pH-Dependent Raman spectra and thermal melting profiles for polycytidylic acid

The Raman spectrum of polycytidylic acid was investigated in the pH range of 6.6–4.1. The thermal melting temperatures and the nature of the thermal melting profiles change in this range as monitored by the three Raman band envelopes, which include the 780-, 805-cm^?1 bands, the 1190-, 1285-cm^?1 bands, and the 1527-cm^?1 band. By coupling these data with the theory of Raman scattering intensity and quantitative pH profiles for cytidine, it is shown that the band envelopes studied exhibit specific, yet different information regarding the thermal melting process. The band envelopes at 1170–1310 and 1527 cm^?1, which are a sensitive function of both the extent of protonation and base stacking (hypochromic), reveal T_m values which agree with values derived from uv melting profiles. The 760–830-cm^?1 envelope, which is not directly sensitive to cytosine residue protonation, but includes information associated with base stacking (the 780-cm^?1 band) and the nature of the phosphodiester backbone (the frequency-dependent 805-cm^?1 component), exhibits T_m values which deviate from the values obtained from the other bands. The observed differences are pH-dependent and correlate well with the extent of deprotonation that takes place in the denaturation process. Details of the spectrum of neutral and protonated poly(C) from pH 7 to 4.1 are discussed and related to the nature of the thermal denaturation process.