• In ICP8, the herpes simplex virus (HSV-1) single-strand DNA-binding protein (ssDNA-binding protein (SSB)), the head consists of the eight alpha helices. (wikipedia.org)
  • Six herpes virus-group-common genes encode proteins that likely constitute the replication fork machinery, including a two-subunit DNA polymerase, a Helicase-primase complex and a single-stranded DNA-binding protein. (wikipedia.org)
  • The human herpesvirus 1 (HHV-1) single-strand DNA-binding protein ICP8 is a 128kDa zinc metalloprotein. (wikipedia.org)
  • The mitochondria of eukaryotic cells contain their own single stranded DNA binding protein. (wikipedia.org)
  • DNA-binding protein Replication protein A Comparison of nucleic acid simulation software Mapelli M, Panjikar S, Tucker PA (2005). (wikipedia.org)
  • In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). (rsc.org)
  • Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. (biomedcentral.com)
  • Therefore, a computational method is required to annotate the DNA binding protein as DSB or SSB automatically. (biomedcentral.com)
  • We created several deletion mutants of this protein based on its conserved motifs, and from these structures functional chimeras were synthesized, supporting the hypothesis that gene duplication and recombination could lead to novel functional forms of single-stranded DNA-binding proteins. (johnshopkins.edu)
  • Biophysical studies showed that the orthologs of the two OB fold/one zinc finger replication protein A in Hethanosarcina acetivorans and Methanopyrus kandleri exhibit two binding modes, wrapping and stretching of DNA. (johnshopkins.edu)
  • Most interestingly, a second single-stranded DNA-binding protein, FacRPA2, in this archaeon exhibited the wrapping mode. (johnshopkins.edu)
  • Domain analysis of this protein, which contains a single OB fold, showed that its architecture is similar to the functional homologs thought to be unique to the Crenarckaeotes. (johnshopkins.edu)
  • The encoded protein contains three K-homologous (KH) domains which may be involved in RNA binding. (nih.gov)
  • Together with PCBP-1, this protein also functions as a translational coactivator of poliovirus RNA via a sequence-specific interaction with stem-loop IV of the IRES, promoting poliovirus RNA replication by binding to its 5'-terminal cloverleaf structure. (nih.gov)
  • Recently the human cardiac myosin binding protein-C (MyBP-C) gene was mapped to chromosome 11p11.2 (ref. 8), making this gene a good candidate for the fourth locus, CMH4 (ref. 5). (nih.gov)
  • Single Stranded DNA Binding Protein, E. coli is available at Gentaur for Next week delivery. (telospub.com)
  • Catalyzed by primosome proteins such as PriA, PriB, PriC, DnaT, and DnaG, DNA replication restart pathways facilitate origin-independent reloading of the replicative helicase onto a repaired DNA replication fork in a process that involves coordinated protein and nucleic acid binding within a nucleoprotein complex called the DNA replication restart primosome [ 2 ]. (biomedcentral.com)
  • A bHLH protein in concert with single stranded-binding proteins. (ox.ac.uk)
  • Bound or free: interaction of the C-terminal domain of E. coli single-stranded DNA binding protein (SSB) with the tetrameric core of SSB. (cipps.org.au)
  • Negative co-operativity in Escherichia coli single strand binding protein-oligonucleotide interactions. (utmb.edu)
  • The interaction of the Escherichia coli single strand binding (SSB) protein with single-stranded DNA is complex, since a number of different binding modes have been observed, with different DNA site sizes and binding properties and the transitions among these binding modes are strongly influenced by solution conditions in vitro. (utmb.edu)
  • In order to probe this negative co-operativity, we have examined the binding of a series of oligonucleotides of varying length, using the quenching of the intrinsic SSB protein fluorescence to monitor binding. (utmb.edu)
  • Dive into the research topics of 'Negative co-operativity in Escherichia coli single strand binding protein-oligonucleotide interactions. (utmb.edu)
  • CusabioAlternative Name(s): DsDNA-binding protein A (rpbB)Gene Names: dsbAResearch Areas: Cell. (joplink.net)
