Introduction: Dinucleotide of deoxy cytidine and deoxy guanosine (CpG) is the most mutable sequence in DNA. The reason why this dinucleotide is mutated highly is assumed to be deamination of cytosine and depurination of guanosine. By experimental analysis it is suggested that methylation of cytosine is the main cause of the alteration in this dinucleotide. Thymidine substitutes cytosine when the cytosine is methylated and consequently the repair system of cell cannot recognize the mutation. In this way, the mutation has been established in the genome. In current study we analyzed the methylation effect of CpG on the stability of this sequence from thermochemical point of view, in order to understand whether methylation affects the energy level or not.

Materials and Methods: To theoretically evaluate the effects of methylation on thermochemical parameters Gaussian software was used. The data used for this study include thermochemical and NMR parameters.

Conclusion: Our results suggested a reliable answer about the effect of methylation on mentioned dinucleotide. Our results theoretically elaborates more chance for instability of the dinucleotide when it is methylated. This can reveal another reason rather than the incompetence of repair system for the high rate mutation in methylated CpG. The novel reason could be the instability increase due to the methylation.