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Nucleic Acids Research Advance Access published online on June 14, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp468
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Classification and energetics of the base-phosphate interactions in RNA

Craig L. Zirbel1,2, Judit E. Sponer3, Jiri Sponer3, Jesse Stombaugh2,4 and Neocles B. Leontis2,4,*

1Department of Mathematics and Statistics, 2Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403 USA, 3Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic and 4Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA

*To whom the correspondence should be addressed. Tel: 419 372 8663; Fax: 419 372 9809; Email: leontis{at}bgsu.edu

Received March 25, 2009. Revised May 13, 2009. Accepted May 17, 2009.

Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson–Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the ‘Find RNA 3D' (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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