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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Monakhova MV, Kubareva EA, Kolesnikov KK, Anashkin VA, Kosaretskiy EM, Zvereva MI, Romanova EA, Friedhoff P, Oretskaya TS, Zatsepin TS. Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model. Molecules 2022; 27:molecules27082438. [PMID: 35458636 PMCID: PMC9031232 DOI: 10.3390/molecules27082438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Covalent protein capture (cross-linking) by reactive DNA derivatives makes it possible to investigate structural features by fixing complexes at different stages of DNA–protein recognition. The most common cross-linking methods are based on reactive groups that interact with native or engineered cysteine residues. Nonetheless, high reactivity of most of such groups leads to preferential fixation of early-stage complexes or even non-selective cross-linking. We synthesised a set of DNA reagents carrying an acrylamide group attached to the C5 atom of a 2′-deoxyuridine moiety via various linkers and studied cross-linking with MutS as a model protein. MutS scans DNA for mismatches and damaged nucleobases and can form multiple non-specific complexes with DNA that may cause non-selective cross-linking. By varying the length of the linker between DNA and the acrylamide group and by changing the distance between the reactive nucleotide and a mismatch in the duplex, we showed that cross-linking occurs only if the distance between the acrylamide group and cysteine is optimal within the DNA–protein complex. Thus, acrylamide-modified DNA duplexes are excellent tools for studying DNA–protein interactions because of high selectivity of cysteine trapping.
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Affiliation(s)
- Mayya V. Monakhova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
- Correspondence: ; Tel.: +7-(903)-593-8905
| | - Elena A. Kubareva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Kirill K. Kolesnikov
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
| | - Viktor A. Anashkin
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Egor M. Kosaretskiy
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia;
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
| | - Elena A. Romanova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany;
| | - Tatiana S. Oretskaya
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Timofei S. Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
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