Water-nucleobase "stacking": H-pi and lone pair-pi interactions in the atomic resolution crystal structure of an RNA pseudoknot.

Sarkhel S, Rich A, Egli M
J Am Chem Soc. 2003 125 (30): 8998-9

PMID: 15369340 · DOI:10.1021/ja0357801

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.

MeSH Terms (7)

Crystallography, X-Ray Frameshifting, Ribosomal Hydrogen Models, Molecular Nucleic Acid Conformation RNA, Viral Water

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