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  • enzyme
  • section describes the catalytic activity of an enzyme, i.e. the chemical reaction it catalyzes. (uniprot.org)
  • The C-terminal segment of this enzyme constitutes the catalytic domain. (ebi.ac.uk)
  • The enzyme is involved in DNA repair and chromosomal DNA replication. (nih.gov)
  • Protein dynamics control the progression and efficiency of the catalytic reaction cycle of the Escherichia coli DNA-repair enzyme AlkB. (nih.gov)
  • Here, we utilize enzymological and biophysical studies, including NMR measurements of conformational dynamics, to develop a quantitative mechanistic scheme for the DNA repair enzyme AlkB. (nih.gov)
  • Understanding how integrase recognizes these features of cellular DNA and identifying the part or parts of integrase responsible for any selectivity in choosing target sites are important for modeling integration, for developing methods of targeted gene delivery that are based on retroviral integration, and for designing a new class of antiretroviral agents that interfere with these enzyme-substrate interactions. (asm.org)
  • Together with the finding of new conformational states via smFRET, and "targeted" supercoiling assays with the full-length enzyme, we end up proposing a detailed catalytic mechanism, similar to the one derived from the reverse gyrase structure, only this time based on and supported by a combination of kinetic, thermodynamic, and structural data. (unibas.ch)
  • Two arms of complementary bases flank the catalytic core ( cyan ) on the enzyme strand and the single ribonucleotide ( red ) on the substrate strand. (wikipedia.org)
  • Once sequenced, this single-stranded "cis"-form of the deoxyribozyme can be converted to the two-stranded "trans"-form by separating the substrate domain (containing the ribonucleotide cleavage site) and the enzyme domain (containing the catalytic core) into separate strands which can hybridize through two flanking arms consisting of complementary base pairs . (wikipedia.org)
  • Genomic DNA
  • Replicates viral genomic DNA in the late phase of lytic infection, producing long concatemeric DNA. (uniprot.org)
  • Genomic DNA (gDNA) isolated from either of the E. coli GM33 strains harboring the pBAD vector with the mutated dam gene was resistant to DpnI digestion and sensitive to DpnII restriction endonuclease cutting. (uky.edu)
  • mechanism
  • Its structure consists of ten alpha helices and a three-strand beta sheet, and resembles the catalytic domains of site-specific recombinases that act via a topoisomerase IB-like mechanism [ PMID: 9529259 ]. (ebi.ac.uk)
  • DNA and p180 binding to an Mcm10 construct that contains both the ID and CTD, provide the first mechanistic insight into how Mcm10 might use a handoff mechanism to load and stabilize pol alpha within the replication fork. (nih.gov)
  • Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX, thereby regulating DNA damage response mechanism. (nih.gov)
  • D, catalytic mechanism and dissociation/rate constants at 10 °C. The two alternative reaction pathways ( lower right ) produce 2OG turnover coupled to ( left branch ) or uncoupled from ( right branch ) DNA repair, depending on the relative rates of substrate hydroxylation versus release. (nih.gov)
  • topoisomerase
  • The addition of histone H1, in stoichiometric amounts, to naked DNA or minichromosomes lessened the activity of topoisomerase II, and required 7-fold less for complete inhibition when the latter was used as the substrate. (iisc.ac.in)
  • To ascertain if the observed differences are specific to topoisomerase II from testis, we examined the effect of nucleosomes on the catalytic efficiency of its isoform from liver. (iisc.ac.in)
  • Interestingly, the suppression of relaxation activity of Liver topoisomerase II required substrates containing higher mass ratios of histone octamer/DNA. (iisc.ac.in)
  • Further, this feature appears to be specific for topoisomerase II-directed drugs and is not shared by the generic class of either DNA-intercalating or non-DNA-intercalating ligands. (iisc.ac.in)
  • Escherichia
  • We mutated aspartic acid and tyrosine residues to alanine within the conserved DPPY catalytic motif of Dam and transformed the pBAD/damD/A, pBAD/damY/A, and pBAD/damAhSSU (with the native dam gene) recombinant plasmids into the Escherichia coli GM33 (dam-deficient) strain. (uky.edu)
  • ANDalyze
  • ANDalyze offers products for testing water contamination using catalytic DNA technologies. (environmental-expert.com)
  • Using DNAzyme technology applied to heavy metals testing in water, ANDalyze has developed a DNA sensor technology that test water samples within 2 minutes giving you results at the push of a button. (environmental-expert.com)
  • ANDalyze has created a product for detecting and quantifying heavy metals in water based on the recent discovery of these catalytic properties of DNA, coupled with established nanoparticle reporter technologies. (environmental-expert.com)
