On the mechanism of preferential incorporation of dAMP at abasic sites in translesional DNA synthesis. Role of proof reading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site

Ide, Hiroshi; Murayama, H; Sakamoto, Shunji; Makino, Keisuke; Honda, Kei-ich; Nakamuta, Hiroyuki; Sasaki, Misao; Sugimoto, Naoki

doi:10.1093/nar/23.1.123

Cited by 25 publications

(15 citation statements)

References 38 publications

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“…50 and 51) particularly when canonical hydrogen bonding and/or stacking interactions are absent. Such a mechanism has been implied for AP sites and thymine glycol on the basis of the lack of apparent correlations between the preference of insertion or proofreading excision of nucleotides and the T m of oligonucleotides containing these lesions (52,53). The mechanism involving steric exclusion also seems consistent with the observation that Endo III recognizes mFapyG paired with purines more efficiently than that paired with pyrimidines (activity with respect to the paired base: A Ϸ G Ͼ T Ͼ C) (22).…”

Section: Figmentioning

confidence: 62%

Effects of a Guanine-derived Formamidopyrimidine Lesion on DNA Replication

Asagoshi

Terato

Ohyama

et al. 2002

Journal of Biological Chemistry

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2,6-Diamino-4-hydroxy-5-formamidopyrimidine derived from guanine (FapyG) is a major DNA lesion formed by reactive oxygen species. In this study, a defined oligonucleotide template containing a 5-N-methylated analog of FapyG (mFapyG) was prepared, and its effect on DNA replication was quantitatively assessed in vitro. The results were further compared with those obtained for 7,8-dihydro-8-oxoguanine and an apurinic/ apyrimidinic site embedded in the same sequence context. mFapyG constituted a fairly strong but not absolute block to DNA synthesis catalyzed by Escherichia coli DNA polymerase I Klenow fragment with and without an associated 3-5 exonuclease activity, thereby permitting translesion synthesis with a limited efficiency. The efficiency of translesion synthesis was G > 7,8-dihydro-8-oxoguanine > mFapyG > apurinic/apyrimidinic site. Analysis of the nucleotide insertion (f ins ‫؍‬ V max /K m for insertion) and extension (f ext ‫؍‬ V max /K m for extension) efficiencies for mFapyG revealed that the extension step constituted a major kinetic barrier to DNA synthesis. When mFapyG was bypassed, dCMP, a cognate nucleotide, was preferentially inserted opposite the lesion (dCMP (relative f ins ‫؍‬ 1) > > dTMP (2.4 ؋ 10 ؊4 ) Ϸ dAMP (8.1 ؋ 10 ؊5 ) > dGMP (4.5 ؋ 10 ؊7 )), and the primer terminus containing a mFapyG:C pair was most efficiently extended (mFapyG:C (relative f ext ‫؍‬ 1) > mFapyG:T (4.6 ؋ 10 ؊3 ) > > mFapyG:A and mFapyG:G (extension not observed)). Thus, mFapyG is a potentially lethal but not premutagenic lesion.Reactive oxygen species formed by aerobic metabolism, phagocytic blood cells upon inflammation, ionizing radiation, and photosensitized reactions generate structurally diverse oxidative damage to DNA that stores vital genetic information of cells (1-3). Base lesions thus formed are generally restored by the base excision repair pathway involving multiple enzymes such as N-glycosylase/AP 1 lyase, AP endonuclease, DNA polymerase, and DNA ligase (4, 5). However, if left unrepaired, they result in mutations and/or cell death. It has also been implied that oxidative DNA damage is involved in carcinogenesis and various degenerative diseases (6, 7). 7,8-Dihydro-8-oxoguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine derived from guanine (FapyG) have been identified as major products in the reaction of DNA with reactive oxygen species (Fig. 1A) (1, 2). When formed in DNA, 8-oxoG in a template directs incorporation of non-cognate dAMP as well as cognate dCMP during translesion synthesis by DNA polymerases, thereby inducing GC-to-TA transversions (8, 9). Similarly, when formed in a cellular nucleotide pool, a 2Ј-deoxyribonucleotide form of 8-oxoG can be incorporated opposite adenine as well as cytosine in a DNA template, inducing AT-to-CG transversions (10 -12). Mispair formation between 8-oxoG and adenine leading to mutation involves an unusual syn-conformer of 8-oxoG that can form two hydrogen bonds between O-6 and N-7-H in 8-oxoG and N-6 -H and N-1 in adenine without introducing significan...

