1. Water-nucleobase 'stacking': H-pi and lone pair-pi interactions in the atomic resolution crystal structure of an RNA pseudoknot
- Author
-
Martin Egli, Sanjay Sarkhel, and and Alexander Rich
- Subjects
Models, Molecular ,Chemistry ,Hydrogen bond ,Intermolecular force ,Stacking ,Ab initio ,Frameshifting, Ribosomal ,Water ,Aromaticity ,General Chemistry ,Crystal structure ,Crystallography, X-Ray ,Biochemistry ,Catalysis ,Nucleobase ,Crystallography ,Colloid and Surface Chemistry ,Nucleic Acid Conformation ,RNA, Viral ,Lone pair ,Hydrogen - Abstract
The hydrogen bond acceptor capability of aromatic rings has been demonstrated both by experimental and theoretical studies, and D-H...pi interactions (H-pi interaction), where D is mainly N, O, and C, are ubiquitous in structures of macromolecules. By comparison, the interaction of a lone pair of water directly with the face of a pi-system (l.p.-pi interaction) seems counterintuitive and to date has only been studied theoretically. In the crystal structure of an RNA pseudoknot at atomic resolution, all nucleobases not involved in either intra- or intermolecular base-base stacking interactions exhibit stacking with water molecules either of the H-pi or the l.p.-pi type. The geometry observed for the l.p.-pi type water-nucleobase stacking is consistent with that predicted in recent ab initio studies.
- Published
- 2004