  • ANDalyze has designed and manufactured a modernized hand held fluorimeter which, in combination with the consumable DNA based sensors can quickly measure water contaminants at the sample site, greatly reducing the time and effort required by current technologies. (environmental-expert.com)
  • enzymes
  • We also demonstrated for the first time its DNA unwinding activity, shedding light on the rarely documented local B-DNA duplex destabilization of helicase-like modules, appended to bigger enzymes. (unibas.ch)
  • Here we show that allosteric regulation of nucleic acid enzymes can be coupled to signal amplification in an entropy-driven DNA circuit. (springeropen.com)
  • substrates
  • Formation of an integrated provirus requires that the viral integrase act on its two DNA substrates with different levels of specificity. (asm.org)
  • To gain insight into the relative catalytic efficiencies of mammalian type I and type II DNA topoisomerases, in the cellular context, we have used naked DNA and DNA incorporated into nucleosomes as substrates. (iisc.ac.in)
  • These first deoxyribozymes were unable to catalyze a full RNA substrate strand, but by incorporating the full RNA substrate strand into the selection process, deoxyribozymes which functioned with substrates consisting of either full RNA or full DNA with a single RNA base were both able to be utilized. (wikipedia.org)
  • ribozymes
  • In addition, DNA lacks the 2'- hydroxyl group found in RNA which limits the catalytic competency of deoxyribozymes even in comparison to ribozymes. (wikipedia.org)
  • The programmability and replicability of RNA and DNA have respectively enabled the design and selection of a number of allosteric ribozymes and deoxyribozymes. (springeropen.com)
  • One of the most important discoveries in the last decade is that DNA/RNA are not only materials for genetic information storage and transfer, but also catalysts for a variety of biological reactions, and thus called catalytic DNA/RNA, (deoxy)ribozymes, or DNA/RNAzymes. (environmental-expert.com)
  • molecule
  • f) obtaining from said amplified subpopulation a single-stranded DNA molecule capable of binding adenosine or an adenosine-5'-phosphate. (google.es)
  • 3. A single-stranded DNA molecule which binds adenosine or an adenosine-5'-phosphate. (google.es)
  • 4. The DNA molecule of claim 3, wherein said DNA comprises a guanosine-rich region. (google.es)
  • 7. The DNA molecule of claim 4, wherein said DNA molecule comprises one or more base-paired nucleic acids adjacent said guanosine-rich region. (google.es)
  • 8. The DNA molecule of claim 7, wherein said base-paired nucleic acids form stem or stem-loop structures. (google.es)
  • phosphorylation
  • Silencing of DNA-PKcs in HeLa cells resulted in a decreased stability of c-Myc protein, which was associated the increasing of c-Myc phosphorylation on Thr58/Ser62 and ubiquitination level. (biomedcentral.com)
  • Phosphorylation of Akt on Ser473, a substrate of DNA-PKcs was found decreased in DNA-PKcs deficient cells. (biomedcentral.com)
  • Consistent with this depressed DNA-PKcs cell model, overexpressing DNA-PKcs in normal human liver L02 cells, by sub-chronically exposing to very low dose of carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), increased c-Myc protein level, the phosphorylation of Akt and GSK3 β, as well as cell proliferation. (biomedcentral.com)
  • Uracil
  • Sensitive and specific detection of uracil-DNA glycosylase (UDG) activity is crucial in biomedical study and disease diagnosis. (rsc.org)
  • Further structural differences between DNA and RNA may also play a role in the lack of biological deoxyribozymes, such as the additional methyl group of the DNA base thymidine compared to the RNA base uracil or the tendency of DNA to adopt the B-form helix while RNA tends to adopt the A-form helix . (wikipedia.org)
  • Structural analysis of uracil DNA glycosylases in complex with DNA reveals that conserved H109 acts as a nucleophile to attack the oxocarbenium ion and makes a covalent bond to the abasic site after uracil excision to form a stable intermediate. (nature.com)
  • activity
  • a href='/help/catalytic_activity' target='_top'>More. (uniprot.org)
  • Depending upon the absence (Pol-delta3) or the presence of POLD4 (Pol-delta4), displays differences in catalytic activity. (uniprot.org)
  • POLgammaA:Y955H is unable to synthesize DNA, POLgammaA:Y955C has strongly impaired DNA synthesis activity.POLgammaA:Y955C has a stronger affinity for primed DNA templates. (nih.gov)
  • It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. (uniprot.org)
  • CDK2 and DNA-PK regulate PR transcriptional activity by distinct mechanisms. (nih.gov)
  • Reactions
  • On the other hand, DNA and RNA can catalyze chemical reactions not only by forming intricate tertiary structures, but also by simply forming Watson-Crick base pairs. (springeropen.com)
  • In fact, by serving as a hybridization template, DNA can control and catalyze a wide range of chemical reactions [ 13 ], some of which can yield products capable of regulating downstream reactions. (springeropen.com)
