Prediction of DNA far-IR absorption spectra based on normal mode analysis

Abstract

We present a computational method which couples normal mode analysis in internal coordinates of a molecule with very far IR spectroscopy. The analytical expression for the dependence of IR absorption on frequency incorporates frequencies and optical activities of each normal mode. In order to predict far-IR spectra of a molecule we evaluate the optical activity of each normal mode. This optical activity is determined by the vibration amplitude of the dipole moment produced by a normal mode. We calculated normal modes of DNA double-helical fragments (dA)12 · (dT)12 and (dA-dT)6 · (dA-dT)6 and evaluated their optical activities. These were found to be very sensitive to the DNA base-pair sequence. The positions of the resonance peaks in the calculated absorption spectrum of (dA)12 · (dT)12 are in a good agreement with those obtained by Fourier transform IR spectroscopy (Powell JW et al. 1987 Phys Rev A 35: 3929–3939).