Identifying and interpreting spectral features of dissolved poly(dA)-poly(dT) DNA polymer in the high-microwave range

The vibrational modes involving the hydrogen-bond fluctuations in B conformation of poly(dA)-poly(dT) DNA homopolymer dissolved in aqueous solution have been theoretically studied within the recently developed effective-field model, including longitudinal as well as radial fields, and a properly frequency-dependent dielectric constant for the surrounding water. We have analyzed the vibrational eigenvectors to characterize two types of motions involving hydrogen bonds, namely, propeller twist and hydrogen-bond breathing. We ran our analysis for five different sets of partial atomic charges, and found that the major mode frequencies are essentially independent of the choice of partial charges. Since hydrogen-bond strength changes with temperature, we simulated the effect of temperature on the hydrogen bonds by varying the hydrogen-bond force constants. Our calculations indicate that a mode near 42 ${\mathrm{cm}}^{\mathrm{-}1}$ with strong propeller twist motion is to be expected. Around 63 ${\mathrm{cm}}^{\mathrm{-}1}$, another mode with strong hydrogen-bond breathing character should be found. We discuss the expected variations of these resonances with temperature as a guide to spectral identification.