  • While DNA circuits may prove useful as diagnostics, strand-exchange reactions have so far been monitored by sophisticated analytical devices. (springeropen.com)
  • regulation
  • We have utilised a cell-free system of concentrated Xenopus laevis egg extracts to investigate the regulation and possible functions of DNA-PK. (biologists.org)
  • These results suggest that cleavage and inactivation of DNA-PKcs prevents this factor from functioning in DNA repair, recombination or transcriptional regulation during apoptosis. (biologists.org)
  • The modification is dependent on DNA and is involved in the regulation of various important cellular processes such as differentiation, proliferation, and tumor transformation and also in the regulation of the molecular events involved in the recovery. (antikoerper-online.de)
  • interferon
  • In the cytosol, responsible for a substantial proportion of the physiological concentration of cytosolic RNA:DNA hybrids, which are necessary to prevent spontaneous activation of type I interferon responses (PubMed:27019227). (rcsb.org)
  • domain
  • The catalytic domain contains five amino acids, conserved in all eukaryotic type IB topoisomerases. (ebi.ac.uk)
  • This entry represents the carboxyl lobe of the catalytic domain (domain 2), and consists of four alpha-helices (helices 6-10). (ebi.ac.uk)
  • The excessive probes would be masked by the ligase reaction that closes the nick and forms a long DNA strand fully complementary to the hairpin domain. (rsc.org)
  • We recently demonstrated that amino acid 119, in the α2 helix of the central domain of the human immunodeficiency virus type 1 integrase, affected the choice of nonviral target DNA sites. (asm.org)
  • Studies using chimeric integrases involving human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus, and visna virus indicate that the central domain of integrase plays a major role in selecting the target sites for insertion of viral DNA ends. (asm.org)
  • We selected the helicase-like domain as a model of study due to its capacity to couple ATP binding and hydrolysis to DNA processing. (unibas.ch)
  • We showed that properties intrinsic to the helicase-like domain, like DNA-stimulated ATP hydrolysis, nucleotide-dependent affinity switch for DNA, and thermodynamic coupling between DNA binding and ATP binding and hydrolysis, are strongly reduced in the context of reverse gyrase. (unibas.ch)
  • Furthermore, we have elucidated the thermodynamic and conformational cycle of the helicase-like domain, and predicted the stages fulfilling the requirements for interdomain communication, local duplex DNA unwinding, and the stages where DNA is in a suitable state to support the supercoiling reaction. (unibas.ch)
  • We demonstrated its strong involvement in DNA binding, DNA-stimulated ATP hydrolysis, and thermodynamic coupling between these processes in the isolated helicase-like domain. (unibas.ch)
  • Additionally, we also elucidated the nucleotide cycle and conformational transitions for this helicase-like domain mutant, which gave the first indications of why no positive supercoiling can be performed by the full-length reverse gyrase lacking the latch, and only DNA relaxation is allowed. (unibas.ch)
  • glycosylases
  • The detection limit is as low as 0.00028 U mL −1 , and UDG can be well distinguished from other DNA glycosylases. (rsc.org)
  • differences
  • However, it has also been shown that DNA can form structures that RNA cannot, which suggests that, though there are differences in structures that each can form, neither is inherently more or less catalytic due to their possible structural motifs. (wikipedia.org)
  • DCLRE1C
  • Promotes processing of hairpin DNA structures in V(D)J recombination by activation of the hairpin endonuclease artemis (DCLRE1C). (nih.gov)
  • repair
  • Under conditions of DNA replication stress, in the presence of POLD3 and POLD4, may catalyze the repair of broken replication forks through break-induced replication (BIR). (uniprot.org)
  • Involved in DNA non-homologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. (nih.gov)
  • Results show that under hypoxia, Ku70 and DNA-PKcs interact with nuclear RON which activates non-homologous end joining DNA repair conferring chemoresistance. (nih.gov)
  • Epistasis, photoreactivation and mutagen sensitivity of DNA repair mutants upr-1 and mus-26 in Neurospora crassa. (semanticscholar.org)
  • DNA repair and specific-locus mutagenesis in Neurospora crassa. (semanticscholar.org)
  • topoisomerases
  • Type I topoisomerases (type IB isomerases) relax positive and negative supercoils and are very important in DNA replication. (ebi.ac.uk)
  • Reverse gyrases are the only topoisomerases capable of introducing positive supercoils into circular DNA. (unibas.ch)
  • coli
  • A conformational transition in the NRL of E. coli AlkB controls the catalytic reaction cycle. (nih.gov)
  • complex
  • this interaction stabilizes the replicative complex and reduces the misincorporation rate of DNA polymerase alpha by acting as a fidelity clamp. (rcsb.org)
  • The assembly of the DNA-PK complex at DNA ends is also required for the NHEJ ligation step. (nih.gov)