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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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Monakhova MV, Milakina MA, Savitskaia VY, Romanova EA, Rao DN, Kubareva EA. MutL Protein from the Neisseria gonorrhoeae Mismatch Repair System: Interaction with ATP and DNA. Mol Biol 2021. [DOI: 10.1134/s0026893321020114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Perry SA, Kubareva EA, Monakhova MV, Trikin RM, Kosaretskiy EM, Romanova EA, Metelev VG, Friedhoff P, Oretskaya TS. DNA with a 2-Pyridyldithio Group at the C2' Atom: A Promising Tool for the Crosslinking of the MutS Protein Preserving Its Functional Activity. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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