Calculation of the stability of mini-duplexes of DNA in an electrolyte solution using a molecular mechanics method in approximating a statistical model of the environment

Approximation of the statistical model of environment (SME) to estimate the energy of the macromolecule in electrolyte solution has been developed and used for calculating the conformational energy of nucleic acids by means of the molecular mechanics method. Calculation of base pairs opening delta Hcalop enthalpies and enthalpies of DNA miniduplexes dissociation delta Hcaldis were performed for 10 types of diduplexes. The approximation SME enable to perform calculations of the absolute base-dependent values of delta Hcalop which coincide in the range of 1 kcal/mol with the experimental base-dependent values of the helix-coil transition enthalpies. Values of dissociation enthalpies delta Hcalop greater than delta Hcaldis for all miniduplexes, the difference of delta Hcalop--delta Hcaldis determine the base-dependent energy of the helix-coil boundary. The values of activation barriers for the strands dissociation delta H d not equal to congruent to 8 kcal/mol and association delta H not equal to as congruent to 4 kcal/mol were obtained for GG/CC and AA/TT duplexes. It is concluded that the approximation SME enables to increase substantially the accuracy of the calculations of the macromolecule conformational rearrangement enthalpies in the electrolytes solution.