Dna binding site. Medical search. Frequent questions

DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins. (wikipedia.org)
DNA binding sites are often associated with specialized proteins known as transcription factors, and are thus linked to transcriptional regulation. (wikipedia.org)
DNA binding sites also encompasses the targets of other proteins, like restriction enzymes, site-specific recombinases (see site-specific recombination) and methyltransferases. (wikipedia.org)
DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for recombination sites) that are specifically bound by one or more DNA-binding proteins or protein complexes. (wikipedia.org)
To quantify the binding affinity of proteins and other molecules to specific DNA binding sites the biophysical method Microscale Thermophoresis is used. (wikipedia.org)
Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
This technique combines DNase I cleavage of protein protected DNA fragments and Maxam-Gilbert sequence determination methods, relying on the relatively low specificity of DNase I in a partial digestion and the ability of DNA-bound proteins to prevent phosphodiester bond hydrolysis between the base pairs they cover. (caltech.edu)
Fe(II) footprinting has been compared with DNase I footprinting in their ability to determine the binding specificities of both small molecules and proteins. (caltech.edu)
The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. (wikipedia.org)
More specifically, Chemicals describes atoms and complete chemical compounds, Polymer-Segments describe regions within polymers such as proteins and DNA, and Organisms describes the biological organism modeled within a PGDB. (ecocyc.org)
Carbapenems inhibit bacterial cell wall synthesis by binding to penicillin-binding proteins. (medscape.com)
Following insulin binding, the insulin receptor (IR) autophosphorylates itself and creates docking sites for IRS proteins. (scielo.br)
One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. (cshlpress.com)
Since the mid-20th century, from discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. (cshlpress.com)
The others are the site-specific TFs or the DNA sequence-specific binding proteins. (intechopen.com)
These agents are characterized by their ability to bind covalently to nucleophilic sites in proteins and DNA. (cdc.gov)
We therefore focus on elucidating the roles of the telomere binding proteins in this process. (lu.se)
DNA FOOTPRINTING utilizes this technique to analyze the DNA contact sites of DNA-BINDING PROTEINS. (bvsalud.org)
It inhibits bacterial cell wall synthesis by binding to 1 or more penicillin-binding proteins. (medscape.com)
In the interaction with proteins, lead binds with virtually every available functional group, including sulfhydryl, amine, phosphate, and carboxyl groups, with sulfhydryl having the highest affinity. (cdc.gov)
Superposition of proteins based on surface shape can enable comparison of highly divergent proteins, identify convergent evolution and enable detailed comparison of surface features and binding sites. (lu.se)
In particular, we find that global surface shape similarity is particular common among DNA binding proteins. (lu.se)
Receptor proteins have specific sites into which certain other proteins, called ligands, fit like keys into locks. (medlineplus.gov)
When the ligand attaches (binds), the PDGFRA receptor protein is turned on (activated), which leads to activation of a series of proteins in multiple signaling pathways. (medlineplus.gov)
Blom A. M . , Berggård K., Webb J. H., Villoutreix B., Lindahl G. and Dahlbäck B. (2000) Human C4b-binding protein has overlapping but not identical binding sites for C4b and streptococcal M-proteins. (lu.se)

On the other hand, DNA binding sites for a given transcription factor are usually all different, with varying degrees of affinity of the transcription factor for the different binding sites. (wikipedia.org)
The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
Here, we describe a novel, high-affinity binding site for I-TevI endonuclease, encoded within the group I td intron of phage T4. (rcsb.org)
I-TevI binds the operator and homing sites with equal affinity, and functions as a transcriptional autorepressor. (rcsb.org)
Alanine substitutions of the interacting CTE residues reduced affinity for inverted repeat HREs separated by three nucleotides, and essentially abrogated binding to a single HRE. (nih.gov)
These results, taken together, support the notion that sequences outside of the HREs influence the DNA binding affinity and specificity of steroid receptors. (nih.gov)
Using mass spectrometry, NMR spectroscopy, and fluorescence experiments we have demonstrated that compound 1 binds reversibly to the ATP-binding site of the 24 kDa N-terminal fragment of DNA gyrase B from Escherichia coli (GyrB24) with low micromolar affinity. (hal.science)
DNA affinity purification sequencing (DAP-seq) and modifications such as sequential DAP-seq (seq-DAP-seq) are robust in vitro methods for mapping individual TF or TF complex binding sites in a genome -wide manner. (bvsalud.org)
DNA libraries are then incubated with an affinity-tagged TF or TF- complex immobilized on magnetic beads. (bvsalud.org)
The TF or TF complex of interest is generally produced using recombinant protein expression and purified prior to DNA affinity purification. (bvsalud.org)
These differences in structure are used to rationalize the lack of affinity of daunomycin-type anthracyclines for d(YGG) and d(YGC) sites. (ox.ac.uk)
Understanding protein-DNA binding affinity is still a mystery for many transcription factors (TFs). (biorxiv.org)

