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 kappa

Biochemistry. 2003 Mar 4;42(8):2456-66. doi: 10.1021/bi026912q.

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 N(2)-guanine (G*) on translesion bypass catalyzed by the Y-family polymerase pol kappa (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, f(ins) = (V(max)/K(m))(ins), are smaller in the XG*Y than in XGY sequences by factors of approximately 50-90 (GG*T and GG*C) or 5000-25000 (TG*G and CG*G). Remarkably, in XG*Y sequences, f(ins) 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 (f(ext)) are generally smaller than f(ins) and also depend on base sequence. However, reasonably efficient translesion bypass of the (+)-trans-[BP]-N(2)-dG adducts is observed in all sequences in running-start experiments with full, or nearly full, primer extension being observed under conditions of [dNTP] > K(m). The key features here are the relatively robust values of the kinetic parameters V(max) that are either diminished to a moderate extent or even enhanced in the presence of the (+)-trans-[BP]-N(2)-dG adducts. In contrast to the small effects of the lesions on V(max), the apparent K(m) values are orders of magnitude greater in XG*Y than in the unmodified XGY sequences. Thus the bypass of (+)-trans-[BP]-N(2)-dG adducts under conditions when [dNTP] < K(m) is quite inefficient. These considerations may be of importance in vivo where [dNTP] <or= K(m), and the translesion bypass of the (+)-trans-[BP]-N(2)-dG by pol kappa 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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide / chemical synthesis*
  • 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide / chemistry
  • Adenine Nucleotides / chemistry
  • Base Sequence
  • Catalysis
  • Chromosomal Proteins, Non-Histone / chemistry*
  • DNA Adducts / chemistry*
  • DNA Damage*
  • DNA Primers / chemistry
  • DNA Replication
  • DNA-Directed DNA Polymerase / chemistry*
  • Deoxycytosine Nucleotides / chemistry
  • Deoxyguanine Nucleotides / chemistry*
  • Electrophoresis, Polyacrylamide Gel
  • Humans
  • Kinetics
  • Mutagenesis
  • Mutagens / chemical synthesis*
  • Mutagens / chemistry
  • Nuclear Proteins / chemistry*
  • Templates, Genetic

Substances

  • Adenine Nucleotides
  • Chromosomal Proteins, Non-Histone
  • DNA Adducts
  • DNA Primers
  • Deoxycytosine Nucleotides
  • Deoxyguanine Nucleotides
  • Mutagens
  • Nuclear Proteins
  • 2'-deoxycytidine 5'-triphosphate
  • 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • DNA-Directed DNA Polymerase
  • POLK protein, human
  • TENT4A protein, human