  • The processes that maintain telomeres employ replication protein A (RPA), a single-stranded DNA binding protein. (massgeneral.org)
  • On the other hand, RNA is a single chain of nucleotides primarily involved in protein synthesis following the master plan outlined by DNA. (aboutdarwin.com)
  • In this platform, catalytically inactive Cas9 serves as an RNA-guided DNA binding protein to silence gene expression in a sequence-specific manner. (berkeley.edu)
  • VEGF inhibitors directly bind to the VEGF protein to disrupt angiogenesis. (medscape.com)
  • Monoclonal antibodies that bind the programmed cell death-1 protein (PD-1) ligands, PD-L1 and PD-L2, to the PD-1 receptor found on T cells, inhibits T cell proliferation and cytokine production. (medscape.com)
  • However, our mesophilic protein also contains a putative single-stranded DNA binding or repA domain. (genengnews.com)
  • Our pAgo candidate nicks and cuts plasmid DNA nonspecifically in the absence of guide in in vitro assays, presumably due to the presence of single-stranded DNA that co-purifies with the protein," the abstract continued. (genengnews.com)
  • A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site. (umassmed.edu)
  • Most recently, I have been involved in two projects involving the biofunctionalization of various surfaces for selective protein binding. (nist.gov)
  • 1) Various complex formation of Histone methyltransferases for repressive chromatin and the molecular basis of their formation, 2) Relationship between heterochromatin formation and repressive histone modification on inactive X chromosome, 3) Involvement of an HP1 binding protein in pathway choice for repairing double-strand breaks. (nii.ac.jp)
  • Improved performance of Pyrosequencing using single-stranded DNA-binding protein. (wikidoc.org)
  • Kurimoto K, Fukai S, Nureki O, Muto Y, Yokoyama S. Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase. (medlineplus.gov)
  • A protein interacting with an A-T-rich region that is a positive control element within the SP6 κ promoter was purified and identified as CArG-box binding factor-A. The purified protein was shown to interact specifically with the coding strand of single-stranded DNA and, with lower affinity, with double-stranded DNA. (lu.se)
  • A mutation that inhibited binding of the protein to the A-T-rich region also aborted the transcriptional stimulatory effect of the region. (lu.se)
  • Two Ets proteins, PU.1 and elf-1, that have previously been shown to bind to an adjacent DNA element were shown to physically interact with CArG- box binding factor.A. An antiserum raised against the protein recognized two different forms indicating either that different splice-forms of. (lu.se)
  • Single-stranded binding protein Pot1, initially up-regulated at 12 wk in the WF+REG group, was later down-regulated in liver tissue at 24 wk along with the WF+HF group. (cdc.gov)
  • 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 hnRNP protein has a strong affinity for polypyrimidine-rich RNA and for single-stranded polypyrimidine-rich DNA. (bvsalud.org)
  • Multiple hnRNP K protein isoforms exist due to alternative splicing and display different nucleic-acid-binding properties. (bvsalud.org)
  • As binding of miRNAs to a target mRNA may result in an airway inflammatory disease closely correlates with either mRNA degradation or inhibition of protein immune regulation, more and more evidences suggest translation.1 More than 2000 miRNAs have been discovered in humans. (cdc.gov)
  • SSB binds with ssDNA with high affinity and low specificity, and is mainly involved in DNA replication, recombination and repair. (biomedcentral.com)
  • And indeed the team found that in cells that use the ALT pathway, RPA binds persistently to telomeres, not detaching after replication. (massgeneral.org)
  • TYPES OF REPLICATION 6 Hypothetically, therecouldbethreepossible waysthat DNAreplication occur: Conservative replication: Bothparental strands stay together afterDNAreplication. (slideshare.net)
  • It's quite an intricate dance aimed at making sure every new chromosome is equipped with one old and one new strand of DNA - this is referred to as semi-conservative replication. (aboutdarwin.com)
  • This enzyme unwinds the double-stranded DNA, paving the way for replication. (aboutdarwin.com)
