Computational Biochemistry and Biophysics
A quantum chemistry study of Ds–Pa unnatural DNA base pair
Article first published online: 9 APR 2012
Copyright © 2012 Wiley Periodicals, Inc.
International Journal of Quantum Chemistry
Special Issue: Seventh Congress of the International Society for Theoretical Chemical Physics
Volume 113, Issue 4, pages 504–509, 15 February 2013
How to Cite
Otsuka, T. and Miyazaki, T. (2013), A quantum chemistry study of Ds–Pa unnatural DNA base pair. Int. J. Quantum Chem., 113: 504–509. doi: 10.1002/qua.24094
- Issue published online: 22 JAN 2013
- Article first published online: 9 APR 2012
- Manuscript Accepted: 21 FEB 2012
- Manuscript Revised: 15 FEB 2012
- Manuscript Received: 8 DEC 2011
- KAKENHI [Japan Society for the Promotion of Science (JSPS)]. Grant Number: 20540401, 22790122, 22104005
- The Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan
- Strategic Programs for Innovative Research (SPIRE), MEXT
- The Computational Materials Science Initiative (CMSI), Japan.
- density functional theory;
- second-order Møller-Plesset perturbation theory;
- unnatural DNA base pair;
- Ds–Pa pair;
- intermolecular interaction
We have performed density functional theory and MP2 calculations of the unnatural DNA base pair, Ds–Pa, (7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa)) in the gas phase. By calculating the interaction energy curve of Ds–Pa pair as a function of intermolecular distance, we have found that the interaction energy between Ds and Pa molecules is very weak. The detailed analysis of the structural properties of the optimized Ds–Pa pair has been also used and compared with those of A–T and G–C natural base pairs. These results clearly show that the Ds–Pa pair does not have any hydrogen bonds and suggest that the pair selectivity in the Ds–Pa pair mainly comes from the interaction of Ds or Pa molecules with other parts in DNA or RNA, such as upper or lower natural bases, sugar phosphate backbones, and water molecules. © 2012 Wiley Periodicals, Inc.