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Lindahl, T.1
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5
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0028863468
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Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: Structural basis for damaged DNA recognition
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Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K: Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell 1995, 83:773-782.
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Vassylyev, D.G.1
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Mikami, Y.3
Ariyoshi, M.4
Iwai, S.5
Ohtsuka, E.6
Morikawa, K.7
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6
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0029904839
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A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
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Slupphaug G, Mol CD, Kavil B, Arvai AS, Krokan HE, Tainer JA: A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 1996, 80:87-92. This paper and the one by Vassylyev et al. (1995; [5]) provide the first two crystal structures of DNA glycosylases bound specifically to their target DNAs. In both cases the mutation of active site residues of the enzymes led to the formation of a stable enzyme-substrate complex. An adenine base opposite the substrate base in the T4 endonuclease V complex, and the targeted uracil itself in the uracil DNA glycosylate both adopt an extrahelical position.
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Nature
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Slupphaug, G.1
Mol, C.D.2
Kavil, B.3
Arvai, A.S.4
Krokan, H.E.5
Tainer, J.A.6
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7
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0026515277
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DNA containing a chemically reduced apurinic site is a high affinity ligand for the E. coli formamidopyrimidine-DNA glycosylase
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Castaing B, Boiteux S, Zelwer C: DNA containing a chemically reduced apurinic site is a high affinity ligand for the E. coli formamidopyrimidine-DNA glycosylase. Nucleic Acids Res 1992, 20:389-394.
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Castaing, B.1
Boiteux, S.2
Zelwer, C.3
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8
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0028924802
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Endonuclease III interactions with DNA substrates. 1. Binding and footprinting studies with oligonucleotides containing a reduced apyrimidinic site
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O'Handley S, Scholes CP, Cunningham RP: Endonuclease III interactions with DNA substrates. 1. Binding and footprinting studies with oligonucleotides containing a reduced apyrimidinic site. Biochemistry 1995, 34:2528-2536.
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O'Handley, S.1
Scholes, C.P.2
Cunningham, R.P.3
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9
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0028604549
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Unified catalytic mechanism for DNA glycosylases
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Dodson ML, Michaels ML, Lloyd RS: Unified catalytic mechanism for DNA glycosylases. J Biol Chem 1994, 52:32709-32712.
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Dodson, M.L.1
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Lloyd, R.S.3
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0023664684
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Oligodeoxynucleotides containing synthetic abasic sites
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Takeshita M, Chang C-N, Johnson F, Will S, Grollman AP: Oligodeoxynucleotides containing synthetic abasic sites. J Biol Chem 1987, 262:10171-10179.
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Takeshita, M.1
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Johnson, F.3
Will, S.4
Grollman, A.P.5
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12
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0028287938
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Transition state analysis and inhibitor design for enzymatic reactions
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Schramm VL, Horenstein BA, Kline PC: Transition state analysis and inhibitor design for enzymatic reactions. J Biol Chem 1994, 269:18259-18262.
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Schramm, V.L.1
Horenstein, B.A.2
Kline, P.C.3
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13
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0030614471
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2-terminal proline acts as a nucleophile in the glycosylase/AP lyase reaction catalyzed by Escherichia coli formaminopyrimidine-DNA glycosylase (Fpg) protein
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2-terminal proline acts as a nucleophile in the glycosylase/AP lyase reaction catalyzed by Escherichia coli formaminopyrimidine-DNA glycosylase (Fpg) protein. J Biol Chem 1997, 272:5335-5341.
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Zharkov, D.O.1
Rieger, R.A.2
Iden, C.R.3
Grollman, A.P.4
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14
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0031239573
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The critical active site amine of the human 8-oxoguanine DNA glycosylase, hOgg1: Direct identification, ablation and chemical reconstitution
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2 group of Lys249 as the active imine.
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Chem Biol
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Nash, H.M.1
Lu, R.2
Lane, W.S.3
Verdine4
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15
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1542763243
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Enzyme-catalyzed organic synthesis: Practical routes to aza sugars and their analogs for use as glycoprocessing inhibitors
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Look GC, Fotsch CH, Wong C-H: Enzyme-catalyzed organic synthesis: practical routes to aza sugars and their analogs for use as glycoprocessing inhibitors. Accounts Chem Res 1993, 26:182-190.
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Accounts Chem Res
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Look, G.C.1
Fotsch, C.H.2
Wong, C.-H.3
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16
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0028868463
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Specific binding of the DNA repair enzyme Alka to a pyrrolidine-based inhibitor
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Schärer OD, Ortholand J-Y, Ganesan A, Ezaz-Nikpay K, Verdine GL: Specific binding of the DNA repair enzyme AIkA to a pyrrolidine-based inhibitor. J Am Chem Soc 1995, 117:6623-6624.
