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Nucleic Acids Research, 1983, Vol. 11, No. 16 5747-5761
© 1983

CHEMISTRY

Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA*

J.M. Benevides and G.J. Thomas, Jr.+

Department of Chemistry, Southeastern Massachusetts University North Dartmouth, MA 02747, USA

+To whom correspondence may be addressed.

Received May 20, 1983. Accepted July 15, 1983.

Raman spectra of poly(dG-dC) poly(dG-dC) in D2O solutions of high (4.0M NaCl) and low-salt (0.1M NaCl) exhibit differences due to different nucleotide conformations and secondary structures of Z and B-DHA. Characteristic carbonyl modes in the 1600-1700 cm–1 region also reflect differences in base pair hydrogen bonding of the respective GC complexes. Comparison with A-DNA confirms the uniqueness of C-0 stretching frequencies in each of the three DNA secondary structures. Most useful for qualitative identification of B, Z and A-DNA structures are the intense Raman lines of the phosphodiester backbone in the 750-850 cm–1 region. A conformation-sensitive guanine mode, which yields Raman lines near 682, 668, or 625 cm–1 in B (C2'-endo, anti), A (C3'-endo, anti) or Z (C3'-endo, syn) structures, respectively, is the most useful for quantitative analysis. In D2O, the guanine line of Z-DNA is shifted to 615 cm–1, permitting its detection even in the presence of proteins.


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