Defect-mediated hydrogen-bond instability of poly(dG)-poly(dC)

A modified self-consistent phonon theory based on the complex Green’s function is developed for a DNA polymer poly(dG)-poly(dC) which contains a defect (dG refers to repeating guanine bases on one strand and dC the repeating cytosine bases on the other strand). The defect simulates a fluctuation in which the hydrogen bonds which bridge the guanine and cytosine in one cell are broken. The theory is then used to analyze the possible instabilities that can arise in neighboring cells as a function of the temperature. A melting or hydrogen-bond instability does occur in the neighboring cells at 350 K. We find a directional effect around the defect when the instability begins to occur. This calculation has no parameters adjusted to fit melting data and is based on the potentials which are adjusted to fit data of the vibrational modes of the DNA homopolymer at room temperature (293 K).