A complete conformational map for RNA

Abstract

A simple stereochemical framework for understanding RNA structure has remained elusive to date. We present a comprehensive conformational map for two nucleoside-5',3'-diphosphates and for a truncated dinucleotide derived from a grid search of all potential conformers using hard sphere steric exclusion criteria to define allowed conformers. The eight-dimensional conformational space is presented as a series of two-dimensional projections. These projections reveal several well-defined allowed and disallowed regions which correlate well with data obtained from X-ray crystallography of both large and small RNA molecules. Furthermore, the two-dimensional projections show that consecutive and ribose ring-proximal torsion angles are interdependent, while more distant torsion angles are not. Remarkably, using steric criteria alone, it is possible to generate a predictive conformational map for RNA.