Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.

ABSTRACT: Molecular dynamics (MD) simulations for RNA tetramers r(AAAA), r(CAAU), r(GACC), and r(UUUU) are benchmarked against ¹H-¹H NOESY distances and ³J scalar couplings to test effects of RNA torsion parametrizations. Four different starting structures were used for r(AAAA), r(CAAU), and r(GACC), while five starting structures were used for r(UUUU). On the basis of X-ray structures, criteria are reported for quantifying stacking. The force fields, AMBER ff99, parmbsc0, parm99χ_Yil, ff10, and parmTor, all predict experimentally unobserved stacks and intercalations, e.g., base 1 stacked between bases 3 and 4, and incorrect χ, ϵ, and sugar pucker populations. The intercalated structures are particularly stable, often lasting several microseconds. Parmbsc0, pa

SUBMITTER: Condon DE 

PROVIDER: S-EPMC4463549 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature