CD Spectral Comparisons of the Acid-Induced Structures of Poly[d(A)]Poly[r(A)], Poly[d(C)], and Poly[r(C)]

Abstract

CD spectra were used to compare the acid-induced structural transitions of polyd(A)] and polyd(C)] with those of polyr(A)] and polyr(C)], respectively. The types of base pairing were probably the same in the acid self-complexes of both A-containing polymers and in the acid self-complexes of both C-containing polymers. Similar base pairings were indicated by similarities in the difference CD spectra showing the changes during the first major acid- induced transitions of the polymers. Information from the CD spectra and pK_a values of the transitions suggested that the transitions for the RNA polymers involved similar structural changes. The two DNA polymers were markedly different. Single-stranded poly d(A)] was in the most stacked structure and had the lowest pK^a for forming an acid self-complex. Single-stranded polyd(C)] was in the least stacked structure and had the highest pK_a for forming a protonated duplex.