CD SPECTRAL COMPARISONS OF THE ACID-INDUCED STRUCTURES OF POLY[D(A)], POLY[R(A)], POLY[D(C)], AND POLY[R(C)]

CD spectra were used to compare the acid-induced structural transitions of poly[d(A)] and poly[d(C)] with those of poly[r(A)] and poly[r(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 poly[d(C)] was in the least stacked structure and had the highest pK(a) for forming a protonated duplex.