University of Sussex
Browse

File(s) not publicly available

Opening mechanism of G.T/U pairs in DNA and RNA duplexes: A combined study of imino proton exchange and molecular dynamics simulation

journal contribution
posted on 2023-06-08, 09:35 authored by Peter Varnai, Muriel Canalia, Jean-Louis Leroy
The opening pathway of wobble pairs dT and rU has been investigated in four DNA and two RNA duplexes. Using NMR spectroscopy, we measured the imino proton exchange of both G(H1) and T/U(H3), catalyzed by ammonia, tris, and OH-, and we calculated the free energy surface related to T/U opening by molecular dynamics simulations. Taken together the experimental and theoretical results, we suggest that wobble pairs open through a coupled rotation of the bases toward the major groove where exchange of both imino protons takes place with the surrounding water.

History

Publication status

  • Published

Journal

Journal of American Chemical Society

ISSN

0002-7863

Publisher

ACS Publications

Issue

44

Volume

126

Page range

14659-14667

Pages

9.0

Department affiliated with

  • Chemistry Publications

Notes

PV+JLL designed research, CM+JLL performed NMR measurements, PV performed simulations and analyzed data, PV+JLL wrote the paper. First combined theoretical and experimental paper using novel computational methodology to study the base opening mechanism that compares the dynamic features of GT and AU base pairs in a number of sequences.

Full text available

  • No

Peer reviewed?

  • Yes

Legacy Posted Date

2012-02-06

Usage metrics

    University of Sussex (Publications)

    Categories

    No categories selected

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC