VIBRATIONAL CD STUDY OF THE THERMAL-DENATURATION OF POLY(RA).POLY(RU)

The vibrational cd (VCD) of a double-stranded RNA, poly(rA) . poly(rU), at pH 7 and moderate added salt concentration (0.1 M) has been measured in both the base-stretching and phosphate-stretching regions of the ir as a function of temperature. The data in both cases show two distinct phase transitions. The first is from double- to a triple-stranded form, and the second is from triple- to single-stranded forms, which still retain substantial local order even up to 80-degrees-C. The nature of these transitions has been identified by comparison of the VCD and ir absorption spectra of the initially double-stranded samples with those of single-stranded poly(rA) and poly(rU) and with triple-stranded poly-(rA) . poly(rU) . poly(rU). The large differences in the VCD band shapes allows positive identification of the intermediate and final states. Thus under VCD-concentration conditions, a simple helix-to-coil transition can be eliminated for poly (rA) . poly (rU) while such a two-step transition can be seen at low salt conditions. All of these observations are consistent with previous studies of the phase transitions of poly (rA) . poly (rU) under various salt conditions. Additionally, the VCD is indicative of premelting for all the triple-, double-, and single-strand complexes studied. The triple-strand complex did not show disproportionation to double strand on heating under these added salt conditions. The unusual VCD pattern for low temperature poly (rA) . poly (rU), as compared to high G-C content RNAs and DNAs, is qualitatively, but not quantitatively, explained using exciton coupling of localized dipolar transitions in each type of base within the strand.