Raman Depolarization Ratios in RNA and DNA are Sensitive for Sugar-Base Coupling

Polarized and depolarized Raman spectra are obtained for a number of synthetic polynucleotides containing adenine, uracil, and thymine bases. The depolarization ratios are determined by two methods: (1) by dividing the -spectrum by the -spectrum and (2) after curve fitting. Overlapping bands, isotope splitting, reorientational broadening, and noncoincidence splitting affect the magnitude of the depolarization ratios over the band-width. For both Lorentz and Gauss curves these influences are simulated. A comparison of the Raman spectra of RNA and DNA molecules shows that the depolarization ratios for a number of similar base vibrations are different. The vibrational modes and the depolarization ratios of sugar vibrations are most sensitive to the structure of the polynucleotide. Base vibrations that have their potential energy distributed over base and sugar atoms also seem to be more sensitive to the structure. For instance the adenine vibrations at 1332 cm-1 and 1344 cm-1 in poly(dA), poly(dA) · poly(dT) and poly(dA-dT) · poly(dA-dT) have different depolarization ratios of, respectively, 0.36 and 0.28. This supports a previous assignment of the 1332 cm-1 band to a different sugar pucker (O4,-endo) than the C2,-endo corresponding with the 1344 cm-1 vibration. Assuming equal Raman scattering coefficients for this vibration, irrespective of the sugar pucker gives rise to the following ratio of the O4,-endo/C2,-endo in poly(dA) of 0.41, in poly(dA) · poly(dT) of 0.37, and in poly(dA-dT) · poly(dA-dT) of 0.41.