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Nucleic Acids Research, 1993, Vol. 21, No. 6 1433-1438
© 1993

STRUCTURAL BIOLOGY

Demonstration of Z-d(5BrCGAT5BrCG) and B-d(CGCGATCGCG) form crystal stuctures in DNA-cobalt hexammine complexes by Kr 647.1 nm excitation of Raman spectra*

J.M. Benevides, A.H.-J. Wang and G.J. Thomas, Jr.+

Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City Kansas City, MO 64110-2499, USA 1Biophysics Division and Department of Cell and Structural Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA

+To whom correspondence should be addressed

Received December 7, 1992. Revised February 5, 1993. Accepted February 5, 1993.

Cobalt hexammine [Co(NH3)63+] Is an efficient ONA complexlng agent which significantly perturbs nucleic acid secondary structure. We have employed red excitation (647.1 nm) from a krypton laser to obtain Raman spectra of the highly colored complexes formed between cobalt hexammine and crystals of the DNA ollgomers, d(5BrCGAT5BrCG) and d(CGCGATCGCG), both of which Incorporate out-of-alternatlon pyrimidlne/purlne sequences. The Co(NH3)63+ complex of d(C5BrGAT5BrCG) exhibits a typical Z-form Raman signature, similar to that reported previously for the alternating d(CGCGCG) sequence. Comparison of the Raman bands of d(5BrCGAT5BrCG) with those of other ollgonucleotide and polynucleotide structures suggests that C3'-endo/syn and C3/-endo/anti thymldlnes may exhibit distinctive nucleoside conformation markers, and tentative assignments are proposed. The Raman markers for C2'-endo/anti adenoslne in this Z-DNA are consistent with those reported previously for B-DNA crystals containing C2'-endo/anti dA. Raman bands of the cobalt hexammine complex of d(CGCGATCGCG) are those of B-DNA, but with significant differences from the previously characterized B-DNA dodecamer, d(CGCAAATTTGCG). The observed differences suggest an unusual deoxyguanoslne conformer, possibly related to a previously characterized structural Intermediate in the B–Z transition. The present results show that crystallization of d(CGCGATCGCG) In the presence of cobalt hexammine is not alone sufficient to Induce the left-handed Z-DNA conformation. This investigation represents the first application of off-resonance Raman spectroscopy for characterization of highly chromophorfc DNA and illustrates the feasibility.

*Paper XLV in the series Raman Spectral Studies of Nucleic Acid


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