Structural and conformational studies of polyriboadenylic acid in neutral and acid solution

Raman spectra of solutions of polyriboadenylic acid have been studied in the pH range of 7.2–5.2. Bands are identified which are sensitive to the characteristics of poly(rA) in the single-and double-stranded helical forms. Thermal melting profiles were obtained as a function of pH to monitor simultaneously the changes in (1) the phosphodiester backbone, (2) the base-stacking interactions, (3) the perturbation of the PO unit, and (4) the degree of protonation at the N-1 position in the adenine base. The temperature dependence of the intensity ratio of the bands at 725 and 705 cm^?1 appears to be sensitive to the noncooperative and the cooperative thermal-melting process for the single-and double-stranded forms of poly(rA), respectively. Concurrently, bands diagnostic of the degree of protonation reveal that the cooperative melting process for the “acid” poly(rA) clearly involves deprotonation. The progressive perturbation of the 1100 cm^?1 band with an increasing degree of protonation of poly(rA) is consistent with earlier suggestions regarding a PO-(6)-NH₂ interaction in the double-helical form of poly(rA). The stability of the double-helix parallels the degree of protonation over the pH range studied as reflected in the t_m values, which increase linearly with decreasing pH.