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Molecules, volume 27, issue 8, pages 2438

Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model

Monakhova Mayya V ¹

KUBAREVA ELENA A. ¹

Kolesnikov Kirill K ²

Anashkin Viktor A ¹

Kosaretskiy Egor M ³

Zvereva Maria ²

Romanova Elena A ¹

Friedhoff P. ⁴

Орецкая Т. С. ¹

Zatsepin Timofei S. ²

Hide authors affiliations Show authors affiliations: 4 affiliations

A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia |

Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia |

Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia |

⁴

Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany |

Publication type: Journal Article

Publication date: 2022-04-10

Multidisciplinary Digital Publishing Institute (MDPI)

Journal: Molecules

Quartile SCImago

Quartile WOS

Impact factor: 4.6

ISSN: 14203049

DOI: 10.3390/molecules27082438

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PubMed ID: 35458636

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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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Monakhova M. V. et al. 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. Vol. 27. No. 8. p. 2438.

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Monakhova M. V., KUBAREVA E. A., Kolesnikov K. K., Anashkin V. A., Kosaretskiy E. M., Zvereva M., Romanova E. A., Friedhoff P., Орецкая Т. С., Zatsepin T. S. 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. Vol. 27. No. 8. p. 2438.

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TY - JOUR

DO - 10.3390/molecules27082438

UR - https://doi.org/10.3390%2Fmolecules27082438

TI - Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model

T2 - Molecules

AU - KUBAREVA, ELENA A.

AU - Kolesnikov, Kirill K

AU - Kosaretskiy, Egor M

AU - Romanova, Elena A

AU - Monakhova, Mayya V

AU - Anashkin, Viktor A

AU - Zvereva, Maria

AU - Friedhoff, P.

AU - Орецкая, Т. С.

AU - Zatsepin, Timofei S.

PY - 2022

DA - 2022/04/10 00:00:00

PB - Multidisciplinary Digital Publishing Institute (MDPI)

SP - 2438

IS - 8

VL - 27

PMID - 35458636

SN - 1420-3049

ER -

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@article{2022_Monakhova,

author = {ELENA A. KUBAREVA and Kirill K Kolesnikov and Egor M Kosaretskiy and Elena A Romanova and Mayya V Monakhova and Viktor A Anashkin and Maria Zvereva and P. Friedhoff and Т. С. Орецкая and Timofei S. Zatsepin},

title = {Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model},

journal = {Molecules},

year = {2022},

volume = {27},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

month = {apr},

url = {https://doi.org/10.3390%2Fmolecules27082438},

number = {8},

pages = {2438},

doi = {10.3390/molecules27082438}

}

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Monakhova, Mayya V., et al. “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, vol. 27, no. 8, Apr. 2022, p. 2438. https://doi.org/10.3390%2Fmolecules27082438.

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Publisher

Multidisciplinary Digital Publishing Institute (MDPI)

Journal

Molecules

Quartile SCImago

Quartile WOS

Impact factor

4.6

ISSN

14203049 (Print)

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