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

Varnai, Peter, Canalia, Muriel and Leroy, Jean-Louis (2004) Opening mechanism of G.T/U pairs in DNA and RNA duplexes: A combined study of imino proton exchange and molecular dynamics simulation. Journal of American Chemical Society, 126 (44). pp. 14659-14667. ISSN 0002-7863

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Abstract

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.

Item Type: Article
Additional Information: 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.
Schools and Departments: School of Life Sciences > Chemistry
Depositing User: Peter Varnai
Date Deposited: 06 Feb 2012 21:18
Last Modified: 19 Mar 2013 14:05
URI: http://sro.sussex.ac.uk/id/eprint/30661
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