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

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

Journal

Nucleic Acids Research
ISSN: 0305-1048 , E-ISSN: 1362-4962

Output data

Year: 2019, Volume: 47, Number: 15, Pages: 7767-7780 Pages count : 14 DOI: 10.1093/nar/gkz620

Authors

Krumkacheva Olesya A. ^1,2,3 , Shevelev Georgiy Yu. ^2,4 , Lomzov Alexander A. ^2,4 , Dyrkheeva Nadezhda S. ⁴ , Kuzhelev Andrey A. ^1,2,3 , Koval Vladimir V. ^2,4 , Tormyshev Victor M. ^1,2 , Polienko Yuliya F. ^1,2 , Fedin Matvey V. ^2,3 , Pyshnyi Dmitrii V. ^2,4 , Lavrik Olga I. ^2,4 , Bagryanskaya Elena G. ^1,2

Affiliations

1	(Данные Web of science) RAS, SB, NN Vorozhtsov Novosibirsk Inst Organ Chem, 9 Lavrentiev Ave, Novosibirsk 630090, Russia
2	(Данные Web of science) Novosibirsk State Univ, Pirogova Str 2, Novosibirsk 630090, Russia
3	(Данные Web of science) RAS, SB, Int Tomog Ctr, Inst Skaya Str 3a, Novosibirsk 630090, Russia
4	(Данные Web of science) RAS, SB, Inst Chem Biol & Fundamental Med, 8 Lavrentiev Ave, Novosibirsk 630090, Russia

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.

Krumkacheva O.A. , Shevelev G.Y. , Lomzov A.A. , Dyrkheeva N.S. , Kuzhelev A.A. , Koval V.V. , Tormyshev V.M. , Polienko Y.F. , Fedin M.V. , Pyshnyi D.V. , Lavrik O.I. , Bagryanskaya E.G.
DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling

Nucleic Acids Research. 2019. V.47. N15. P.7767-7780. DOI: 10.1093/nar/gkz620 WOS Scopus РИНЦ OpenAlex

Full text from publisher

Published online:	Jul 22, 2019
Published print:	Sep 5, 2019

Web of science:	WOS:000490574300010
Scopus:	2-s2.0-85072058932
Elibrary:	43206949
OpenAlex:	W2963949730

DB	Citing
Web of science	21
Scopus	22
Elibrary	21
OpenAlex	22