Homopairing possibilities of the DNA bases cytosine and guanine: An ab initio DFT study

All the planar homopairings of cytosine and guanine are reported for the first time in this study. The idea of binding sites suggested for the simple case of adenine homopairs (J. Phys. Chem. B 2005, 109, 11933) is shown to be applicable to more complicated molecules binding to each other via multiple hydrogen bonds and can be considered as a general method for constructing hydrogen bonding structures. As an example we consider homopairs formed by DNA bases cytosine and guanine, suggesting that there may be 13 cytosine and 17 guanine homopairs. However, only I I cytosine and 15 guanine homopairs remain after atomic relaxation performed using ab initio density functional theory. Most of the homopairs obtained have not been studied before. The homopairs have significant binding energies, varying from -0.19 to -1.12 eV, that are explained by multiple hydrogen bonds formed between monomers in the pairs, up to four hydrogen bonds in most energetically favorable cases. The detailed information on all guanine and cytosine planar homopairs contained in this work can be used to construct various cytosine and guanine superstructures observed on different surfaces.