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 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.

本数据集系统性地探究了所有氢键平面结构，包括互补（腺嘌呤-胸腺嘧啶、胞嘧啶-鸟嘌呤、腺嘌呤-尿嘧啶）和非互补（腺嘌呤-胞嘧啶、腺嘌呤-鸟嘌呤、胞嘧啶-胸腺嘧啶、胞嘧啶-尿嘧啶、鸟嘌呤-胸腺嘧啶、鸟嘌呤-尿嘧啶、胸腺嘧啶-尿嘧啶）异源配对。借鉴我们先前关于同源配对的研究（凯利等，物理化学B，2005，109，11933−11939；22045−22052；物理化学B，2006，110，2249−2255）中提出的结合位点概念以及从头算密度泛函理论（DFT），我们发现了9对腺嘌呤-胸腺嘧啶、9对腺嘌呤-尿嘧啶、7对胞嘧啶-鸟嘌呤、6对腺嘌呤-胞嘧啶、9对腺嘌呤-鸟嘌呤、6对胞嘧啶-胸腺嘧啶、6对胞嘧啶-尿嘧啶、7对鸟嘌呤-胸腺嘧啶、7对鸟嘌呤-尿嘧啶以及9对胸腺嘧啶-尿嘧啶的强异源配对。这些配对的稳定化能展现出从-0.45至-1.12 eV的广泛变化，其中最稳定的是沃森-克里克胞嘧啶-鸟嘌呤对。在可获取高质量量子化学和/或DFT计算结果的情况下，所选配对的几何构型和稳定性与我们的计算结果极为吻合。所获得的75对稳定异源配对可用于模拟基于DNA和RNA异源配对的大规模超结构（见于各种表面）。