footprints, DNA - Related but not broader or narrower Concept UI. ... DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. ... DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. ...
WikiGenes - GCR1 - Gcr1p
A simple in vivo footprinting method to examine DNA-protein interactions over the yeast PYK UAS element. Dumitru, I., McNeil, J ... DNA gel mobility shift assays and in-vitro DNase I protection experiments mapped a DNA binding site for Gcr1p in the ... In this report, I demonstrate that GCR1 encodes a DNA binding protein whose ability to bind DNA is dependent on the CTTCC ... Characterization of the DNA-binding activity of GCR1: in vivo evidence for two GCR1-binding sites in the upstream activating ...
Department of Chemistry - Research output - Experts@Syracuse
Pesquisa | Portal Regional da BVS
Nucleic Acids to Amino Acids: DNA Specifies Protein | Learn Science at Scitable
Thus, the shortest code of DNA bases that could possibly encode all the necessary amino acids in proteins is a triplet code - ... Indeed, various experiments established that DNA has a triplet code and also determined which triplets specify which amino ... How can the four bases that make up DNA specify the 20 amino acids that make up proteins? Clearly, each base cannot specify a ... Do Transcription Factors Actually Bind DNA? DNA Footprinting and Gel Shift Assays ...
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria ...
... and DNase I footprinting assays. The results indicate that phosphorylated ArcA proteins bind to a DNA site similar in sequence ... In Dub-seq, a shotgun expression library is cloned between dual random DNA barcodes and the precise breakpoints of DNA ... In Dub-seq, a shotgun expression library is cloned between dual random DNA barcodes and the precise breakpoints of DNA ... High-throughput functional variant screens via in vivo production of single-stranded DNA. Journal Article Schubert, Max G. ; ...
Xromatin - Vikipediya
"DNAse footprinting: a simple method for the detection of protein-DNA binding specificity". Nucleic Acids Research. 5 (9). 1978 ... DNA kimi həqiqi polimerlər üçün bu, çox kobud bir təxmindir; vacib olan in vivo DNA üçün mövcud yerin məhluldakı sərbəst ... B və Z-DNA qovşağında bir baza cütü normal bağlanmadan qopur. İkiqat rol oynayırlar: bir çox zülalın tanınma yeri və RNT ... "DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139". J. Biol. Chem. 273 (10). 1998: 5858-68. doi: ...
Hot Topics of the Day|PHGKB
Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer A Vanderstichel et al, NPJ ... DNA germline genetic testing can identify individuals with cancer susceptibility. However, DNA sequencing alone is limited in ... However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the ... Sequences of the human genome have typically included gaps in repetitive regions of DNA. A combination of state-of-the-art ...
Androgel malaysia price, anadrol achat | Kingneon
The Role of Fatty Acid Metabolism in Drug Tolerance of Mycobacterium tuberculosis : WestminsterResearch
Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. Odell, M. and Shuman, S. 1999. Footprinting of ... DNA Ligases: Stuctures. Odell, M. 2004. DNA Ligases: Stuctures. in: Lennarz, W.J. and Lane, M.D. (ed.) Encyclopedia of ... Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate ... Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate ...
Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by...
Epigenetic modifications, such as DNA methylation at position five in cytosine, has been shown to play a role in the ... The overall levels of methylation in CG, CHG, and CHH contexts were similar between flight and ground DNA, however, thousands ... Whole Genome Bisulfite Sequencing of DNA of Arabidopsis grown on the ISS from seed revealed organ-specific patterns of ... In vivo footprinting and high-resolution methylation analysis of the mouse hypoxanthine phosphoribosyltransferase gene 5′ ...
Metadata detail: PRJDB675
Genome footprinting by high-throughput sequencing (GeF-seq) resolves DNA-binding sites of targeted proteins with an accuracy ... The binding sites of AbrB determined by GeF-seq are comparable to the resolution achieved by in vitroDNase I footprinting. The ... Here, we describe a new method, "Genome Footprinting by high-throughput sequencing (GeF-seq)", to attain high-resolution ... comparable to in vitro DNase I footprinting. description. Chromatin immunoprecipitation (ChIP) is a common method to map ...
