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N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry
Of the Siberian Branch of Russian Academy of Science

В  журнале Nucleic Acids Research (IF 11,147I) опубликована статья с участием сотрудников Института  - О.А. Крумкачева, А. А. Кужелев,  В.М. Тормышев, Ю.Ф. Полиенко, Е. Г. Багрянская:

DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling

Olesya A Krumkacheva, Georgiy Yu Shevelev, Alexander A Lomzov, Nadezhda S Dyrkheeva, Andrey A Kuzhelev, Vladimir V Koval, Victor M Tormyshev, Yuliya F Polienko, Matvey V Fedin, Dmitrii V Pyshnyi, Olga I Lavrik, Elena G Bagryanskaya

Nucleic Acids Research, Volume 47, Issue 15, 05 September 2019, Pages 7767–7780

First published: 22 July 2019


 https://doi.org//10.1093/nar/gkz620





2019 07 27 NAR

 

Abstract

A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5′ ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1. 

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