Water-nucleobase "stacking": H-pi and lone pair-pi interactions in the atomic resolution crystal structure of an RNA pseudoknot.
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.
Sarkhel
Sanjay
S
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Rich
Alexander
A
Egli
Martin
M
D018360:Crystallography, X-Ray; D018965:Frameshifting, Ribosomal; D006859:Hydrogen / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D012367:RNA, Viral; D014867:Water; D006859:Hydrogen