title: Conformational insights into the lesion and sequence effects for arylamine-induced translesion DNA synthesis: 19F NMR, surface plasmon resonance, and primer kinetic studies.
abstract: Adduct-induced DNA damage can affect transcription efficiency and DNA replication and repair. We previously investigated the effects of the 3'-next flanking base (G*CT vs G*CA; G*, FABP, N-(2'-deoxyguanosin-8-yl)-4'-fluoro-4-aminobiphenyl; FAF, N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) on the conformation of arylamine-DNA lesions in relation to E. coli nucleotide excision repair ( Jain , V. , Hilton , B. , Lin , B. , Patnaik , S. , Liang , F. , Darian , E. , Zou , Y. , Mackerell , A. D. , Jr. , and Cho , B. P. ( 2013 ) Nucleic Acids Res. , 41 , 869 - 880 ). Here, we report the differential effects of the same pair of sequences on DNA replication in vitro by the polymerases exofree Klenow fragment (Kf-exo(-)) and Dpo4. We obtained dynamic (19)F NMR spectra for two 19-mer modified templates during primer elongation: G*CA [d(5'-CTTACCATCG*CAACCATTC-3')] and G*CT [d(5'-CTTACCATCG*CTACCATTC-3')]. We found that lesion stacking is favored in the G*CT sequence compared to the G*CA counterpart. Surface plasmon resonance binding results showed consistently weaker affinities for the modified DNA with the binding strength in the order of FABP > FAF and G*CA > G*CT. Primer extension was stalled at (n) and near (n - 1 and n + 1) the lesion site, and the extent of blockage and the extension rates across the lesion were influenced by not only the DNA sequences but also the nature of the adduct's chemical structure (FAF vs FABP) and the polymerase employed (Kf-exo(-) vs Dpo4). Steady-state kinetics analysis with Kf-exo(-) revealed the most dramatic sequence and lesion effects at the lesion (n) and postinsertion (n + 1) sites, respectively. Taken together, these results provide insights into the important role of lesion-induced conformational heterogeneity in modulating translesion DNA synthesis.
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States.
authors.forename: Vipin
authors.initials: V
authors.lastname: Jain
authors.forename: Vaidyanathan G
authors.initials: VG
authors.lastname: Vaidyanathan
authors.forename: Satyakam
authors.initials: S
authors.lastname: Patnaik
authors.forename: Sathyaraj
authors.initials: S
authors.lastname: Gopal
authors.forename: Bongsup P
authors.initials: BP
authors.lastname: Cho
mesh_terms: D000611:Aminobiphenyl Compounds / Q000737:chemistry*; D001483:Base Sequence; D018736:DNA Adducts; D004249:DNA Damage; D004256:DNA Polymerase I / Q000378:metabolism; D004260:DNA Repair; D004261:DNA Replication; D005449:Fluorenes / Q000737:chemistry*; D005461:Fluorine / Q000737:chemistry; D007700:Kinetics; D009690:Nucleic Acid Conformation; D020349:Surface Plasmon Resonance
chemical_list: D000611:Aminobiphenyl Compounds; D018736:DNA Adducts; D005449:Fluorenes; C006757:4-biphenylamine; D005461:Fluorine; C012177:2-aminofluorene; D004256:DNA Polymerase I