C-H...O and C-H...N interactions in RNA structures

Small molecule studies indicate that C-H...X interactions (X: O,N) constitute weak H-bonds. We have performed a comprehensive analysis of their occurrence and geometry in RNA structures. Here, we report on statistical properties of the total set of interactions identified and discuss selected motifs. The distance/angle distribution of all interactions exhibits an excluded region where the allowed C--H...X angle range increases with an increasing H...X distance. The preferred short C--H...X interactions in RNA are backbone-backbone contacts between neighbour nucleotides. Distance/angle distributions generated for various interaction types can be used for error recognition and modelling. The axial C2'(H)...O4' and C5'(H)...O2' interactions connect two backbone segments and form a seven-membered ring that is specific for RNA. An AA base pair with one standard H-bond and one C-H...N interaction has been identified in various structures. Despite the occurrence of short C--H...X contacts their free energy contribution to RNA stability remains to be assessed.