Physical Sciences and Mathematics Commons^™

Classification And Energetics Of The Base-Phosphate Interactions In Rna, Craig L. Zirbel, Judit E. Šponer, Jiri Šponer, Jesse Stombaugh, Neocles B. Leontis

Chemistry Faculty Publications

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 …