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Nucleic Acids Research, 1978, Vol. 5, No. 10 3679-3696
© 1978

Articles

A comparison of the circular dichroism spectra of synthetic DNA sequences of the homopurine homopyrimidine and mixed purine- pyrunidine types

Donald M. Gray*, A. Richard Morgan+ and Robert L. Ratiliff{dagger}

*Program in Mol. Biol., University of Texas at Dallas, Box 688, Richardson TX 75080, USA +Dep. Biochem., University of Alberta, Edmonton Alberta, T6G 2H7, Canada {dagger}Cell. and Mol. Biol. Group, Los Alamos Scientific Laboratory, University of California Los Alamos, NM 87545, USA

Received September 1, 1978. We have obtained the ultraviolet circular dichroism spectra of two repeating trinucleotide DNAs, poly and [d(A-G-G)·d(C-C-T)] poly [d(A-A-G)·(C-T-T)], that have all purines on one strand and all pyrimidines on the other. These spectra, together with spectra of other synthetic polymers, can be combined to give 3 first-neighbor calculations of the spectrum of poly[d(A)·d(T)] and 2 first-neighbor calculations of the spectrum of poly-[d(G)·d(C)]. The results show (1) that first-neighbor calculations utilizing only spectra of hoimpurine·homopyrimidine DNA sequences are no more accurate than are similar calculations that involve spectra of mixed purine-pyrimidine sequences, desonstrating that double-stranded homopurine·homopyrimidine sequences do not obviously belong to a special class of secondary conformations, and (2) that the wavelength region above 250 run in the CD spectra of synthetic DNAs is least predictable from first-neighbor equations, probably because this region is especially sensitive to sequence-dependent conformational differences.


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