The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation

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Abstract
CD spectra were obtained for eight synthetic double‐stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A‐C) · d(G‐T)] and poly[d(A‐G) · d(C‐T)], (b) poly[d(A‐C‐C) · d(G‐G‐T)] and poly[d(A‐C‐G) · d(C‐G‐T)], and (c) poly[d(A) · d(T)], poly[d(A‐T) · d(A‐T)], poly[d(A‐A‐T) · d(A‐T‐T)], and poly[d(A‐A‐T‐T) · d(A‐A‐T‐T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G · C)‐containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180–191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right‐handed conformations. Among the set of sequences containing only A · T base pairs, poly[d(A) · d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A · T)‐rich polymers and was absent from two first‐neighbor estimations of the poly[d(A) · d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A · T)‐rich polymers was due in part of the fact that poly[d(A) · d(T)] exists in a noncanonical B conformation.