Moreover, due to the limited success of bioinformatics in producing efficient DNA binding site prediction tools (large false positive rates are often associated with in-silico motif discovery / site search methods), there has been no systematic effort to computationally annotate these features in sequenced genomes. (wikipedia.org)
Below is a non-exhaustive table of available databases: A collection of DNA binding sites, typically referred to as a DNA binding motif, can be represented by a consensus sequence. (wikipedia.org)
These matrices give information on the frequency of each base at each position of the DNA binding motif. (wikipedia.org)
We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.com)
If you want to search for a protein sequence or a DNA motif use the Sequence Search Form . (csic.es)
For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue. (wikipedia.org)

Restriction enzymes, like transcription factors, yield a gradual, though sharp, range of affinities for different sites and are thus also best represented by PSFM. (wikipedia.org)
From then on, DNA binding sites for many transcription factors, restriction enzymes and site-specific recombinases have been discovered using a profusion of experimental methods. (wikipedia.org)
Due to the diverse nature of the experimental techniques used in determining binding sites and to the patchy coverage of most organisms and transcription factors, there is no central database (akin to GenBank at the National Center for Biotechnology Information) for DNA binding sites. (wikipedia.org)
There are, however, several private and public databases devoted to compilation of experimentally reported, and sometimes computationally predicted, binding sites for different transcription factors in different organisms. (wikipedia.org)
Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes. (lu.se)
Published September 5, 2007 transcription factors and replicating extra DNA, rather than going directly into growth of the cell. (lu.se)

On the one hand, restriction sites can be generally represented by consensus sequences. (wikipedia.org)
This makes it difficult to accurately represent transcription factor binding sites using consensus sequences, and they are typically represented using position specific frequency matrices (PSFM), which are often graphically depicted using sequence logos. (wikipedia.org)
Even though NCBI contemplates DNA binding site annotation in its reference sequences (RefSeq), most submissions omit this information. (wikipedia.org)
Using structural, biochemical, and cell-based assays, we show that GR binding sequences, differing by as little as a single base pair, differentially affect GR conformation and regulatory activity. (rcsb.org)
In this paper, we present a threshold-free framework based on a novel ensemble learning algorithm in order to locate TFBSs in DNA sequences. (biorxiv.org)
Our proposed approach creates TF-specific classifier models using genome-wide DNA-binding experiments and a prior biological knowledge on DNA sequences and TF binding preferences. (biorxiv.org)
Finally, the created classifier models are used to scan new DNA sequences and identify potential binding sites. (biorxiv.org)

Transcriptional regulation information for a gene, including any predicted DNA binding site motifs ( YeTFaSCo ) for the gene's protein product, as well as any of its targets (genes it regulates) or regulators (genes that regulate it), based on experimental evidence. (yeastgenome.org)
Binding sites motifs as predicted by YeTFaSCo . (yeastgenome.org)
Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)
Upon binding of insulin to the insulin receptor (IR), IRS1 is phosphorylated at several YXXM motifs creating docking sites for the binding of PI3Kp85, which activates AKT kinase. (scielo.br)

Although several approaches have been proposed in the literature to model the DNA-binding specificity of TFs, they still have some limitations. (biorxiv.org)
Site-specificity of and cell proliferation would allow DPX and cell proliferation formaldehyde-induced lesions in rats and monkeys implicates data to be interpolated from measurement sites to the rest of the regional tissue susceptibility and dose as factors potentially nasal passage. (cdc.gov)

