Opening mechanism of G.T/U pairs in DNA and RNA duplexes: a combined study of imino proton exchange and molecular dynamics simulation.
The opening pathway of wobble pairs dG.T and rG.U 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 G.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.
Várnai
Péter
P
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS UPR 9080, 13 Rue Pierre et Marie Curie, Paris 75005, France.
Canalia
Muriel
M
Leroy
Jean-Louis
JL
D000641:Ammonia / Q000737:chemistry; D020029:Base Pairing; D002384:Catalysis; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D007097:Imines / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013816:Thermodynamics
D007097:Imines; D012330:RNA, Double-Stranded; D000641:Ammonia; D004247:DNA