Sequence Effects on Translesion Synthesis of an Aminofluorene–DNA Adduct: Conformational, Thermodynamic, and Primer Extension Kinetic Studies

• Published in: Biochemistry (Easton) 2012-03, Vol.51 (9), p.1983-1995
• Main Authors: Vaidyanathan, V. G, Cho, Bongsup P
• Format: Article
• Language: English
• Subjects: Base Pairing; Base Sequence; Deoxyguanosine - analogs & derivatives; Deoxyguanosine - chemistry; DNA - chemistry; DNA Adducts - chemistry; DNA Polymerase I - chemistry; DNA Polymerase I - metabolism; DNA Replication; Fluorenes - chemistry; Kinetics; Molecular Conformation; Molecular Sequence Data; Nucleic Acid Conformation; Stereoisomerism; Thermodynamics
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi2017443

The DNA sequence effect is an important structural factor for determining the extent and nature of carcinogen-induced mutational and repair outcomes. In this study, we used two 16-mer template sequences, TG*A [d­(5′-CTTCTTG*ACCTCATTC-3′)] and CG*A [d­(5′-CTTCTCG*ACCTCATTC-3′)], to study the impact of the 5′-flanking nucleotide (T vs C) on aminofluorene (AF)-induced stacked (S)/major groove (B)/wedge (W) conformational heterogeneity during a simulated translesion synthesis. In addition, we probed the sequence effect on nucleotide insertion efficiencies catalyzed by the Klenow fragment (exonuclease-deficient) of DNA polymerase I. Our 19F NMR/ICD/DSC results showed that AF in the CG*A duplex sequence adopts a greater population of S-conformer than the TG*A sequence. We found that the S conformer of CG*A thermodynamically favors insertion of A over C at the lesion site (n). Significant stalling occurred at both the prelesion (n – 1) and lesion (n) sites; however, the effect was more persistent for the S conformer of CG*A than TG*A at the lesion site (n). Kinetics show that relative nucleotide insertion frequencies (f ins) were greater for TG*A than the S conformer of CG*A for either dCTP or dATP at the lesion site (n), and the insertion rate was significantly reduced at immediate upstream base pairs (n, n + 1). Taken together, the results provide insight into how the mutagenic AF could exhibit an S/B/W equilibrium in the active site of a polymerase, causing different mutations. This work represents a novel structure–function relationship in which adduct structure is directly linked to nucleotide insertion efficiency in a conformation-specific manner during translesion DNA synthesis.