Nucleoside free energy perturbation calculations: Mutation of purine-to-pyrimidine and pyrimidine-to-purine nucleosides

Free energy perturbation calculations were conducted on the mutations of pyrimidine-to-pyrimidine, purine-to-purine, purine-to-pyrimidine, and pyrimidine-to-purine nucleosides. The parameters and technique required for these perturbations is presented. Each of the four nucleosides in DNA were mutated into the other three nucleosides, and the calculated change in free energy for each of the 12 mutations is reported.