MH DELETED MN ADDED MN
DNA Footprinting E5.393.600.300 DNA Tumor Viruses B4.909.204.210 B4.280.210 B4.909.574.204 B4.613.204 DNA Viruses B4.909.204 ... DNA, A-Form G2.111.570.790.486.128 G2.111.570.820.486.128 DNA, B-Form G2.111.570.790.486.142 G2.111.570.820.486.142 DNA, C-Form ... DNA, Circular G2.111.570.790.486.212 G2.111.570.820.486.212 DNA, Concatenated G2.111.570.790.486.268 G2.111.570.820.486.268 DNA ... DNA, Superhelical G2.111.570.790.486.212.250 G2.111.570.820.486.212.250 DNA, Z-Form G2.111.570.790.486.493 G2.111.570.820. ...
MH DELETED MN ADDED MN
DNA Footprinting E5.393.600.300 DNA Tumor Viruses B4.909.204.210 B4.280.210 B4.909.574.204 B4.613.204 DNA Viruses B4.909.204 ... DNA, A-Form G2.111.570.790.486.128 G2.111.570.820.486.128 DNA, B-Form G2.111.570.790.486.142 G2.111.570.820.486.142 DNA, C-Form ... DNA, Circular G2.111.570.790.486.212 G2.111.570.820.486.212 DNA, Concatenated G2.111.570.790.486.268 G2.111.570.820.486.268 DNA ... DNA, Superhelical G2.111.570.790.486.212.250 G2.111.570.820.486.212.250 DNA, Z-Form G2.111.570.790.486.493 G2.111.570.820. ...
MH DELETED MN ADDED MN
DNA Footprinting E5.393.600.300 DNA Tumor Viruses B4.909.204.210 B4.280.210 B4.909.574.204 B4.613.204 DNA Viruses B4.909.204 ... DNA, A-Form G2.111.570.790.486.128 G2.111.570.820.486.128 DNA, B-Form G2.111.570.790.486.142 G2.111.570.820.486.142 DNA, C-Form ... DNA, Circular G2.111.570.790.486.212 G2.111.570.820.486.212 DNA, Concatenated G2.111.570.790.486.268 G2.111.570.820.486.268 DNA ... DNA, Superhelical G2.111.570.790.486.212.250 G2.111.570.820.486.212.250 DNA, Z-Form G2.111.570.790.486.493 G2.111.570.820. ...
Negative regulation of ectoine uptake and catabolism in Sinorhizobium meliloti: Characterization of the EhuR gene<...
Electrophoretic mobility shift assays and DNase I footprinting assays revealed that EhuR bound specifically to the DNA regions ... Electrophoretic mobility shift assays and DNase I footprinting assays revealed that EhuR bound specifically to the DNA regions ... Electrophoretic mobility shift assays and DNase I footprinting assays revealed that EhuR bound specifically to the DNA regions ... Electrophoretic mobility shift assays and DNase I footprinting assays revealed that EhuR bound specifically to the DNA regions ...
Broad-spectrum binding to human papillomavirus DNA | James K Bashkin | University of Missouri-St. Louis, USA | Medicinal...
James K Bashkin abstract presented on Broad-spectrum binding to human papillomavirus DNA at Medicinal Chemistry 2019 , ... Binding constants were determined by quantitative DNase I footprinting and capillary electrophoresis. Binding constants do not ... We have measured binding constants for a group of active anti-HPV compounds on viral DNA, largely but not exclusively in the ... These and other recent results, including new observations of polyamide-DNA binding stoichiometry, are of interest. In ...
2020/03/27: Ultra-deep Coverage Single-molecule R-loop Footprinting using SMRF-seq - Chedin lab
2021/10/01: New review published in DNA Repair. Congrats Daisy! * - 2021/08/01: Talysa Ogas-Viera joins the lab effective ... 2020/03/27: Ultra-deep Coverage Single-molecule R-loop Footprinting using SMRF-seq. By flchedin in Uncategorized on March 15, ... Home » Uncategorized » - 2020/03/27: Ultra-deep Coverage Single-molecule R-loop Footprinting using SMRF-seq ... near nucleotide resolution profiling of R-loops on single DNA molecules at ultra-deep coverage. Great work! ...
Imaging - IBMC
Abstract , Links , BibTeX , Tags: Animals, Antibodies, Base Sequence, Binding Sites, DNA, DNA-Binding Proteins, Epitopes, ... Genomic footprinting and transfection experiments suggest that this activation occurs through a ternary complex that includes ... Animals DNA ENNIFAR ERIANI Female FLORENTZ FRUGIER Genetic hoffmann Humans I2CT imler Immunity M3i MARQUET Mice Molecular Non-U ... keywords = {Animals, Antibodies, Base Sequence, Binding Sites, DNA, DNA-Binding Proteins, Epitopes, Escherichia coli, ets- ...
