EFFECT OF DRUG-BINDING-INDUCED DEFORMATION ON THE VIBRATIONAL-SPECTRUM OF A DNA DAUNOMYCIN COMPLEX

Vibrational frequencies of a DNA-daunomycin complex and those of a fre e DNA helix and an isolated daunomycin are calculated and compared wit h the infrared spectrum of similar systems at frequencies above 600 cm (-1). Our study indicates that the binding induces a considerable chan ge in the vibrational spectrum of both DNA and the binding drug. The f requency shifts appear to be closely related to the conformational def ormation in the complex caused by drug binding. Significant frequency shift is found in the normal modes in the DNA drug complex that are pr imarily vibrations localized to the sugar-phosphate backbone of the bi nding site. Sizable frequency-change is also found in the modes associ ated with base atoms involved in the drug binding and in the modes in regions of the binding daunomycin that are deformed by the binding. In contrast the frequency of the modes in the region with no significant deformation is relatively unchanged. The modification of the DNA dyna mical force field by the nonbonded interactions between DNA and the dr ug is found to have little effect on the modes in DNA above 600 cm(-1) . The modification to the daunomycin dynamical force field appears to be sizable since the frequency of several daunomycin modes is changed by several cm(-1). The close relationship between structure and spectr um revealed in this work is of potential application in the identifica tion of sites and types of deformation of a biomolecule from Raman and infrared spectra.