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Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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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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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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