  • They pair with bases on the old strand during replication. (aboutdarwin.com)
  • An artist in its own right, Ligase dutifully connects Okazaki fragments (short sequences produced at the lagging strand) during replication. (aboutdarwin.com)
  • formed by continuously copying the parent strand 3' to 5' toward the replication fork. (flashcardmachine.com)
  • More recently, recombinases have been used in isothermal nucleic acid amplification methods, mainly in recombinase polymerase amplification RPA and strand invasion based amplification SIBA. (helsinki.fi)
  • Target amplification assays are based on the ability of complementary oligonucleotide primers to specifically anneal and allow enzymatic amplification of the target nucleic acid strands. (cdc.gov)
  • Most recently, GeneXpert MTB/RIF (Cepheid) advanced nucleic acid-based detection by integrating PCR and a highly sensitive molecular-beacon assay into a single, automated system. (cdc.gov)
  • Recombinases exhibit ATP hydrolysis coupled DNA-binding activity and strand exchange activities during homologous recombination. (helsinki.fi)
  • Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. (lu.se)
  • There are two kinds of DNAs, single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). (biomedcentral.com)
  • The function of DnaT is not well understood, but it has been proposed that DnaT binding leads to dissociation of single-stranded DNA (ssDNA) from PriB through a competition mechanism, possibly exposing the ssDNA on the lagging strand template for reloading the replicative helicase, which ultimately leads to fork reactivation [ 8 ]. (biomedcentral.com)
  • Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. (nist.gov)
  • The stochastic nature of single-molecule charge transport measurements requires collection of large data sets to capture the full complexity of a molecular system. (imperial.ac.uk)
  • Here we present such an approach based on multivariate pattern analysis and apply it to simulated and experimental single-molecule charge transport data. (imperial.ac.uk)
  • A quenching of 50(± 2)% is observed upon filling only half of the subunits with either one molecule of dT(pT) 34 or two molecules of dT(pT) 15 , which agrees with the quenching and site size observed in the (SSB) 35 polynucleotide binding mode. (utmb.edu)
  • DNA, a double-stranded molecule, is the primary genetic material directly responsible for development and inheritable traits. (aboutdarwin.com)
  • A single-stranded chemiluminescent DNA probe, which is complementary to a region of the target amplicon, is labeled with different acridinium ester molecule. (cdc.gov)
  • Examples DNA repair and apoptosis path- concept is that there is a distinct dif- of DNA damage are DNA adducts ways, which are described in detail ference between DNA damage and (i.e. a molecule bound covalently to by Ciccia and El edge (2010) . (who.int)
  • METHODS: : The entire CDKN2A coding region and exon 2 of the CDK4 gene of an affected member of each of 52 families from southern Sweden with at least two cases of melanoma in first- or second-degree relatives were screened for mutations by use of polymerase chain reaction-single-strand conformation polymorphism analysis. (lu.se)
  • 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)
  • The telomeric repeat-binding factor 1 (Trf1) and 2 (Trf2), and the protection of telomere 1 (Pot1) are involved in telomere maintenance by preventing telomere end-to-end fusion through proper folding of the telomere. (cdc.gov)
  • In conclusion, our data suggest that disruption/down-regulation of single-stranded Pot1 and double-stranded Trf1/Trf2 expression in liver might act as an anti-apoptotic mechanism in the DNA-damage response leading to multistep liver injury by involvement in the telomere response to diet changes and WF exposure. (cdc.gov)
  • The recent Encyclopedia of studies in the 1950s and 1960s in Escherichia coli and then by DNA Elements (ENCODE) project showed binding of carcinogens to nu- Szybalski (1958) , who tested more indicates that at least 80% of the cleic acids ( Wiest and Heidelberger, than 400 compounds in E. coli . (who.int)
  • The great progress of the structure genomics project [ 9 ] results that more and more high resolution 3D structures for DSBs and SSBs are available now, which makes it possible to investigate the common structural differences between SSB and DSB that are responsible for the binding specificity. (biomedcentral.com)
