Jain V, Vaidyanathan VG, Patnaik S, Gopal S, Cho BP. Conformational insights into the lesion and sequence effects for arylamine-induced translesion DNA synthesis: 19F NMR, surface plasmon resonance, and primer kinetic studies.
Biochemistry 2014;
53:4059-71. [PMID:
24915610 PMCID:
PMC4075988 DOI:
10.1021/bi5003212]
[Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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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 (JainV., HiltonB., LinB., PatnaikS., LiangF., DarianE., ZouY., MackerellA. D.Jr., and ChoB. P. (2013) Nucleic Acids Res., 41, 869−88023180767). 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 19F 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.
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