Structural Stability of Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments: Molecular Dynamics Studies of Functional RNA

Abstract

Noncanonical basepairs have gained importance over the past few years because of their various functions in RNA biochemistry. These basepairs appear quite frequently in different double helical stems also, but whether they are stabilized by contextual pressure or act as seeds of folding is not yet clear. We have used all-atom molecular dynamics simulations to characterize the stability and functional features of a few noncanonical basepairs within two RNA double helical fragments obtained from ribosome crystal structures. It is anticipated that the noncanonical basepairs would open up spontaneously if they had appeared due to contextual pressure. However, we have found from MD simulations that the noncanonical basepairs occurring in tandem at the central regions of double helical stretches are quite stable. Analysis of basepairing parameters carried out in terms of H-bonding edge-specific axis system indicates that dynamics of the noncanonical basepairs are very similar to those of the canonical ones. The stacking parameters for dinucleotide steps consisting of noncanonical basepairs are rather unusual, but the variability patterns indicate their significant stability. The stacking free-energy values as presumed from the distributions of structural parameters also appear to be similar for both canonical and noncanonical basepair steps.