Fast Picosecond Dynamics in Polynucleotides by Raman Spectroscopy

Abstract

Spontaneous Raman scattering can be used to study the fast dynamics in molecules. The reorientational correlation times can be obtained from a comparison of the bandwidth in the anisotropic Raman spectrum with that in the isotropic Raman spectrum [1]. Macromolecular motion in fluids is in general too slow to be observable in the Raman time window that is accessible in the frequency domain (~0.1 ps. to ~8ps.). In principle motion of molecular sub-groups can be fast enough. We have studied the isotropic bandwidths of vibrations in a large number of synthetic polynucleotides and compared them with mononucleotides. Also temperature melting profiles were obtained from a number of polynucleotides. A comparison of rAMP and poly(rA) in stacked and unstacked form were previously published [2]. It was concluded that the bandwidths of base vibrations are sensitive for the formation of stacked structures in the sense that stacking leads to a decreased bandwidth of a number of in-plane vibrations. Temperature induced melting of the stacked stnicture of poly(rA) causes the 1336 cm-1 band to acquire a bandwidth identical to that in rAMP. Not so, however, for the 727 cm-1 band which retains a much narrower bandwidth (12.6 – 0.3 cm-1) at elevated temperatures (75–90 C.) than in rAMP (15.4 - 0.3 cm-1). Also it was determined that the perturbation correlation time of this band was shorter then 0.13 ps., which is significantly shorter than the amplitude correlation time (0.86 ps.) indicating that this band is in the fast modulation regime.