Calculation of temperature dependence of interbase breathing motion of a guanine-cytosine DNA double helix with adenine-thymine insert

Abstract

The modified self-consistent phonon approximation is generalized to calculate the critical temperature of a DNA double helix with block inserts of different base pair sequences. An iterative method based entirely on the Green’s function is developed to compute efficiently the self-consistent anharmonic force constants and thermal mean-squared vibrational amplitudes in hydrogen bonds. The calculation is carried out for a long guanine-cytosine (G-C) type helix with an insert of d(A${)}_4$-d(T${)}_4$. The melting-associated behavior is predicted to initiate in major groove bonds in the inserted adenine-thymine (A-T) base pairs at 349 K. This temperature is above the mean-field melting temperature of poly(dA)-poly(dT) due to stabilization of the A-T bonds by the G-C helix and below the mean-field melting temperature of poly(dG)-poly(dC), where dA refers to repeating ade- nine bases on one strand and dT the repeating thymine bases on the other strand.