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Schärer, O.D.1
Ortholand, J.-Y.2
Ganesan, A.3
Ezaz-Nikpay, K.4
Verdine, G.L.5
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17
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0029730708
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Structural determinants for specific recognition by T4 endonuclease V
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McCullough AK, Schärer OD, Verdine GL, Lloyd RS: Structural determinants for specific recognition by T4 endonuclease V. J Biol Chem 1996, 271:32147-32152.
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J Biol Chem
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McCullough, A.K.1
Schärer, O.D.2
Verdine, G.L.3
Lloyd, R.S.4
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18
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0030602838
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Structural basis for the excision repair of alkylation-damaged DNA
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Labahn J, Schärer OD, Long A, Ezaz-Nikpay K, Verdine GL, Ellenberger TE: Structural basis for the excision repair of alkylation-damaged DNA. Cell 1996, 86:321-329. The cyrstal structure of the DNNA glycosylase Alka reveals a binding pocket for the alkylated bases recognized by the enzyme lined with electron rich aromatic amino acids. An aspartate residue (Asp238) that points into the binding pocket is shown to be essential for catalysis by site-directed mutagenesis, Mutation of Asp138 diminishes binding of a pyrrolidine inhibitor by 50 fold, indicating that the positively charged pyrrolidine ring interact with Asp238 in the active site.
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Cell
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Labahn, J.1
Schärer, O.D.2
Long, A.3
Ezaz-Nikpay, K.4
Verdine, G.L.5
Ellenberger, T.E.6
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19
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0030986454
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Unusually strong binding of a designed transition state analog to a base-excision DNA repair protein
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Deng L, Schärer OD, Verdine GL: Unusually strong binding of a designed transition state analog to a base-excision DNA repair protein. J Am Chem Soc 1997, 119:7865-7866. This paper describes the synthesis of an oligonucleotide containing an pyrro-lidine homoadenine residue as a transition state mimic of the DNA glycosylase MutY. This inhibitor binds to its target DNA glycosylase MutY more than an order of magnitude more tightly than any other DNA glycosylase inhibitor to date.
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J Am Chem Soc
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Deng, L.1
Schärer, O.D.2
Verdine, G.L.3
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20
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0028804386
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A designed inhibitor of base-excision DNA repair
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Schärer OD, Verdine GL: A designed inhibitor of base-excision DNA repair, J Am Chem Soc 1995, 117:10781-10782.
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J Am Chem Soc
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Schärer, O.D.1
Verdine, G.L.2
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21
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0030911354
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Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors
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Schärer OD, Kawate T, Gallinari P, Jiricny J, Verdine GL: Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors. Proc Natl Acad Sci USA 1997, 94:4878-4883. The concecpt of transition state destabilizalion for the inhibition of DAN glycosylases is developed in this paper. Introduction of a fluorine atom at C-2′ of the substrate nucleotide results in a substrate analog that is bound specifically by DNA glycosylase but no longer processed. Methylation interference analysis of an G/T glycosylase-inhibitor complex revealed a specific contact of the enzyme to a G residue adjacent to the G/T mismatch, which helps to explain the observed sequence preference of the enzyme.
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Proc Natl Acad Sci USA
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Schärer, O.D.1
Kawate, T.2
Gallinari, P.3
Jiricny, J.4
Verdine, G.L.5
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22
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0028904903
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Reaction mechanism of T4 endonuclease V determined by analysis using modified oligonucleotide duplexes
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Iwai S, Maeda M, Shirai M, Shimada Y, Osafune T, Murata T, Ohtsuka E: Reaction mechanism of T4 endonuclease V determined by analysis using modified oligonucleotide duplexes. Biochemistry 1995, 11:4601-4609.
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Biochemistry
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Iwai, S.1
Maeda, M.2
Shirai, M.3
Shimada, Y.4
Osafune, T.5
Murata, T.6
Ohtsuka, E.7
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23
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0029836886
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Specific recognition of substrate analogs by the mismatch repair enzyme MutY
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Porello SL, Williams SD, Kuhn H, Michaels ML, David SS: Specific recognition of substrate analogs by the mismatch repair Enzyme MutY. J Am Chem Soc 1996, 118:10684-10692. Oligonucleotides containing modified adenine bases derived from the natural products tubercidine and formycin A are bound specifically, but not processed, by the DNA glycosylase MutY.
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J Am Chem Soc
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Porello, S.L.1
Williams, S.D.2
Kuhn, H.3
Michaels, M.L.4
David, S.S.5
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24
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0029800969
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Substrate specificity of Escherichia coli MutY protein
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Bulychev NV, Varaprasad CV, Dorman G, Miller JH, Eisenberg M, Grollman AP, Johnson F: Substrate specificity of Escherichia coli MutY protein. Biochemistry 1996, 35:13147-13156.
