2′-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis

Jack S. Hardwick, Marius M. Haugland, Afaf H. El-Sagheer, Denis Ptchelkine, Frank R. Beierlein, Andrew N. Lane, Tom Brown, Janet E. Lovett, Edward A. Anderson

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2′ position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2′-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation.

Original languageEnglish
Pages (from-to)2830-2840
Number of pages11
JournalNucleic Acids Research
Volume48
Issue number6
DOIs
StatePublished - Apr 6 2020

Bibliographical note

Publisher Copyright:
© 2020 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

ASJC Scopus subject areas

  • Genetics

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