  • A parallel development has been the preparation of imaging agents which can bind their targets with high specificity and affinity [ 10 ]. (hindawi.com)
  • We report that N. gonorrhoeae PriA's DNA binding and unwinding activities are similar to those of E. coli PriA, and N. gonorrhoeae PriA's helicase activity is stimulated by its cognate PriB, as it is in E. coli . (biomedcentral.com)
  • This finding is significant because N. gonorrhoeae PriB's single-stranded DNA binding activity is weak relative to that of E. coli PriB, and in E. coli , PriB's single-stranded DNA binding activity is important for PriB stimulation of PriA helicase. (biomedcentral.com)
  • Furthermore, a N. gonorrhoeae PriB variant defective for binding single-stranded DNA can stimulate PriA's helicase activity, suggesting that DNA binding by PriB might not be important for PriB stimulation of PriA helicase in N. gonorrhoeae . (biomedcentral.com)
  • While it remains unclear if N. gonorrhoeae PriB's weak DNA binding activity is required for PriB stimulation of PriA helicase, the ability of PriB to stimulate PriA-catalyzed ATP hydrolysis could play an important role. (biomedcentral.com)
  • Recruitment of PriB to a PriA:DNA complex stabilizes PriA on the DNA [ 6 ] and enhances its helicase activity through a mechanism that involves PriB's single-stranded DNA-binding activity [ 7 ]. (biomedcentral.com)
  • Though there are some researches [ 5 - 7 ] on the SSB and DSB respectively, few attentions have been paid on investigating what makes SSB and DSB have such different kind of binding specificity. (biomedcentral.com)
  • Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. (umassmed.edu)
  • This creates a second or double strand of nucleotides. (cdc.gov)
  • CONCLUSIONS: : Our findings confirm that the majority of CDKN2A-associated melanoma families in Sweden are due to a single founder mutation. (lu.se)
  • The nitrogen bases protruding from the existing strand bind to bases of the strand being synthesized according to the base pairing rules: Adenine binds to Thymine, and Cytosine binds to Guanine. (cdc.gov)
  • We identified several putative THA8L-binding sites, enriched with purine sequences, in the group II introns. (rcsb.org)
  • They work by binding to topoisomerase and causing single-strand DNA breaks. (medscape.com)
  • Photoaffinity labeling has shown that the region encompassing amino acid residues 368-902 contains the single-strand DNA-binding site of ICP8. (wikipedia.org)
  • Since telomerase is recruited to and elongates the single-stranded telomeric 3 ′ overhangs, the generation of 3 ′ overhangs is an essential step in the maintenance process. (lu.se)
  • Therefore, a single-stranded DNA of at least 64 nucleotides is required to wrap around an SSB tetramer fully and interact with all four subunits. (utmb.edu)
  • The real-time PCR assays for parasite detection at CDC use either the DNA-binding dye SYBR Green or sequence-specific TaqMan probes as fluorescence detection mechanisms. (cdc.gov)
  • As the reaction proceeds and PCR product accumulates, the amount of double-stranded DNA increases and with it the fluorescence signal (4-5). (cdc.gov)
  • Levels of TERRA fluctuate during the cell cycle as RPA binds and detaches from telomeres. (massgeneral.org)
  • While DSBs involve in binding to particular dsDNA sequences, to modulate the process of transcription, to cleave DNA molecules, or to be involved in chromosome packaging and transcription in the cell nucleus, etc. (biomedcentral.com)
  • It is observed that both biological effects and epidemiological effects appear to be the same or very similar from ELF exposure and from RF/MW exposures, including calcium ion efflux, melatonin reduction, DNA strand breakage, chromosome aberrations, leukaemia, brain cancer, breast cancer, miscarriage and neurological effects. (whale.to)
  • The 113insArg mutant p16(INK4a) was unable to bind cdk4 and cdk6 in an in vitro binding assay. (lu.se)
  • Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. (yeastgenome.org)
  • The star enzyme that plays a critical role in synthesizing new DNA strands by following the older DNA as a template. (aboutdarwin.com)
  • Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. (rochester.edu)
  • Direct binding measurements indicate that the binding of dT(pT) 27 to its second site is influenced by the oligonucleotide that occupies the first binding site (either dT(pT) 27 or dT(pT) 34 ), providing proof for the existence of a true negative co-operativity. (utmb.edu)
  • Latest platform of Pyrosequencing (GS FLX from 454 Life Sciences which is owned by Roche) can generate 100 million nucleotide data in a 7 hour run with a single machine. (wikidoc.org)
  • Two double-stranded DNA molecules. (aboutdarwin.com)
  • During the hybridization step, the sequence specific regions of the capture oligomers bind to specific regions of the target molecules. (cdc.gov)
  • The microparticles, including the captured target molecules bound to them, are pulled to the side of the reaction vessel using magnets and the supernatant is aspirated. (cdc.gov)
  • Predicted to enable DNA binding activity and nuclease activity. (mcw.edu)
  • RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. (rochester.edu)
  • At the start of the reaction, very little double stranded DNA is present, and so the fluorescent signal detected by the thermocycler is low (3). (cdc.gov)
  • Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. (lu.se)
  • The assay, which we show is amenable to multiplexed detection in a single lateral-flow strip incorporating an internal control for ribonuclease contamination, should facilitate SARS-CoV-2 detection in settings with limited resources. (nature.com)
  • This negative co-operativity is observed also for the binding of the shorter oligonucleotide, dT(pT) 15 . (utmb.edu)
  • Like other arenaviruses, Lassa virus lacks a ogy and clinical presentation, treatment, prevention conventional negative-strand coding arrangement and control as well as the current theories of its patho- and the isolates of the virus differ in their genetic, genesis and efforts in vaccine development. (folkhalsomyndigheten.se)
  • On the basis of these data, we constructed a model of THA8L-RNA binding that is dependent on two forces: one is the interaction between nucleotide bases and specific amino acids in the PPR motifs (codes), and the other is the interaction between the negatively charged RNA backbone and positively charged residues of PPR motifs. (rcsb.org)
  • Now that the molecular structure determines its biological function, structural information is expected to provide insight on the binding mechanism of SSB or DSB. (biomedcentral.com)
  • The compatibility of the produced recombinases in strand invasion based amplification SIBA method was evaluated. (helsinki.fi)
  • Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. (imperial.ac.uk)
  • It has a structure of three beta-strands to a single six-stranded beta-sheet to form a dimer. (wikipedia.org)
  • SYBR Green is a DNA binding dye that fluoresces strongly when bound to double-stranded DNA. (cdc.gov)
  • Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it. (wikidoc.org)
  • The front side of the neck region consists of a five-stranded beta-sheet and two alpha helices, whereas the back side is a three-stranded beta-sheet The shoulder part of the N-terminal domain contains an alpha-helical and beta-sheet region. (wikipedia.org)
  • Each one consists of one old strand (original template) and one newly synthesized strand. (aboutdarwin.com)
  • According to the researchers, this finding suggests that lethality is due to unrepaired double-stranded DNA breaks. (genengnews.com)
  • Mutations in these two positively charged patches greatly reduced THA8L RNA-binding activity. (rcsb.org)
  • Structural analysis revealed that THA8L contains two extensive patches of positively charged residues next to the residues that are proposed to comprise the RNA-binding codes. (rcsb.org)
  • In some genomic regions, the lack of protospacer adjacent motifs (PAMs) means that CRISPR is bound to lose its grip. (genengnews.com)
  • Human mitochondrial SSB (mtSSB) binds to single-stranded mitochondrial DNA as a tetramer and has sequence similarity to bacterial SSB. (wikipedia.org)
  • SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. (cdc.gov)
  • They then unfold themselves to form the DNA strands. (whale.to)