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

Medium length (500-200 bp) alternating purine-pyrimidine DNAs 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 five sequences studied, two DNAs, poly(dG-dC).poly(dG-dC) and poly(dA-dU).poly(dA-dU), gave singlet 31P resonances, while three others, poly(dA-dT).poly(dA-dT), poly(dA-br5U).poly(dA-br5U), and poly(dI-dC).poly(dI-dC), exhibited two resolved signals of equal area. This indicates the existence of two distinct alternating phosphodiester backbone conformations for these latter three B-DNAs in solution. Controls of homopolymers, which were also prepared by sonication, showed only singlet 31P resonances. Of the alternating sequences DNAs, only sonicated poly(dG-dC).poly(dG-dC) exhibited a conformational transition to a high salt (greater than 2.5 M) form which exhibited two well-resolved 31P resonances of equal area. This indicates that the high salt form of poly(dG-dC).poly(dG-dC) 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.

Molecular orbital studies on the structure of nucleoside analogs. III. Conformation of 3-deazapyrimidine nucleosides.

PCILO computations ahve been carried out on the conformational properties of 3-deazapyrimidine nucleosides namely: 3-deazauridine and 3-deazacytidine. These nucleoside analogs result as a consequence of the replacement of N(3) by a carbon atom and they become nucleoside antibiotics having cytostatic and antiviral properties. Both C(2')-endo and C(3')-endo sugar geometries have been considered and the results indicate that the conformational preferences of these nucleoside antibiotics are very similar to those of their parent nucleosides and more particularly so in the situations that occur in aqueous solutions. The important biological significance of the results has been discussed.