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 free DNA helix and an isolated daunomycin are calculated and compared with the infrared spectrum of similar systems at frequencies above 600 ${\mathrm{cm}}^{\mathrm{-}1}$. Our study indicates that the binding induces a considerable change in the vibrational spectrum of both DNA and the binding drug. The frequency shifts appear to be closely related to the conformational deformation in the complex caused by drug binding. Significant frequency shift is found in the normal modes in the DNA⋅drug complex that are primarily vibrations localized to the sugar-phosphate backbone of the binding site. Sizable frequency change is also found in the modes associated 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 dynamical force field by the nonbonded interactions between DNA and the drug is found to have little effect on the modes in DNA above 600 ${\mathrm{cm}}^{\mathrm{-}1}$. The modification to the daunomycin dynamical force field appears to be sizable since the frequency of several daunomycin modes is changed by several ${\mathrm{cm}}^{\mathrm{-}1}$. The close relationship between structure and spectrum revealed in this work is of potential application in the identification of sites and types of deformation of a biomolecule from Raman and infrared spectra.