LOCAL MODES IN A DNA POLYMER WITH HYDROGEN-BOND DEFECT

Vibrations of a homopolymer DNA with localized hydrogen bond defects h ave been examined using the recently developed decaying mode theory fo r long-chain polymers with local structural defects. For a poly(dA)-po ly(dT) homopolymer having perturbed hydrogen bonds in one base pair, a localized mode at 63.2 cm(-1) has been found. This mode has a very ne arly pure H-bond stretch or ''breathing'' character, although the back bones do not separate. This agrees in frequency with a similar result found by other authors using a different approach. We search the full microwave frequency range for other local modes for several models of weakened H bonds. Besides the local mode with breathing characteristic s, local modes with other characteristic motions were found, but only for asymmetrically perturbed bonds. We find in general that local mode s are not very robust, requiring quite specific, narrow ranges in para meter space. They are also not abundant, there being only three in our most prolific model.