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

Abstract

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.

Lack of Z-DNA conformation in mitomycin-modified polynucleotides having inverted circular dichroism.

“…[Recently a similar inhibition of the B-UZ transition was observed in aflatoxin B1-poly(dG-dC).poly(dG-dC) complexes (22 (5,15,16). Only one peak is evident, however, at the position of that of the control (4.30 ppm).…”

“…(ii) MC [10][11][12][13][14][15][16][17][18][19][20] nucleotides; CD, highly inverted (Fig. 1B); and base composition, 42.5% G, 43.1% C, 7.5% T, and 6.9% A.…”

Sequence preferences in the binding to DNA of triostin A and TANDEM as reported by DNase I footprinting

“…The similarity of the footprints for the two antibiotics is surprising since their relative binding affinities for poly(dA-dT) and poly(dG-dC) are quite different, implying definite differences in the precise base sequence(s) of their preferred binding site(s) 151. However, these polynucleotides may adopt different helical structures as compared to natural DNAs [15,16], so that binding data obtained with them may tend to exaggerate small differences in the intrinsic sequence preferences of the antibiotics. It may therefore be advisable to assess the footprinting patterns in the light of equilibrium binding data for natural DNAs.…”

31P-NMR analysis of the B to Z transition in double-stranded (dC-dG)3, and (dC-dG)4in high salt solution

“…Also, 31P NMR spectra of the left handed Z DNA of polynucleotides show two characteristic signals with separation or ca. 0.5-1.5 ppm, which can be used to detect the presence of Z DNA in solution (3,6,8,9,(15)(16)(17)(18)(19)(20)(21)(22)(23). It is usual to assume that the downfield and upfield components correspond to predominantly gt and gg conformations, respectively, of the i and a torsion angles (24) in the 03'-P-05' linkages (6,(15)(16)(17)(18)(19)(20)(21)(22)(23) …”