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Open Access Open Badges Research article

Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

Svetlana Kirillova1* and Oliviero Carugo2

Author Affiliations

1 Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria

2 Department of Chemistry, Pavia University, Viele Taramelli 12, I-27100 Pavia, Italy

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BMC Structural Biology 2011, 11:41  doi:10.1186/1472-6807-11-41

Published: 19 October 2011



Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing.


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.