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Biochemistry
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Bulychev, N.V.1
Varaprasad, C.V.2
Dorman, G.3
Miller, J.H.4
Eisenberg, M.5
Grollman, A.P.6
Johnson, F.7
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25
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0030766474
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The role of base flipping in damage recognition and catalysis by T4 endonuclease V
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McCullough AK, Dodson ML, Schärer OD, Lloyd RS: The role of base flipping in damage recognition and catalysis by T4 endonuclease V. J Biol Chem, 1997, 232:27210-27217.
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J Biol Chem
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McCullough, A.K.1
Dodson, M.L.2
Schärer, O.D.3
Lloyd, R.S.4
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26
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0030220956
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Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA repair protein superfamily
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Nash HM, Bruner SD, Schärer OD, Kawate T, Addona TA, Spooner E, Lane WS, Verdine GL: Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA repair protein superfamily. Curr Biol 1996, 6:968-980.
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(1996)
Curr Biol
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Nash, H.M.1
Bruner, S.D.2
Schärer, O.D.3
Kawate, T.4
Addona, T.A.5
Spooner, E.6
Lane, W.S.7
Verdine, G.L.8
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27
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0029896229
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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-methylformylamidopyrimidine
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Van Der Kamp PA, Thomas D, Barbey R, de Olivera 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-methylformylamidopyrimidine. Proc Natl Acad Sci USA 1996, 93:5197-5202. This paper and that of Nash et al. [27] report the cloning and characterization of a yeast 8-oxoguanine DNA glycosylase. Nash et al. [26] used the sodium borohydride trapping assay to reveal the presence of a 8-oxoguanine DNA glycosyalse / lyase activity in yeast cell extracts. The protein was then isolated using affinity chromatography with an oligonucleotide containing a reduced absic site residue.Van der Kamp et al. [27] isolated the same protein using a genetic screen by expressing a yeast cDNA library in an E.coli strain deficient in 8-oxoguanine DNA glycosylase activity. The yeast 8-oxoguanine DNA glycosylase is not homologous to the corresponding bacterial enzyme and therefore coulld not be cloned based on homology alone. The two papers demonstrate that chemical and genetic approaches can be complementary in isolation and cloning of eukaryotic DNA repair enzymes.
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(1996)
Proc Natl Acad Sci USA
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Van Der Kamp, P.A.1
Thomas, D.2
Barbey, R.3
De Olivera, R.4
Boiteux, S.5
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28
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0029132769
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Studies on the catalytic mechanism of five DNA glycosylases. Probing for DNA enzyme imion intermediates
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Sun B, Lathan KA, Dodson M, Lloyd RS: Studies on the catalytic mechanism of five DNA glycosylases. Probing for DNA enzyme imion intermediates. J Biol Chem 1995, 270:32709-32712.
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J Biol Chem
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Sun, B.1
Lathan, K.A.2
Dodson, M.3
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0027301692
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Evidence for an imino intermediate in the T4 endonuclease V reaction
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Dodson ML, Schrock RD, Lloyd RS: Evidence for an imino intermediate in the T4 endonuclease V reaction. Biochemisty 1993, 32:8284-8290.
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Biochemisty
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Dodson, M.L.1
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0031172802
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A mammalian DNA repair enzyme that excises oxidatively damaged guanines maps to a locus frequently lost in lung cancer
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Lu R, Nash HM, Verdine GL: A mammalian DNA repair enzyme that excises oxidatively damaged guanines maps to a locus frequently lost in lung cancer. Curr Biol 1997, 7:397-407. The use of borohydride trapping for the identification and characterization of 8-oxoguanine DNA glycosylase/lyase activities in human and nurine cells is described. The cloning of corresponding glycosylases identifies them as members of the superfamily of BER proteins.
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Curr Biol
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Lu, R.1
Nash, H.M.2
Verdine, G.L.3
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31
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5544239019
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Purification of a mammalian homologue of Escherichia coli endonuclease III: Identification of a bovine pyrimidine hydrate thymine glycol DNA glycosylase/AP lyase by irreversible cross linking to a thymine glycol-containing oligonucleotide
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3. An enzymatic activity from calf thymus was purified over several chromatographic separations and isolated by monitoring its DNA glycosylase/AP lyase activity using the trapping assay.
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(1996)
Biochemistry
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Hilbert, T.P.1
Boorstein, R.J.2
Kung, H.C.3
Bolton, P.H.4
Xing, D.H.5
Cunningham, R.P.6
Teebor, G.W.7
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