Temperature-Dependent Signatures of Coherent Vibrational Openings in DNA

We report numerical simulations of the contribution of the transverse hydrogen bond stretching vibrations in the dynamic structure factor of a DNA sequence. We apply a simple nonlinear dynamical model to a finite segment of the bacteriophage T7 core promoter DNA. The temperature dependence of the dynamic structure factor is investigated. A distinct feature is identified and attributed to coherent localized thermal openings (hot-spots) due to nonlinearity combined with sequence specificity. We present the variation of the position and the width of the corresponding dynamic structure factor feature with temperature. Finally, a strong deviation of the Debye−Waller factor from the usual harmonic form is evaluated.