Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis.

ABSTRACT: Guanine:adenine (G:A) mismatches and in particular tandem G:A (tG:A) mismatches are frequently observed in biological RNA molecules and can serve as sites for tertiary interaction, metal binding and protein recognition. Depending on the surrounding sequence tG:A mismatches can adopt different basepairing topologies. In the sequence context (5'-) GGAC (tandem G:A in bold) a face-to-face (imino or Watson-Crick-like) pairing is preferred whereas in the CGAG context, G and A adopt a sheared arrangement. Systematic conformational searches with a generalized Born continuum model and molecular dynamics simulations including explicit water molecules and ions have been used to generate face-to-face and sheared tG:A mismatches in both CGAG and GGAC sequence contexts. Conformations from both approach

SUBMITTER: Villescas-Diaz G 

PROVIDER: S-EPMC1303097 | biostudies-literature | 2003 Jul

REPOSITORIES: biostudies-literature