Efficiency of coaxial stacking depends on the DNA duplex structure

Abstract Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X, Y = A, C, T, G; *—nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear regression analysis has revealed that the free-energy increments of interaction for the contacts GX*pYG/CZVC and CX*pYC/GZVG can be described by a set of uniform ΔG°X*pY/zv values. The difference in the observed free-energy of the coaxial stacking between the two sets is defined by the contribution from the factors reflecting structural differences between compared DNA duplexes.