Planar heteropairing possibilities of the DNA and RNA bases: An ab initio density functional theory study

All hydrogen-bonded planar structures of complementary (adenine-thymine, cytosine-guanine, and adenineuracil) 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.