Predictive TFBS models are generated from the bound regions using downstream bioinformatics analysis pipelines . (bvsalud.org)
Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. (cshlpress.com)

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
Kornberg 7 has presented that the interactions between DNA and histones are involved in chromosome packaging in the cell nucleus. (nature.com)
Crystallographic studies showed that the overall interactions of the DNA-binding domain with the operator and homing sites are similar, but have some different hydrogen-bonding contacts. (rcsb.org)
We present a model in which the flexibility in protein-DNA interactions allows I-TevI to bind variant intronless alleles to promote intron mobility while facilitating its function in autorepression, and thereby persistence in its host. (rcsb.org)
While it is possible by spectroscopic means to determine the overall affinities and stoichiometries of these small molecule/DNA interactions, the exact locations and sizes of these sites of interaction are not known. (caltech.edu)
binding cooperativity of different small molecules) on the interactions of small molecules with native DNA. (caltech.edu)
The eponymous FinO protein was discovered as a regulator of F plasmid conjugation nearly 50 years ago, and acts to bind a single partner sRNA called FinP to stabilize FinP and facilitate its interactions with its antisense partner, the mRNA encoding the major F plasmid transcription factor, TraJ 5 . (nature.com)
Anthracycline-DNA interactions at unfavourable base-pair triplet-binding sites: structures of d(CGGCCG)/daunomycin and d(TGGCCA)/adriamycin complexes. (ox.ac.uk)
Both complexes are essentially isomorphous with related structures but differ in terms of the number of favourable van der Waals interactions of the amino sugars of the drug molecules with the DNA duplexes and the formation in the minor groove of heterodromic pentagonal arrangements of hydrogen bonds involving water molecules which link the amino sugars to the DNA. (ox.ac.uk)
A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create a unified view of the field and a fuller understanding of protein-DNA interactions. (cshlpress.com)
Researchers started with an assembly of nanoparticles already linked in a regular array by the complementary binding of the A, T, G, and C bases on single-stranded DNA tethers, and then added reprogramming DNA strands to alter the interparticle interactions. (acm.org)
Common among these 10 interactions of organic compounds, their power to detect excess cancer agents is the electrophilic nature of or their metabolites, with DNA and R 1 risk at particular sites. (who.int)

The different subclasses of Polymer-Segments include different types of DNA sites such as transcription start sites and terminators, and longer regions such as genes. (ecocyc.org)
We therefore propose that DNA is a sequence-specific allosteric ligand of GR that tailors the activity of the receptor toward specific target genes. (rcsb.org)
The fuzzy dot images were not precise enough on the nanometer level to truly tell us how these markers reflect DNA, but this system allows us to collect quantitative data and prove - not hypothesize - how genes are behaving. (sciencedaily.com)
For example, steroid and thyroid hormones directly bind to nuclear receptors, which induce expression of specific genes. (intechopen.com)

Fe(II) footprinting provided greater resolving capacity and importantly more precisely defined the binding locations and sizes of small molecule: DNA complexes. (caltech.edu)
However, determining the genome -wide binding of specific TFs or TF complexes remains a technical challenge. (bvsalud.org)
After incubation of the DNA library with the immobilized TF of interest, multiple wash steps are performed to reduce non-specific DNA binding and the TF- DNA complexes eluted. (bvsalud.org)
Buehl CJ, Goff NJ, Hardwick SW, Gellert M, Blundell TL, Yang W, Chaplin AK , Meek K. Two distinct long-range synaptic complexes promote different aspects of end processing prior to repair of DNA breaks by non-homologous end joining. (le.ac.uk)

Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. (lu.se)

Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)
Early studies showed that FinO specifically binds the 3' transcriptional terminator structure of FinP in a manner that critically relies on both the GC-rich hairpin and 3' polypyrimidine tail that define the terminator 16 , and further work showed that the base of the hairpin and 3' tail are both strongly protected from ribonuclease degradation by FinO 17 . (nature.com)
The identification of genome -wide transcription factor binding sites (TFBS) is a critical step in deciphering gene and transcriptional regulatory networks. (bvsalud.org)

