The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics

摘要

The sequence dependence of RNA energetics is important for predicting RNA structure. Hairpins with C_n loops are consistently less stable than hairpins with other loops, which suggests the structure of C_n regions could be unusual in the "unfolded" state. For example, previous nuclear magnetic resonance (NMR) evidence suggested that polycytidylic acid forms a left-handed helix. In this study, UV melting experiments show that the hairpin formed by r(5′GGACCCCCGUCC) is less stable than r(5′GGACUUUUGUCC). NMR spectra for single-stranded C_4 oligonucleotide, mimicking the unfolded hairpin loop, are consistent with a right-handed A-form-like helix. Comparisons between NMR spectra and molecular dynamics (MD) simulations suggest that recent reparametrizations, parm99χ-YIL and parm99TOR, of the AMBER parm99 force field improve the agreement between structural features for C_4 determined by NMR and predicted by MD. Evidently, the force field revisions to parm99 improve the modeling of RNA energetics and therefore structure.