• Pathway
  • Apurinic/apyrimidinic (AP) endonuclease is an enzyme that is involved in the DNA base excision repair pathway (BER). (wikipedia.org)
  • Because APE1 performs an essential function in DNA base-excision repair pathway, it has become a target for researchers looking for means to prevent cancer cells from surviving chemotherapy. (wikipedia.org)
  • Not only is APE1 needed in and of itself to create the nick in the DNA backbone so that the enzymes involved later in the BER pathway can recognize the AP-site, it also has a redox function that helps activate other enzymes involved in DNA repair. (wikipedia.org)
  • Parikh SS, Mol CD and Tainer JA (1997) Base excision repair enzyme family portrait: integrating the structure and chemistry of an entire DNA repair pathway. (els.net)
  • The deletion of nth1 in the apn2 mutant strain partially relieves the MMS sensitivity of the apn2 single mutant, indicating that the Apn2 and Nth1 act in the same pathway for the repair of abasic sites. (biomedsearch.com)
  • Using this method, we have investigated the role of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a member of the phosphatidylinositol 3-kinase-related protein kinases (PIKK) family, in the TCR pathway of UV-induced DNA damage. (biomedcentral.com)
  • On the basis of the above methodology verification, we found that the depletion of DNA-PKcs mediated by siRNA significantly decreased the TCR capacity of repairing the UV-induced CPDs damage in DHFR gene in HeLa cells, indicating that DNA-PKcs may also be involved in the TCR pathway of DNA damage repair. (biomedcentral.com)
  • Our data suggest that DNA-PKcs plays a role in the TCR pathway of UV-damaged DNA. (biomedcentral.com)
  • RNA polymerase II plays a critical role in the recognition of DNA damage in the TCR pathway. (biomedcentral.com)
  • While human cells utilize both short- and long-patch BER, the yeast Saccharomyces cerevisiae was long thought to lack a short-patch pathway because it does not have homologs of several mammalian short-patch proteins, including pol β, DNA ligase III, XRCC1, and the kinase domain of PNKP. (wikipedia.org)
  • The recent emerging concept to sensitize cancer cells to DNA-alkylating drugs is by inhibiting various proteins in the base excision repair (BER) pathway. (aacrjournals.org)
  • APE1
  • APE1 is a gene that codes for DNA AP lyase in humans which binds to AP DNA loops into both the DNA major and minor grooves and binds a flipped-out AP site in a pocket that excludes DNA bases and racemized-anomer AP sites. (wikipedia.org)
  • Human AP Endonuclease (APE1), like most AP endonucleases, is of class II and requires an Mg2+ in its active site in order to carry out its role in base excision repair. (wikipedia.org)
  • Meanwhile, an Asp210 in the active site, which is made more reactive due to the increase in its pKa (or the negative log of acid dissociation constant) caused through its stabilization through its hydrogen bonding between Asn68 and Asn212, activates the nucleophile that attacks and cleaves the phosphodiester backbone and probably results in the observed maximal APE1 activity at a pH of 7.5. (wikipedia.org)
  • Both also contain lots of H-bond acceptors which may interact with the H-bond donors in the active site of APE1, causing these inhibitors to stick in the active site and preventing the enzyme from catalyzing other reactions. (wikipedia.org)
  • We determined the specificity of this small molecular weight inhibitor for Pol-β by using in vitro activities of APE1, Fen1, DNA ligase I, and Pol-β-directed single-nucleotide and long-patch BER. (aacrjournals.org)
  • It blocked Pol-β-directed single-nucleotide and long-patch BER without affecting the activity of APE1, Fen1, and DNA ligase I. Fluorescence anisotropy data suggested that NSC-666715 directly and specifically interacts with Pol-β and interferes with binding to damaged DNA. (aacrjournals.org)
  • lesions
  • AP sites are pre-mutagenic lesions that can prevent normal DNA replication so the cell contains systems to identify and repair such sites. (abnova.com)
  • AP sites are pre-mutagenic lesions that can prevent normal DNA replication. (wikipedia.org)
  • To counteract this threat, cells have evolved a series of intricate DNA repair pathways that correct DNA lesions affecting base pairing or structure of DNA. (slideshare.net)
  • DNA lesions repaired by base excision repair. (els.net)
  • One of the most frequent lesions formed in cellular DNA are abasic (apurinic/apyrimidinic, AP) sites that are both cytotoxic and mutagenic, and must be removed efficiently to maintain genetic stability. (biomedsearch.com)
  • For example, incorporation of adenine across from 8-oxoguanine (right) during DNA replication causes a G:C base pair to be mutated to T:A. Other examples of base lesions repaired by BER include: Oxidized bases: 8-oxoguanine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG, FapyA) Alkylated bases: 3-methyladenine, 7-methylguanosine Deaminated bases: hypoxanthine formed from deamination of adenine. (wikipedia.org)
  • Some lesions, such as oxidized or reduced AP sites, are resistant to pol β lyase activity and, therefore, must be processed by long-patch BER. (wikipedia.org)
  • Besides opening AP sites, they possess 3' phosphodiesterase activity and can remove a variety of 3' lesions including phosphates, phosphoglycolates, and aldehydes. (wikipedia.org)
  • The chemotherapeutic drugs that induce DNA-alkylation damage elicit lesions that are repaired primarily by the O 6 -methylguanine DNA methyltransferase (MGMT), mismatch repair (MMR), and base excision repair (BER) pathways. (aacrjournals.org)
  • sequence
  • Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect. (abnova.com)
  • A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map. (waw.pl)
  • 42. A polypeptide comprising a first amino acid sequence substantially identical to SEQ ID NO:1 linked to a second amino acid sequence substantially identical to SEQ ID NO:2, wherein the first and second amino acid sequences are linked directly or by a linker having between 1-300 amino acids and wherein the polypeptide excises methylated cytosines in DNA when contacted to DNA comprising methylated cytosines. (patentsencyclopedia.com)
  • polymerase beta
  • Gu H, Marth JD, Orban PC, Mossmann H and Rajewsky K (1994) Deletion of a DNA polymerase beta gene segment in T cells using cell type‐specific gene targeting. (els.net)
  • OGG1
  • Examples of DNA glycosylases include Ogg1, which recognizes 8-oxoguanine, Mag1, which recognizes 3-methyladenine, and UNG, which removes uracil from DNA. (wikipedia.org)
  • The OGG1 gene of Saccharomyces cerevisiae codes for a DNA glycosylase that excises 7,8-dihydro-8- oxoguanine (8-OxoG) and 2,6-diamino-4-hydroxy-5- N -methylformamidopyrimidine (Fapy) from damaged DNA. (pubmedcentralcanada.ca)
  • Mutations of K241 to Gln (K241Q) and Arg (K241R) have been obtained after site directed mutagenesis of OGG1. (pubmedcentralcanada.ca)
  • However, the K241Q mutant still binds DNA duplexes containing 8-OxoG/C. In contrast, K241R mutation results in a catalytically active form of Ogg1. (pubmedcentralcanada.ca)
  • van der Kemp PA, Thomas D, Barbey R, de Oliveira R, Boiteux S. Cloning and expression in Escherichia coli of the OGG1 gene of Saccharomyces cerevisiae, which codes for a DNA glycosylase that excises 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine. (pubmedcentralcanada.ca)
  • excision
  • AP sites can be formed by spontaneous depurination, but also occur as intermediates in base excision repair. (wikipedia.org)
  • This insight led him to discover a molecular machinery, base excision repair, which constantly counteracts the collapse of our DNA. (slideshare.net)
  • The altered DNA base, and in some cases a few nucleotides adjacent to the altered base, is removed by excision, and the DNA is repaired by DNA synthesis and ligation. (els.net)
  • Krokan HE, Standal R and Slupphaug G (1997) DNA glycosylases in the base excision repair of DNA. (els.net)
  • 1996) Specific interaction of DNA polymerase β and DNA ligase I in a multiprotein base excision repair complex from bovine testis. (els.net)
  • 1996) Requirement of mammalian DNA polymerase β in base excision repair. (els.net)
  • Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. (waw.pl)
  • A mutant lacking the DNA glycosylase/AP lyase Nth1 is very sensitive to the alkylating agent methyl methanesulfonate (MMS), suggesting a role for Nth1 in base excision repair (BER) of alkylation damage. (biomedsearch.com)
  • activity
  • 5'dRP/AP lyase activity of purified NHEJ factors. (nih.gov)
  • Mn2+ stabilizes the reaction of the lyase activity. (wikipedia.org)
  • DNA AP lyase activity is documented to have similar function in both E. Coli and in humans. (wikipedia.org)
  • One possible mechanistic hypothesis is that DNA-PKcs may function through associating with CyclinT2/CDK9 (P-TEFb) to modulate the activity of RNA Pol II, which has already been identified as a key molecule recognizing and initializing TCR. (biomedcentral.com)
  • The recent discovery that the poly-A polymerase Trf4 possesses 5' dRP lyase activity has challenged this view. (wikipedia.org)
  • Mutation K241Q completely abolishes DNA glycosylase activity and covalent complex formation in the presence of NaBH4. (pubmedcentralcanada.ca)
  • 1993
  • Lindahl T (1993) Instability and decay of the primary structure of DNA. (els.net)
  • 1993) Yeast open reading frame YCR14C encodes a DNA beta‐polymerase‐like enzyme. (els.net)
  • HeLa
