Can G-C Hoogsteen-wobble pairs contribute to the stability of d(G{middle dot}C-C) triplexes? | Zendy

Robert Soliva | Zendy; F. Javier Luque | Zendy; Modesto Orozco | Zendy

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Can G-C Hoogsteen-wobble pairs contribute to the stability of d(G{middle dot}C-C) triplexes?

Author(s) -

Robert Soliva,

F. Javier Luque,

Modesto Orozco

Publication year - 1999

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/27.11.2248

Subject(s) - speed wobble , wobble base pair , pairing , stacking , physics , molecular dynamics , ab initio , computational chemistry , biology , rna , chemistry , quantum mechanics , transfer rna , nuclear magnetic resonance , biochemistry , superconductivity , gene

Quantum mechanics, molecular dynamics and statistical mechanics methods are used to analyze the importance of neutral Hoogsteen-wobble G.C pairing in the stabilization of triple helices based on the poly-(G.C-C) trio at neutral pH and low ionic strength. In spite of the existence of a single hydrogen bond, the Hoogsteen-wobble G.C pair is found to be quite stable both in gas phase and solvated DNA. Molecular dynamics simulations of different triplexes based on the d(G.C-C) trio leads to stable structures if the neutral d(G.C-C) steps stabilized by Hoogsteen-wobble pairs are mixed with d(G.C-C+) steps. Finally, high level ab initio calculations and thermodynamic integration techniques are used to determine the relative stability of G.C wobble and G.C imino pairings. It is found that triplexes containing the imino pairing are slightly more stable structures than those with the wobble one, due mainly to a better stacking.

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