Conformational studies of d(AAAAATTTTT)2 using constraints from nuclear Overhauser effects and from quantitative analysis of the cross-peak fine structures in two-dimensional proton nuclear magnetic resonance spectra

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Abstract
The conformation of the dA-dT junction in d-(AAAAATTTTT)2 was investigated by using a variety of phase-sensitive two-dimensional nuclear magnetic resonance experiments at 500 MHz for detailed studies of the deoxyribose ring puckers. Conformational constraints were collected from two-dimensional nuclear Oerhauser enhancement spectra recorded with short mixing times and from quantitative simulations of the cross-peaks in two-dimensional correlated spectra. Overall, the decamer duplex adopts a conformation of the B-DNA type, and for dA4 and dA5 the pseudorotation phase angle P is in the standard range 150-180.degree.. The deoxyribose puckers for the other nucleotides deviate significantly from the standard B-DNA structure. Spectrum simulations assuming either static deviations from standard B-DNA or a simple two-state dynamic equilibrium between the C2''-endo and C3''-endo forms of the deoxyribose were used to analyze the experimental data. It was thus found that the ring pucker for dT6 deviates from the regular C2''-endo form of B-DNA by a static distortion, which the pseudorotation phase angle P in the range 100-130.degree., and a similar value of P is indicated for dT7. For the peripheral base pairs dynamic distortions of the C2''-endo form of the deoxyribose were found. In agreement with recent papers on related duplexes containing (dA)n tracts, we observed prominent nuclear Overhauser effects between adenine-2H and deoxyribose-1''H, which could be largely due to pronounced propeller twisting as observed in the crystal structures of (dA)n-containing compounds.