Effects of base sequence context on translesion synthesis past a bulky (+)-trans-anti-B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol κ

Xuanwei Huang, Alexander Kolbanovskiy, Xiaohua Wu, Yanbin Zhang, Zhigang Wang, Ping Zhuang, Shantu Amin, Nicholas Geacintov

Research output: Contribution to journalArticle

Abstract

The effects of bases flanking single bulky lesions derived from the binding of a benzo[a]-pyrene 7,8-diol 9,10-epoxide derivative ((+)-7R,8S,9S,10R stereoisomer) to N2-guanine (G*) on translesion bypass catalyzed by the Y-family polymerase pol κ (hDinB1) were examined in vitro. The lesions were positioned near the middle of six different 43-mer 5′-...XG*Y... sequences (X, Y = C, T, or G, with all other bases remaining fixed). The complementary dCTP is preferentially inserted opposite G* in all of the sequences; however, the proportions of other dNTPs inserted varies as a function of X and Y. The dCTP insertion efficiencies, fins = (Vmax/Km)ins, are smaller in the XG*Y than in XGY sequences by factors of ∼50-90 (GG*T and GG*C) or 5000-25000 (TG*G and CG*G). Remarkably, in XG*Y sequences, fins varies by as much as 3 orders of magnitude, being smallest with G flanking the lesions on the 3′-side and highest with G flanking the adducts on the 5′-side. One-step primer extension efficiencies just beyond the lesions (fext) are generally smaller than fins and also depend on base sequence. However, reasonably efficient translesion bypass of the (+)-trans-[BP]-N2-dG adducts is observed in all sequences in runningstart experiments with full, or nearly full, primer extension being observed under conditions of [dNTP] > Km. The key features here are the relatively robust values of the kinetic parameters Vmax that are either diminished to a moderate extent or even enhanced in the presence of the (+)-trans-[BP]-N2-dG adducts. In contrast to the small effects of the lesions on Vmax, the apparent Km values are orders of magnitude greater in XG*Y than in the unmodified XGY sequences. Thus the bypass of (+)-trans-[BP]-N2-dG adducts under conditions when [dNTP] < Km is quite inefficient. These considerations may be of importance in vivo where [dNTP] < Km, and the translesion bypass of the (+)-trans-[BP]-N2-dG by pol κ may be significantly less efficient than in vitro at higher dNTP concentrations. The base sequence-dependent features of translesion bypass are discussed in terms of the possible conformations of the adducts and the known structural features of bypass polymerases.

Original languageEnglish (US)
Pages (from-to)2456-2466
Number of pages11
JournalBiochemistry
Volume42
Issue number8
DOIs
StatePublished - Mar 4 2003

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7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
Stereoisomerism
Guanine
Kinetic parameters
Conformations
Derivatives
Experiments
2'-deoxycytidine 5'-triphosphate
benzo(a)pyrene N2-dG adduct
In Vitro Techniques

ASJC Scopus subject areas

  • Biochemistry

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Effects of base sequence context on translesion synthesis past a bulky (+)-trans-anti-B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol κ. / Huang, Xuanwei; Kolbanovskiy, Alexander; Wu, Xiaohua; Zhang, Yanbin; Wang, Zhigang; Zhuang, Ping; Amin, Shantu; Geacintov, Nicholas.

In: Biochemistry, Vol. 42, No. 8, 04.03.2003, p. 2456-2466.

Research output: Contribution to journalArticle

Huang, Xuanwei ; Kolbanovskiy, Alexander ; Wu, Xiaohua ; Zhang, Yanbin ; Wang, Zhigang ; Zhuang, Ping ; Amin, Shantu ; Geacintov, Nicholas. / Effects of base sequence context on translesion synthesis past a bulky (+)-trans-anti-B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol κ. In: Biochemistry. 2003 ; Vol. 42, No. 8. pp. 2456-2466.
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title = "Effects of base sequence context on translesion synthesis past a bulky (+)-trans-anti-B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol κ",
abstract = "The effects of bases flanking single bulky lesions derived from the binding of a benzo[a]-pyrene 7,8-diol 9,10-epoxide derivative ((+)-7R,8S,9S,10R stereoisomer) to N2-guanine (G*) on translesion bypass catalyzed by the Y-family polymerase pol κ (hDinB1) were examined in vitro. The lesions were positioned near the middle of six different 43-mer 5′-...XG*Y... sequences (X, Y = C, T, or G, with all other bases remaining fixed). The complementary dCTP is preferentially inserted opposite G* in all of the sequences; however, the proportions of other dNTPs inserted varies as a function of X and Y. The dCTP insertion efficiencies, fins = (Vmax/Km)ins, are smaller in the XG*Y than in XGY sequences by factors of ∼50-90 (GG*T and GG*C) or 5000-25000 (TG*G and CG*G). Remarkably, in XG*Y sequences, fins varies by as much as 3 orders of magnitude, being smallest with G flanking the lesions on the 3′-side and highest with G flanking the adducts on the 5′-side. One-step primer extension efficiencies just beyond the lesions (fext) are generally smaller than fins and also depend on base sequence. However, reasonably efficient translesion bypass of the (+)-trans-[BP]-N2-dG adducts is observed in all sequences in runningstart experiments with full, or nearly full, primer extension being observed under conditions of [dNTP] > Km. The key features here are the relatively robust values of the kinetic parameters Vmax that are either diminished to a moderate extent or even enhanced in the presence of the (+)-trans-[BP]-N2-dG adducts. In contrast to the small effects of the lesions on Vmax, the apparent Km values are orders of magnitude greater in XG*Y than in the unmodified XGY sequences. Thus the bypass of (+)-trans-[BP]-N2-dG adducts under conditions when [dNTP] < Km is quite inefficient. These considerations may be of importance in vivo where [dNTP] < Km, and the translesion bypass of the (+)-trans-[BP]-N2-dG by pol κ may be significantly less efficient than in vitro at higher dNTP concentrations. The base sequence-dependent features of translesion bypass are discussed in terms of the possible conformations of the adducts and the known structural features of bypass polymerases.",
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T1 - Effects of base sequence context on translesion synthesis past a bulky (+)-trans-anti-B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol κ

