Temperature dependence of Raman vibrational bandwidths in poly(rA) and rAMP

Abstract

Isotropic and anisotropic spontaneous Raman spectra were obtained from solutions of poly(ra) and rAMP in buffer. The temperature dependence of these spectra was measured to elucidate the influence of macromolecular dynamics and solvent dynamics on the bandwidths of base vibrations in the single stranded polynucleotide poly(rA). The temperature dependence of a bandwidth depends upon the particular vibration under study. The bands can for the larger part be described by Lorentz functions. When fitted by Voigt functions, maximally 10% of each bandprofile of the adenine base vibrations can be attributed to a Gaussian component. The second moment has been determined from the spectra for the 725 cm −1 band. From the second moment and the bandwidth, we were able to deduce that the vibrational oscillator is in the fast modulation limit. The determined timescale (perturbation correlation time ⩽0.13 ps) eliminate perturbations connected to long range diffusion like concentration fluctuations (timescale in the order of 10 ps). The spectra were analyzed by an extensive curve fitting procedure providing accurate bandparameters (position, width and integrated intensity). The 725 cm −1 band of adenine has a bandwidth which is dependent upon the degree of polymerization. In RAMP it is 17.6 cm −1, in stacked (i.e. low temperature 5°C) poly(rA) it is 11.5 cm −1. The bandwidth of the adenine vibration at 1336 cm −1 cm −1 has a temperature dependence which is similar to the intensity changes of the Raman and the absorption hypochromic effect as a function of temperature. The melting transition can therefore be followed by the changes in bandwidth of suitable vibrations.