Abstract.
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.
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Received: 17 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998
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Brandl, M., Lindauer, K., Meyer, M. et al. C–H...O and C–H...N interactions in RNA structures. Theor Chem Acc 101, 103–113 (1999). https://doi.org/10.1007/s002140050415
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DOI: https://doi.org/10.1007/s002140050415