Characterization of alternating deoxyribonucleic acid conformations in solution by phosphorus-31 nuclear magnetic resonance spectroscopy

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Abstract
Medium length (50-200 bp [base-pairs]) alternating purine-pyrimidine DNA were prepared by sonication of synthetic polymers at low temperature. The products, and the hairpin structures derived from them after melting, were sufficiently small for high-resolution 31P NMR studies. Of the 5 sequences studied, 2 DNA, poly(dG-dC).cntdot.poly(dG-dC) and poly(dA-dU).cntdot.poly(dA-dU), gave singlet 31P resonances, while 3 others, poly(dA-dT).cntdot.poly(dA-dT), poly(dA-br5U).cntdot.poly(dA-br5U) and poly(dI-dC).cntdot.poly(dI-dC), exhibited 2 resolved signals of equal area. This indicates the existence of 2 distinct alternating phosphodiester backbone conformations for these latter 3 B-DNA in solution. Controls of homopolymers, which were also prepared by sonication, showed only singlet 31P resonances. Of the alternating sequence DNA, only sonicated poly(dG-dC).cntdot.poly(dG-dC) exhibited a conformational transition to a high salt (> 2.5 M) form which exhibited 2 well-resolved 31P resonances of equal area. The high salt form of poly(dG-dc).cntdot.poly(dG-dC) evidently also has an alternating backbone structure, and it is presumed to be a Z-DNA. These results indicate a general response of the DNA backbone conformation to alternating purine-pyrimidine base sequences but with a degree of sequence and environmental specificity which might have functional genetic significance.