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Probing the Effect of Bulky Lesion-Induced Replication Fork Conformational Heterogeneity Using 4-Aminobiphenyl-Modified DNA

Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI 02881, USA
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Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Derek J. McPhee
Molecules 2019, 24(8), 1566; https://doi.org/10.3390/molecules24081566
Received: 27 February 2019 / Revised: 14 April 2019 / Accepted: 17 April 2019 / Published: 20 April 2019
(This article belongs to the Special Issue Structural and Functional Aspects of DNA Polymerases)
Bulky organic carcinogens are activated in vivo and subsequently react with nucleobases of cellular DNA to produce adducts. Some of these DNA adducts exist in multiple conformations that are slowly interconverted to one another. Different conformations have been implicated in different mutagenic and repair outcomes. However, studies on the conformation-specific inhibition of replication, which is more relevant to cell survival, are scarce, presumably due to the structural dynamics of DNA lesions at the replication fork. It is difficult to capture the exact nature of replication inhibition by existing end-point assays, which usually detect either the ensemble of consequences of all the conformers or the culmination of all cellular behaviors, such as mutagenicity or survival rate. We previously reported very unusual sequence-dependent conformational heterogeneities involving FABP-modified DNA under different sequence contexts (TG1*G2T [67%B:33%S] and TG1G2*T [100%B], G*, N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl) (Cai et al. Nucleic Acids Research, 46, 6356–6370 (2018)). In the present study, we attempted to correlate the in vitro inhibition of polymerase activity to different conformations from a single FABP-modified DNA lesion. We utilized a combination of surface plasmon resonance (SPR) and HPLC-based steady-state kinetics to reveal the differences in terms of binding affinity and inhibition with polymerase between these two conformers (67%B:33%S and 100%B). View Full-Text
Keywords: 4-aminobiphenyl; bulky DNA lesion; conformational heterogeneity; surface plasmon resonance (SPR) binding kinetics; steady state enzyme kinetics; Klenow fragment 4-aminobiphenyl; bulky DNA lesion; conformational heterogeneity; surface plasmon resonance (SPR) binding kinetics; steady state enzyme kinetics; Klenow fragment
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Cai, A.; Bian, K.; Chen, F.; Tang, Q.; Carley, R.; Li, D.; Cho, B.P. Probing the Effect of Bulky Lesion-Induced Replication Fork Conformational Heterogeneity Using 4-Aminobiphenyl-Modified DNA. Molecules 2019, 24, 1566.

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