Thus, we can distinguish between transcription factor-binding sites, restriction sites and recombination sites. (wikipedia.org)
Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. (lu.se)

The existence of something akin to DNA binding sites was suspected from the experiments on the biology of the bacteriophage lambda and the regulation of the Escherichia coli lac operon. (wikipedia.org)

This gDNA library can be used directly or an amplification step may be performed to remove DNA modifications such as cytosine methylation . (bvsalud.org)
and research using the Sequenom MassArray system for SNP genotyping, DNA methylation analysis, and somatic mutation profiling. (genomeweb.com)

We have determined the structure of the progesterone receptor (PR)-DBD-CTE DNA complex at a resolution of 2.5 A, which revealed binding of the CTE to the minor groove flanking the HREs. (nih.gov)
In addition to binding to the insulin receptor, IRS1 also binds to and transmits signals from the receptors of prolactin, growth hormone (GH), leptin, vascular endothelial growth factor (VEGF), tropomyosin receptor kinase B (TrkB), anaplastic lymphoma kinase (ALK), insulin like growth factor (IGF1), and integrins ( Vuori and Ruoslathi , 1994 Vuori K and Ruoslahti E (1994) Association of insulin receptor substrate-1 with integrins. (scielo.br)
Post-attachment inhibitors bind to the CD4 receptor and prevent HIV (that also binds to the CD4 receptor) from entering the cell. (msdmanuals.com)

DAP-seq protocols use a genomic DNA (gDNA) library from any target organism with or without amplification, allowing the determination of TF binding on naked or endogenously modified DNA , respectively. (bvsalud.org)

Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
Both methods provided similar information in the case of a sequence-specific DNA binding protein, lac repressor. (caltech.edu)

hSSB1 is a newly discovered single-stranded DNA (ssDNA)-binding protein that is essential for efficient DNA double-strand break signalling through ATM. (st-andrews.ac.uk)
Strikingly, silencing of hSSB1 prevents foci formation as well as recruitment of MRN to sites of DSBs and leads to a subsequent defect in resection of DSBs as evident by defective RPA and ssDNA generation. (st-andrews.ac.uk)
Based on the structure evidence that other KH-I superfamily members bind RNA/ssDNA. (nih.gov)

However, the fusion protein does not require ligand binding to be activated. (medlineplus.gov)
Similarly, point mutations in the PDGFRA gene can result in a PDGFRA protein that is activated without ligand binding. (medlineplus.gov)

Need some help purifying genomic DNA with the Monarch Genomic DNA Purification Kit ( NEB #T3010 )? (neb.com)
You can also find guidance on choosing appropriate input amounts in our online resource, Choosing Input Amounts for the Monarch Genomic DNA Purification Kit . (neb.com)
Some organ tissues (e.g. spleen, kidney, liver) are extremely rich in genomic DNA. (neb.com)

Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila . (nature.com)

DNA binding sites are a type of binding site found in DNA where other molecules may bind. (wikipedia.org)
Many small molecules, such as antibiotics used in cancer chemotherapy, are believed to execute their therapeutic action through binding to the DNA template and impeding the progress of transcription and replication. (caltech.edu)
Fe(II) footprinting, which allows the determination of the preferred binding sites of several small molecules on heterogeneous double helical DNAs. (caltech.edu)
Fe(II) as a small synthetic scissor one is capable of footprinting the preferred locations and binding site sizes of small molecules bound on native DNA. (caltech.edu)
From a collection of their preferred binding sites, binding models for these small molecules have been derived. (caltech.edu)
Unit-cell dimensions are a = 28.07 (2), c = 53.35 (1) and a = 28.01 (1), c = 52.99 (1) A, respectively, and the asymmetric unit of both structures consists of one strand of DNA, one drug molecule and approximately 50 water molecules. (ox.ac.uk)
Two DNA molecules held by a quad-optical trap (Lumicks) are held together by a Cohesin complex, which can slide on the DNA without letting go of the DNA strands. (imperial.ac.uk)
Now, Georgia Tech and Emory researchers have created a technology based on stellar photometry software that provides more precise images of single molecules tagged with nanoprobes, particles specially designed to bind with a certain type of cell or molecule and illuminate when the target is found. (sciencedaily.com)
While less than precise nanoprobe images yield valuable information, the Georgia Tech and Emory research team knew that better technology was needed to pinpoint the exact distance in nanometers between probes to reveal important information about the size and binding geometry of targeted molecules. (sciencedaily.com)

