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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 LeroyThe 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 SocietyISSN
0002-7863Publisher
ACS PublicationsExternal DOI
Issue
44Volume
126Page range
14659-14667Pages
9.0Department 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
2012-02-06Usage metrics
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