Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Classification and Energetics of the Base-Phosphate Interactions in RNA

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 the 3D structures of 16S and 23S rRNA 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 Protein Data Bank (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 correspond to energy minima on the potential energy hypersurface. We modified the ?Find RNA 3D? (FR3D) software suite to automatically find and classify these interactions. The 3D structures of the 16S and 23S rRNAs of E.coli and T.thermophilus were compared to identify conserved BPh interactions. Most conserved BPh interactions occur in hairpin, internal, or junction loops or as part of tertiary interactions. Bases which form BPh interactions that are conserved in the 3D structures are also conserved in rRNA sequence alignments. In addition, bases involved in BPh interactions show a higher degree of conservation than those not involved, even after adjusting the analysis for the other types of molecular interactions. In summary, we identified BPh interactions as important extension of base pairing of structured RNAs with selective effect on RNA sequences. Thus consideration of BPh interactions in RNA bioinformatics is very vital.

Craig L. Zirbel1,4
Judit E. Sponer5
Jiri Sponer5
Jesse Stombaugh2,4
Neocles B. Leontis3,4*

1Dept of Mathematics and Statistics
2Dept of Biological Sciences
3Dept of Chemistry
4Ctr for Biomolecular Sciences
Bowling Green State Univ.
Bowling Green, OH 43403
5Inst of Biophysics
Academy of Sci. of the Czech Rep.
Kralovopolska 135
612 65 Brno, Czech Republic

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