By a structure-based approach we have previously discovered compound 1, an indolinone derivative, possessing inhibitory activity against DNA gyrase. (hal.science)
Sjöberg A., Trouw L., McGrath F., Hack E. C. and Blom A. M. (2006) Regulation of complement activation by C-reactive protein: targeting of the inhibitory activity of C4b-binding protein. (lu.se)

Historically, the experimental techniques of choice to discover and analyze DNA binding sites have been the DNAse footprinting assay and the Electrophoretic Mobility Shift Assay (EMSA). (wikipedia.org)

DNA binding sites can be categorized according to their biological function. (wikipedia.org)
While these studies have built the case that certain ProQ/FinO family members bind to only a very limited number of partners in a highly specific manner, other family members appear to have multiple biological sRNA targets. (nature.com)

Webb, J. H., Villoutreix, B. O., Dahlbäck, B. and Blom A. M. (2001) Localization of a hydrophobic binding site for protein S on the b-chain of C4BP. (lu.se)

These targets were identified based on the presence of predicted regulator binding sites or experimental regulator binding in the target promoter, and/or changes in the target gene's transcript levels in regulator mutant strains. (yeastgenome.org)

The resulting sequence reads are mapped to the corresponding reference genome , identifying direct potential bound regions and binding sites of the TF or TF complex of interest. (bvsalud.org)
The telomeres are the DNA-protein structures at the ends of eukaryotic chromosomes, which serve to protect and stabilize the genome. (lu.se)

Distinct sequence and spacing requirements of the catalytic domain result in reduced cleavage activity on operator DNA. (rcsb.org)
The DNA binding domain (DBD) of nuclear hormone receptors contains a highly conserved globular domain and a less conserved carboxyl-terminal extension (CTE). (nih.gov)
Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
The FH domain is a winged helix DNA-binding domain. (nih.gov)
GAL4 DNA-binding-domain clonned upstream of the multiple cloning site in pCMX. (addgene.org)

Attachment inhibitors bind directly to the viral envelope glycoprotein 120 (gp120), close to the CD4+ binding site, which prohibits the conformational change necessary for initial interaction between the virus and the surface receptors on CD4 cells, thereby preventing attachment and subsequent entry into host T cells and other immune cells. (msdmanuals.com)

The analogous question of protein: DNA binding specificities has been answered through the use of DNase I footprinting. (caltech.edu)
Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. (nih.gov)

The predicted binding mode explains the competitive inhibitory mechanism with respect to ATP and forms a useful basis for further development of potent DNA gyrase inhibitors. (hal.science)
Nucleoside reverse transcriptase inhibitors (NRTIs) are phosphorylated to active metabolites that compete for incorporation into viral DNA. (msdmanuals.com)
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) bind directly to the reverse transcriptase enzyme. (msdmanuals.com)
Integrase inhibitors prevent HIV DNA from being integrated into human DNA. (msdmanuals.com)

The molecular mechanism by which Cas9 binds and cleaves off-targets remains largely unknown, which is a significant problem that hinders the development of new and improved CRISPR/Cas9 systems with high accuracy and efficiency. (imperial.ac.uk)

In its binding with sulfhydryl groups, lead may interfere with the activity of zinc metalloenzymes, as zinc binds to a sulfhydryl group at the active site. (cdc.gov)
Lead also binds to metallothionein, a sulfhydryl-rich protein, but does not appear to displace cadmium or zinc. (cdc.gov)

The reprogramming DNA strands adhere to open binding sites to exert additional forces on the linked-up nanoparticles. (acm.org)

Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)

