%0 Journal Article
%T Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures
%A Svetlana Kirillova
%A Oliviero Carugo
%J BMC Structural Biology
%D 2011
%I BioMed Central
%R 10.1186/1472-6807-11-41
%X A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed.The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.Water plays an important role in the function of biological molecules [1]. In the case of RNA, water is regarded as "an integral part of nucleic acid structure" because it defines structure and folding and participates in intra-molecular interactions [2]. For example, the free energy of RNA hairpins is considerably influenced by the presence of acceptor groups that do not form hydrogen bonds [3]. Moreover, RNA interactions with other molecules can be mediated by water molecules that link the two partners and water molecules bound to RNA can be replaced by polar groups of other molecules [4,5]. Furthermore, water molecules having large dipole moments modulate electrostatic interactions [6]. For these reasons, the understanding of RNA hydration is of crucial importance in drug design and modeling interactions [7]. Additionally, molecular dynamics simulations require the definition of the initial positions of the solvent atoms and the last stages of crystallographic refinements involve RNA hydration sites [8].The most frequently used experimental methods to study RNA hydration are X-ray crystallography and NMR spectroscopy. NMR spe
%U http://www.biomedcentral.com/1472-6807/11/41