Localized fluctuational hydrogen-bond stretch modes in homopolymer DNA

The effect of a particular type of thermal fluctuation in a DNA molecule is to reduce the hydrogen-bond force constants locally. In this paper we study the effect of such thermal fluctuations on the vibrational spectra of B-form poly(dG){·}poly(dC) and B-form poly(dA){·}poly(dT). We find the fluctuations create a defect (decrease in H-bond force constants) that is localized to a single base pair. In both polymers the presence of such a defect induces prominent defect modes in the frequency region between 60 and 72 cm^-1. The mode found in poly(dG){·}poly(dC) is quasilocal (inband), whereas the mode found in poly(dA){·}poly(dT) is local (lies in the band gap). Our calculations indicate that it is easier to create the defect mode in poly(dA){·}poly(dT) than in poly(dG){·}poly(dC). The local mode in poly(dA){·}poly(dT) is at a frequency where infrared absorption occurs.