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Planar Heteropairing Possibilities of the DNA and RNA Bases:  An ab Initio Density Functional Theory Study

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posted on 15.03.2007, 00:00 by Ross E. A. Kelly, Lev N. Kantorovich
All hydrogen-bonded planar structures of complementary (adenine−thymine, cytosine−guanine, and adenine−uracil) and noncomplementary (adenine−cytosine, adenine−guanine, cytosine−thymine, cytosine−uracil, guanine−thymine, guanine−uracil, and thymine−uracil) heteropairings are systematically investigated. Using the idea of binding sites discussed in our previous work on homopairs [Kelly et al. J. Phys. Chem. B 2005, 109, 11933−11939; 22045−22052; J. Phys. Chem. B 2006, 110, 2249−2255] and the ab initio density functional theory (DFT), we found 9 adenine−thymine, 9 adenine−uracil, 7 cytosine−guanine, 6 adenine−cytosine, 9 adenine−guanine, 6 cytosine−thymine, 6 cytosine−uracil, 7 guanine−thymine, 7 guanine−uracil, and 9 thymine−uracil strong heteropairs. The stabilization energies of the pairs show a wide variation from −0.45 up to −1.12 eV, the most stable being the Watson−Crick cytosine−guanine pair. The geometries and stabilities of the selected pairs, where high quality quantum chemistry and/or DFT calculations are available, are found to compare extremely well with our calculations. The obtained set of 75 stable heteropairs can be used in modeling larger super-structures (based on DNA and RNA heteropairs) seen on various surfaces.