Molecular Neuroscience: A Laboratory Manual
DNA BASICS. Preparation of Plasmid DNA by Alkaline Lysis with Sodium Dodecyl Sulfate: Minipreparation. Joseph Sambrook and ... RNase Footprinting to Map Sites of RNA-Protein Interactions. Timothy W. Nilsen. Identification of RNA Cargoes by Antibody- ... SECTION 2. WORKING WITH DNA. BACTERIA BASICS. Bacteria. Kathy Barker. Making Media for Bacterial Culture. Kathy Barker. ... Quantitation of DNA and RNA. Carlos F. Barbas III, Dennis R. Burton, Jamie K. Scott, and Gregg J. Silverman. The Basic ...
Track Data Hubs
Digital genomic footprinting from 243 cell & tissue types hg38. DNA Methylation Hundreds of analyzed methylomes from bisulfite ... ENCODE DNA Trackhub ENCODE Trackhub for DNA-based assays hg19, hg38, mm10. ... UCD DNA methylation data [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...[-]. hg19, hg18, mm10, mm9, bosTau7, bosTau6, ... UniBind 2021 hub for robust direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, sacCer3, rn6, araTha1...[-]. hg38, ...
Track Data Hubs
Digital genomic footprinting from 243 cell & tissue types hg38. DNA Methylation Hundreds of analyzed methylomes from bisulfite ... ENCODE DNA Trackhub ENCODE Trackhub for DNA-based assays hg19, hg38, mm10. ... UCD DNA methylation data [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...[-]. hg19, hg18, mm10, mm9, bosTau7, bosTau6, ... UniBind 2021 hub for robust direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, sacCer3, rn6, araTha1...[-]. hg38, ...
Track Data Hubs
Digital genomic footprinting from 243 cell & tissue types hg38. DNA Methylation Hundreds of analyzed methylomes from bisulfite ... ENCODE DNA Trackhub ENCODE Trackhub for DNA-based assays hg19, hg38, mm10. ... UCD DNA methylation data [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...[-]. hg19, hg18, mm10, mm9, bosTau7, bosTau6, ... UniBind 2021 hub for robust direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, sacCer3, rn6, araTha1...[-]. hg38, ...
NIH VideoCasting - Past Events
Site information for: LexA
in species Listeria monocytogenes;
genome accession: NC 003210.1
DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or ... More recently, motif discovery algorithms that make use of phylogenetic foot-printing (the idea that TF-binding site will be ... plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) ...
Members - Zaugg Group
Sebastian Doniach's Profile | Stanford Profiles
The 0.22 value of the scaling exponent for short DNA segments is consistent with theoretical predictions for a branched DNA ... Here, we use hydroxyl radical footprinting and small-angle X-ray scattering (SAXS) to study the conformations of this tandem ... Understanding biological and physical processes involving nucleic acids, such as the binding of proteins to DNA and RNA, DNA ... Counterion distribution around DNA probed by solution X-ray scattering PHYSICAL REVIEW LETTERS Das, R., Mills, T. T., Kwok, L. ...
Genomic3
- In vivo genomic DMS footprinting revealed upstream of the major transcription initiation sites, the presence of at least three protein binding sites, two of which were constitutively occupied. (cnrs.fr)
- As a demonstration of this approach, we constructed a Dub-seq library with total Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified 813 genes with high-confidence overexpression phenotypes across 4,151 genes assayed. (osti.gov)
- Genomic footprinting and transfection experiments suggest that this activation occurs through a ternary complex that includes the serum response factor (SRF) and the ternary complex factor p62. (cnrs.fr)
Assays2
- In Dub-seq, a shotgun expression library is cloned between dual random DNA barcodes and the precise breakpoints of DNA fragments are associated to the barcode sequences prior to performing assays. (osti.gov)
- Electrophoretic mobility shift assays and DNase I footprinting assays revealed that EhuR bound specifically to the DNA regions overlapping the -35 region of the ehuA promoter and the +1 region of the ehuR promoter. (elsevierpure.com)
Proteins4
- A method for determining the sequence specificity of DNA-binding proteins. (bvsalud.org)
- Once it was determined that messenger RNA ( mRNA ) serves as a copy of chromosomal DNA and specifies the sequence of amino acids in proteins, the question of how this process is actually carried out naturally followed. (nature.com)
- Elk-1 and p62TCF have the same DNA sequence requirements and antibodies against Elk-1 block the binding of both proteins. (cnrs.fr)
- recent Advances in the biology of DNA have shown that a very large part of the genome in eukaryotes codes for small RNA molecules that appear to be centralto the way the genes (coding for proteins) are put together. (stanford.edu)
