DNA with damage in both strands as affinity probes and nucleotide excision repair substrates
- Authors: Lukyanchikova N.V.1,2, Petruseva I.O.1, Evdokimov A.N.1, Silnikov V.N.1, Lavrik O.I.1,2,3
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Affiliations:
- Institute of Chemical Biology and Fundamental Medicine
- Novosibirsk State University
- Altai State University
- Issue: Vol 81, No 3 (2016)
- Pages: 263-274
- Section: Article
- URL: https://journals.rcsi.science/0006-2979/article/view/150807
- DOI: https://doi.org/10.1134/S0006297916030093
- ID: 150807
Cite item
Abstract
Nucleotide excision repair (NER) is a multistep process of recognition and elimination of a wide spectrum of damages that cause significant distortions in DNA structure, such as UV-induced damage and bulky chemical adducts. A series of model DNAs containing new bulky fluoro-azidobenzoyl photoactive lesion dCFAB and well-recognized nonnucleoside lesions nFlu and nAnt have been designed and their interaction with repair proteins investigated. We demonstrate that modified DNA duplexes dCFAB/dG (probe I), dCFAB/nFlu+4 (probe II), and dCFAB/nFlu−3 (probe III) have increased (as compared to unmodified DNA, umDNA) structure-dependent affinity for XPC—HR23B (Kdum > KdI > KdII ≈ KdIII) and differentially crosslink to XPC and proteins of NER-competent extracts. The presence of dCFAB results in (i) decreased melting temperature (ΔTm = −3°C) and (ii) 12° DNA bending. The extended dCFAB/dG-DNA (137 bp) was demonstrated to be an effective NER substrate. Lack of correlation between the affinity to XPC—HR23B and substrate properties of the model DNA suggests a high impact of the verification stage on the overall NER process. In addition, DNAs containing closely positioned, well-recognized lesions in the complementary strands represent hardly repairable (dCFAB/nFlu+4, dCFAB/nFlu−3) or irreparable (nFlu/nFlu+4, nFlu/nFlu−3, nAnt/nFlu+4, nAnt/nFlu−3) structures. Our data provide evidence that the NER system of higher eukaryotes recognizes and eliminates damaged DNA fragments on a multi-criterion basis.
About the authors
N. V. Lukyanchikova
Institute of Chemical Biology and Fundamental Medicine; Novosibirsk State University
Email: lavrik@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090; Novosibirsk, 630090
I. O. Petruseva
Institute of Chemical Biology and Fundamental Medicine
Email: lavrik@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090
A. N. Evdokimov
Institute of Chemical Biology and Fundamental Medicine
Email: lavrik@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090
V. N. Silnikov
Institute of Chemical Biology and Fundamental Medicine
Email: lavrik@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090
O. I. Lavrik
Institute of Chemical Biology and Fundamental Medicine; Novosibirsk State University; Altai State University
Author for correspondence.
Email: lavrik@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090; Novosibirsk, 630090; Barnaul, 656049
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