Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies

Abstract

Asymmetric bulge loop motifs are widely dispersed in all types of functional RNAs. They are frequently occurring structural motifs in folded RNA structures and appear commonly in pre-microRNA and ribosomes, where they are involved in specific RNA–RNA and RNA–protein interactions. It is therefore necessary to understand such motifs from a structural point of view. We analyzed all available RNA structures and identified quite a few fragments of double helices that contain bulges. We found that these discontinuities often introduce kinks into the double helices, which also affects the stacking overlap between the base pairs across the irregularity. In order to understand the influence of these bulges on stability and flexibility, we carried out molecular dynamics simulations of three different single-residue bulge-containing RNA helices using the CHARMM36 force field. The structural variability at the junctions of RNA bulges is expected to differ from that in continuous double-helical stretches. The structural features of the junction region were observed to vary noticeably depending on the orientation of the bulge residue. When the base of the bulge residue is looped out, the RNA stretch behaves like a standard long A-form RNA double helix, whereas the entire RNA behaves differently when the base of the bulge residue is intercalated between base pairs inside the RNA stem. Such single-base intercalation was found to introduce a permanent kink into the composite double helix, which could be a recognition element for Dicer during the maturation of miRNA.