The clearer images allow researchers to collect more detailed information about a single molecule, such as how the molecule is binding in a gene sequence, taking scientists a few steps closer to truly personalized and predictive medicine as well as more complex biomolecular structural mapping. (sciencedaily.com)
The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. (lu.se)
Blom A. M. , Kask L. and B. Dahlbäck (2001) Structural requirements for the complement regulatory activities of C4b-binding protein. (lu.se)
Kask L., Hillarp A., Ramesh B., Dahlbäck B., and Blom A. M. (2002) Structural requirements for the intra-cellular subunit polymerization of the complement inhibitor C4b-binding protein. (lu.se)

Biophysical characterization of an indolinone inhibitor in the ATP-binding site of DNA gyrase. (hal.science)
DNA gyrase represents a validated antibacterial target and has drawn much interest in recent years. (hal.science)
Fluoroquinolones inhibit bacterial DNA synthesis and, consequently, growth by inhibiting DNA gyrase and topoisomerases, which are required for replication, transcription, and translation of genetic material. (medscape.com)

Here, we show that hSSB1 is recruited rapidly to sites of double-strand DNA breaks (DSBs) in all interphase cells (G1, S and G2) independently of, CtIP, MDC1 and the MRN complex (Rad50, Mre11, NBS1). (st-andrews.ac.uk)
ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. (nih.gov)
Confocal time-lapse movie initially shows a single dCas9 complex (green dot) bound on-target to λ-DNA held between two beads by optical tweezers at low force (5 pN). (imperial.ac.uk)
Off-targets dissociate while decreasing the force back to 5 pN, and only the on-target complex remains bound. (imperial.ac.uk)
These complex multi-subunit machines carry out multiple tasks on nucleosomes including chemical modifications, histone exchange and sliding them on DNA in what appears to be a highly coordinated process. (imperial.ac.uk)
Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. (lu.se)
The LIG4-XRCC4 heteromer associates in a DNA-dependent manner with the DNA-dependent protein kinase complex DNA-PK, formed by the KU p70/p86 dimer (g22p1/g22p2) and PRKDC. (lu.se)

The sum of DNA binding sites of a specific transcription factor is referred to as its cistrome. (wikipedia.org)
Likewise, site-specific recombinases also show a varied range of affinities for different target sites. (wikipedia.org)
A more accurate way of representing binding sites is through Position Specific Frequency Matrices (PSFM). (wikipedia.org)
Find support for a specific problem in the support section of our website. (mdpi.com)

Whether you are performing your first cloning experiment or constructing multi-fragment DNA assemblies, NEB ® has the solution for you. (neb.com)

Despite previous observations that the CTEs of some classes of nuclear receptors are structured and interact with DNA outside of the hexanucleotide hormone response element (HRE), there has been no evidence for such a CTE among the steroid receptors. (nih.gov)
Throughout the life of a eukaryotic cell, chromosomes undergo drastic conformational rearrangements that play essential roles in almost all nuclear processes, including gene expression, DNA repair and cell division. (imperial.ac.uk)

This chromatin remodelling activity is associated with regulation of gene expression in heterochromatin regions of plant and mammal chromosomes and with the cellular response to DNA damage. (imperial.ac.uk)

Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. (lu.se)

We also offer solutions for automation, site-directed mutagenesis, as well as your favorite restriction enzyme, ligase or competent cell products. (neb.com)

Chromomycin A 3 , mithramycin, and olivomycin all shared similar binding specificities, demonstrating typically 3 base pair binding site sizes and preferring a 5'-GC-3' sequence within. (caltech.edu)

3 classes inhibit reverse transcriptase by blocking its RNA-dependent and DNA-dependent DNA polymerase activity. (msdmanuals.com)

They inhibit the HIV reverse transcriptase enzyme competitively and terminate synthesis of DNA chains. (msdmanuals.com)

It has been reported that some binding sites have potential to undergo fast evolutionary change. (wikipedia.org)

Force stretching λ-DNA from 5 to 50 pN induces reversible off-target binding at multiple sites. (imperial.ac.uk)

We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. (nih.gov)

Anatomy12

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Chemicals and Drugs111

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