  • Although depletion of DNA-PKcs sensitized HeLa cells to UV radiation, it did not affect the ggNER efficiency of UV-induced cyclobutane pyrimidine dimers (CPD) damage. (biomedcentral.com)
  • occur
  • Paul Modrich has demonstrated how the cell corrects errors that occur when DNA is replicated during cell division. (slideshare.net)
  • substrate
  • Recovered DNA was then assessed for efficiencies of substrate recovery and joining by qPCRs using substrate and junction primer pairs, respectively. (nih.gov)
  • b , Addition of NaBH 4 at the start of the reaction reduces the Schiff base covalent intermediate, forming a stable adduct between an abasic site within a radiolabeled DNA substrate and the 5'dPR/AP lyase. (nih.gov)
  • SMUG1 prefers single-stranded DNA as substrate, but also removes U from double-stranded DNA. (wikipedia.org)
  • phosphate
  • The AP site is then further stabilized through hydrogen bonding of the phosphate group 5´ to the AP site with Asn174, Asn212, His309, and the Mg2+ ion while its orphan base partner is stabilized through hydrogen bonding with Met270. (wikipedia.org)
  • The phosphate group 3' to the AP site is stabilized through hydrogen bonding to Arg177. (wikipedia.org)
  • First, the Asp210 residue in the active site deprotonates a water molecule, which can then perform a nucleophilic attack on the phosphate group located 5´ to the AP site. (wikipedia.org)
  • Next, electrons from one of the oxygen atom in the phosphate group moves down, kicking off one of the other oxygen to create a free 5´ phosphate group on the AP site and a free 3´-OH on the normal nucleotide, both of which are stabilized by the Mg2+ ion. (wikipedia.org)
  • The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. (waw.pl)
  • Some glycosylase-lyases can further perform δ-elimination, which converts the 3' aldehyde to a 3' phosphate. (wikipedia.org)
  • vitro
  • In vitro biochemical experiments have demonstrated that the replicative mitochondrial DNA (mtDNA) polymerase gamma, Polg, is a sensitive target for inhibition by metabolically active forms of NRTIs, nucleotide reverse transcriptase inhibitors (NtRTIs). (frontiersin.org)
  • Similar to Polg, in vitro work has demonstrated both Pol beta and PrimPol incorporate NtRTIs into nascent DNA. (frontiersin.org)
  • Much of the seminal work elucidating these repair systems has taken advantage of defined DSB substrates, either constructed in vitro or formed in cells by site-specific nucleases [ 9 ]. (hindawi.com)
  • The effect of NSC-666715 on the cytotoxicity of the DNA-alkylating drug temozolomide (TMZ) to colon cancer cells was determined by in vitro clonogenic and in vivo xenograft assays. (aacrjournals.org)
  • Repairs oxidative DNA damages in vitro. (genesilico.pl)
  • base
  • An AP site in DNA appears when the glycosylic bond that connects the purine or pyrimidine base to the deoxyribose sugar is cleaved. (wikipedia.org)
  • During every cell division, more than three billion DNA base pairs are replicated and copies of the genome are transferred to the daughter cells. (slideshare.net)
  • Both of these structures possess rings attached to short chains, which appear similar to the deoxyribose sugar ring without a base attached and phosphodiester bond in DNA. (wikipedia.org)
  • These modifications can affect the ability of the base to hydrogen-bond, resulting in incorrect base-pairing, and, as a consequence, mutations in the DNA. (wikipedia.org)
  • This structure revealed that the enzyme flips the damaged base out of the double helix into an active site pocket in order to excise it. (wikipedia.org)
  • damage
  • DNA damage is ubiquitous amongst all forms of life. (wikipedia.org)
  • 2. 1 (15) The Royal Swedish Academy of Sciences has decided to award Tomas Lindahl, Paul Modrich and Aziz Sancar the Nobel Prize in Chemistry 2015 for their "Mechanistic studies of DNA repair" Damage to the genetic material poses a threat to all organisms. (slideshare.net)
  • T . A transversions in Saccharomyces cerevisiae: evidence for endogenous oxidative damage to DNA in eukaryotic cells. (pubmedcentralcanada.ca)
  • The balance between DNA damage and repair determines the final therapeutic consequences of these drugs. (aacrjournals.org)
  • structures
  • Since DNA AP lyase is a class of structures who have numerous target genes that encode for different variations of the enzyme, there is no one single enzyme structure that can be used as an example that encompasses all versions of the enzyme. (wikipedia.org)
  • molecular
  • The reason our genetic material does not disintegrate into complete chemical chaos is that a host of molecular systems continuously monitor and repair DNA. (slideshare.net)
  • In the present study, we used structure-based molecular docking of DNA polymerase β (Pol-β) and identified a potent small molecular weight inhibitor, NSC-666715. (aacrjournals.org)