Assigning the 625cm -1 and other high frequency Raman bands of the Z 1 form of DNA using a normal modes analysis and computer graphics

Abstract The left-handed zigzag conformation of the ribose phosphate backbone of the double helix of Z-DNA is well established. A normal modes analysis has been performed using the crystal form of d(CpGpCpGpCpG); this is a half turn of double helical Z-DNA. The calculated 625 cm −1 band, which has been shown to be specific for the Z conformation of DNA is discussed with reference to previous work. It would seem that the classical description of vibrational modes in terms of internal coordinates is inadequate for macromolecular systems. The great number of internal coordinates involved in one vibrational mode makes the assignment complex. A new method of interpreting the vibrational modes is described. It is based on the use of Cartesian displacement coordinates to describe the vibrational mode together with computer graphics for its direct visualization.