AU - Huang, Xuanwei

AU - Kolbanovskiy, Alexander

AU - Wu, Xiaohua

AU - Zhang, Yanbin

AU - Wang, Zhigang

AU - Zhuang, Ping

AU - Amin, Shantu

AU - Geacintov, Nicholas

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Y1 - 2003/3/4

N2 - The effects of bases flanking single bulky lesions derived from the binding of a benzo[a]-pyrene 7,8-diol 9,10-epoxide derivative ((+)-7R,8S,9S,10R stereoisomer) to N2-guanine (G*) on translesion bypass catalyzed by the Y-family polymerase pol κ (hDinB1) were examined in vitro. The lesions were positioned near the middle of six different 43-mer 5′-...XG*Y... sequences (X, Y = C, T, or G, with all other bases remaining fixed). The complementary dCTP is preferentially inserted opposite G* in all of the sequences; however, the proportions of other dNTPs inserted varies as a function of X and Y. The dCTP insertion efficiencies, fins = (Vmax/Km)ins, are smaller in the XG*Y than in XGY sequences by factors of ∼50-90 (GG*T and GG*C) or 5000-25000 (TG*G and CG*G). Remarkably, in XG*Y sequences, fins varies by as much as 3 orders of magnitude, being smallest with G flanking the lesions on the 3′-side and highest with G flanking the adducts on the 5′-side. One-step primer extension efficiencies just beyond the lesions (fext) are generally smaller than fins and also depend on base sequence. However, reasonably efficient translesion bypass of the (+)-trans-[BP]-N2-dG adducts is observed in all sequences in runningstart experiments with full, or nearly full, primer extension being observed under conditions of [dNTP] > Km. The key features here are the relatively robust values of the kinetic parameters Vmax that are either diminished to a moderate extent or even enhanced in the presence of the (+)-trans-[BP]-N2-dG adducts. In contrast to the small effects of the lesions on Vmax, the apparent Km values are orders of magnitude greater in XG*Y than in the unmodified XGY sequences. Thus the bypass of (+)-trans-[BP]-N2-dG adducts under conditions when [dNTP] < Km is quite inefficient. These considerations may be of importance in vivo where [dNTP] < Km, and the translesion bypass of the (+)-trans-[BP]-N2-dG by pol κ may be significantly less efficient than in vitro at higher dNTP concentrations. The base sequence-dependent features of translesion bypass are discussed in terms of the possible conformations of the adducts and the known structural features of bypass polymerases.

AB - The effects of bases flanking single bulky lesions derived from the binding of a benzo[a]-pyrene 7,8-diol 9,10-epoxide derivative ((+)-7R,8S,9S,10R stereoisomer) to N2-guanine (G*) on translesion bypass catalyzed by the Y-family polymerase pol κ (hDinB1) were examined in vitro. The lesions were positioned near the middle of six different 43-mer 5′-...XG*Y... sequences (X, Y = C, T, or G, with all other bases remaining fixed). The complementary dCTP is preferentially inserted opposite G* in all of the sequences; however, the proportions of other dNTPs inserted varies as a function of X and Y. The dCTP insertion efficiencies, fins = (Vmax/Km)ins, are smaller in the XG*Y than in XGY sequences by factors of ∼50-90 (GG*T and GG*C) or 5000-25000 (TG*G and CG*G). Remarkably, in XG*Y sequences, fins varies by as much as 3 orders of magnitude, being smallest with G flanking the lesions on the 3′-side and highest with G flanking the adducts on the 5′-side. One-step primer extension efficiencies just beyond the lesions (fext) are generally smaller than fins and also depend on base sequence. However, reasonably efficient translesion bypass of the (+)-trans-[BP]-N2-dG adducts is observed in all sequences in runningstart experiments with full, or nearly full, primer extension being observed under conditions of [dNTP] > Km. The key features here are the relatively robust values of the kinetic parameters Vmax that are either diminished to a moderate extent or even enhanced in the presence of the (+)-trans-[BP]-N2-dG adducts. In contrast to the small effects of the lesions on Vmax, the apparent Km values are orders of magnitude greater in XG*Y than in the unmodified XGY sequences. Thus the bypass of (+)-trans-[BP]-N2-dG adducts under conditions when [dNTP] < Km is quite inefficient. These considerations may be of importance in vivo where [dNTP] < Km, and the translesion bypass of the (+)-trans-[BP]-N2-dG by pol κ may be significantly less efficient than in vitro at higher dNTP concentrations. The base sequence-dependent features of translesion bypass are discussed in terms of the possible conformations of the adducts and the known structural features of bypass polymerases.

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