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Section: Figmentioning

confidence: 62%

Effects of a Guanine-derived Formamidopyrimidine Lesion on DNA Replication

Asagoshi

Terato

Ohyama

et al. 2002

Journal of Biological Chemistry

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“…The terminal Og:C mismatch was visibly excised by Kf exo+ in 180 s (Figure 2A, lanes 10-12 and Figure 3A); however, the addition of two GC base pairs on the 5′ side of the Og:C mismatch stabilized it significantly (Figure 3b). At the same time, terminal and internal Gh:C and Sp:C mismatches were recognized by Kf exo+ in 180 s with similar efficiency (Figure 2A, lanes [16][17][18][19][20][21][22][23][24][25][26][27]. The absence of the mismatch position effect in this case correlates with the low overall stability of these duplexes (46).…”

Section: Substrate Design and Analysismentioning

confidence: 85%

“…Each template/primer system was incubated with an excess of Kf exo+ (see Experimental Procedures) to ensure proper binding of the substrate by polymerase (22,23,49). Templates with X ) G (CGG and TGA) were used as important controls in these studies.…”

Section: Substrate Design and Analysismentioning

confidence: 99%

Effect of the Oxidized Guanosine Lesions Spiroiminodihydantoin and Guanidinohydantoin on Proofreading by Escherichia coli DNA Polymerase I (Klenow Fragment) in Different Sequence Contexts

Kornyushyna

Burrows

2003

Biochemistry

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Oxidative damage to DNA by endogenous and exogenous reactive oxygen species has been directly linked to cancer, aging, and a variety of neurological disorders. The potential mutagenicity of the primary guanine oxidation product 8-oxo-7,8-dihydroguanine (Og) has been studied intensively, and much information is available about its miscoding potential in vitro and in vivo. Recently, a variety of DNA lesions have been identified as oxidation products of both guanine and 8-oxoguanine, among them spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). To address questions concerning the mutagenic potential of these secondary products of guanine oxidation, the effect of the lesions on proofreading by DNA polymerase was studied in vitro using the Klenow fragment of Escherichia coli polymerase I (Kf exo+). For the first time, k(cat)/K(m) values were obtained for proofreading of the X:N mismatches (X = Og, Gh, or Sp; N = A, G, or C). Proofreading studies of the terminal mismatches demonstrated the significance of the sequence context flanking the lesion on the 3' side. In addition, a sequence dependence was observed for Gh based on the identity of the base on the 5' side of the lesion providing evidence for a primer slippage mode if N was complementary to the 5' base. Internal mismatches were recognized by Kf exo+ resulting in the excision of the correct base pairs flanking mismatches from the 5' side. The absence of a sequence effect for the Gh- and Sp-containing duplexes can be attributed to the severe destabilization of the lesion-containing duplexes that promotes interaction with the exonuclease domain of the Klenow fragment.

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“…This mechanism is both errorprone and biased toward A1T nucleotides. The polymerases involved in the SOS system (notably polII and polV), which undertake ''translesion'' synthesis, are known to follow the ''A-rule'' (Strauss 1991;Ide et al 1995), that is, the preferential incorporation of a dAMP at abasic sites. Since these lesions can arise from several spontaneous and induced mechanisms and are therefore very frequent (Ide et al 1995), the A-rule could be responsible for the A1T enrichment of a region lacking recombination-dependent repair.…”

Section: Why Peculiar Patterns For Genes Near the Terminus?mentioning

confidence: 99%

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

Daubin

Perrière²

2003

Molecular Biology and Evolution

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The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and after translation (affecting codon and amino acid choice); (2) genes undergo different mutational pressure whether they are on the leading or lagging strand; and (3) genes may have different phylogenetic origins as a result of lateral transfers. However, this view neglects the necessity of organizing genetic information on a chromosome that needs to be replicated and folded, which may add constraints to single gene evolution. As a consequence, genes are potentially subjected to different mutation and selection pressures, depending on their position in the genome. In this paper, we analyze the structuring of different codon usage measures along completely sequenced bacterial genomes. We show that most of them are highly structured, suggesting that genes have different base content, depending on their location on the chromosome. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, is found in most bacterial phyla and may reflect common chromosome constraints. Several species may have lost this pattern, probably because of genome rearrangements or integration of foreign DNA. We show that in several species, this enrichment is associated with an increase of evolutionary rate and we discuss the evolutionary implications of these results. We argue that structural constraints acting on the circular chromosome are not negligible and that this natural structuring of bacterial genomes may be a cause of overestimation in lateral gene transfer predictions using codon composition indices.

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On the mechanism of preferential incorporation of dAMP at abasic sites in translesional DNA synthesis. Role of proof reading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site

Cited by 25 publications

References 38 publications

Effects of a Guanine-derived Formamidopyrimidine Lesion on DNA Replication

Effects of a Guanine-derived Formamidopyrimidine Lesion on DNA Replication

Effect of the Oxidized Guanosine Lesions Spiroiminodihydantoin and Guanidinohydantoin on Proofreading by Escherichia coli DNA Polymerase I (Klenow Fragment) in Different Sequence Contexts

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

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