Genome4
- It's been more than 20 years since the initial draft of the human genome-a single, incomplete sequence based largely on one person's DNA-was unveiled. (cdc.gov)
- Whole Genome Bisulfite Sequencing of DNA of Arabidopsis grown on the ISS from seed revealed organ-specific patterns of differential methylation compared to ground controls. (biomedcentral.com)
- Here, we describe a new method, "Genome Footprinting by high-throughput sequencing (GeF-seq)", to attain high-resolution mapping of protein-binding sites by combining in vivo DNase I digestion and ChIP-seq. (nig.ac.jp)
- DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. (umbc.edu)
Vitro1
- In vitro, DNA binding by EhuR could be directly inhibited by a degradation product of ectoine. (elsevierpure.com)
Protein-DNA interactions1
- To understand the mechanisms underlined in this regulation in normal human cells, we have analysed in vivo protein-DNA interactions at the Cyclin A locus in primary T lymphocytes. (cnrs.fr)
Sequences1
- Last month, scientists published the first draft of a human "pangenome" in Nature, a collection of 94 nearly complete, high-quality DNA sequences, representing both sets of chromosomes from 47 individuals with diverse ancestral backgrounds. (cdc.gov)
Molecule2
- The presence of proflavine in a DNA molecule thus interferes with the molecule's replication such that the resultant DNA copy has a base inserted or deleted. (nature.com)
- Repair by HR begins by resection of the broken DNA molecule leaving a single-stranded DNA (ssDNA) with a free 3′-OH end. (elifesciences.org)
Experiments3
- ReMap 2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. (ucsc.edu)
- ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. (ucsc.edu)
- ReMap 2022: A database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments Go to ReMap2022 for more info. (ucsc.edu)
Single-stranded1
- The D-loop comprises a single-stranded displaced strand, an hDNA, and a DNA strand-exchange junction at each extremity of the hDNA. (elifesciences.org)
Binds1
- DNA cleavage is inhibited where the ligand binds to DNA. (bvsalud.org)
Extension1
- D-loops containing an annealed 3′-OH end are primed for an extension by a DNA polymerase and are less likely to be reversed ( Li and Heyer, 2009 ). (elifesciences.org)
Largely1
- We have measured binding constants for a group of active anti-HPV compounds on viral DNA, largely but not exclusively in the long control region (LCR). (pharmaceuticalconferences.com)
Biology1
- A wide variety of powerful molecular techniques have been applied to biology in recent decades, ranging from recombinant DNA technologies to state-of-the-art imaging methods. (cshlpress.com)
Experimental1
- Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a strategy that couples systematic gene overexpression with DNA barcode sequencing for large-scale interrogation of gene fitness under many experimental conditions at low cost. (osti.gov)
Results1
- These and other recent results, including new observations of polyamide-DNA binding stoichiometry, are of interest. (pharmaceuticalconferences.com)
Major1
- It consists of five major sections: Working with Cells, Working with DNA, Working with RNA, Gene Transfer, and Imaging. (cshlpress.com)
Specifically1
- The overall levels of methylation in CG, CHG, and CHH contexts were similar between flight and ground DNA, however, thousands of specifically differentially methylated cytosines were discovered, and there were clear organ-specific differences in methylation patterns. (biomedcentral.com)
Base1
- DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. (bvsalud.org)
Method1
- This method permits S9.6-independent, strand-specific, near nucleotide resolution profiling of R-loops on single DNA molecules at ultra-deep coverage. (ucdavis.edu)
Repair1
- Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of crossover outcome. (elifesciences.org)
Resolution1
- The binding sites of AbrB determined by GeF-seq are comparable to the resolution achieved by in vitroDNase I footprinting. (nig.ac.jp)
Shown1
- Epigenetic modifications, such as DNA methylation at position five in cytosine, has been shown to play a role in the physiological adaptation to adverse terrestrial environments, and may play a role in spaceflight as well. (biomedcentral.com)
Normal1
- B və Z-DNA qovşağında bir baza cütü normal bağlanmadan qopur. (wikipedia.org)
Environment1
- Fundamental techniques include maintaining a sterile working environment, purifying and culturing neural cells, isolating and manipulating DNA and RNA, and understanding and using a microscope. (cshlpress.com)