Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.

ABSTRACT: The ability to accurately predict RNA hairpin structure and stability for different loop sequences and salt conditions is important for understanding, modeling, and designing larger RNA folds. However, traditional RNA secondary structure models cannot treat loop-sequence and ionic effects on RNA hairpin folding. Here, we describe a general, three-dimensional (3D) conformation-based computational method for modeling salt concentration-dependent conformational distributions and the detailed 3D structures for a set of three RNA hairpins that contain a variable, 15-nucleotide loop sequence. For a given RNA sequence, the new, to our knowledge, method integrates a Vfold2D two-dimensional structure folding model with IsRNA coarse-grained molecular dynamics 3D folding simulations and Monte Carlo t

SUBMITTER: Zhao C 

PROVIDER: S-EPMC7568001 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature