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

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(^5BrCGAT^5BrCG) and d(CGCGATCGCG), both of which Incorporate out-of-alternatlon pyrimidlne/purlne sequences. The Co(NH₃)₆³⁺ complex of d(C^5BrGAT^5BrCG) 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(^5BrCGAT^5BrCG) 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.