Proton two-dimensional nuclear Overhauser effect and relaxation studies of poly(dA).cntdot.poly(dT)

Abstract

The structure of poly(dA) .cntdot. poly(dT) in aqueous solution has been studied by using 1H two-dimensional nuclear Overhauser effect (2D NOE) spectroscopy and relaxation rate measurements on the imino and nonexchangeable protons. The assignments of the 1H resonances are determined from the observed cross-relaxation patterns in the 2D NOE experiments. The cross-peak intensities together with the measured relaxation rates show that the purine and pyrimidine strands in poly(dA) .cntdot. poly(dT) are equivalent in aqueous solution. The results are consistent with a right-handed B-form helix where the sugars on both strands are in the C2''-endo/anti configuration. These observations are inconsistent with a proposed heteronomous structure for poly(dA) .cntdot. poly(dT) [Arnott, S., Chandrasekaran, R., Hall, I. H., and Puigjaner, L. C. (1983) Nucleic Acids Res. 11, 4141-4155]. The measured relaxation rates also show that poly(dA) .cntdot. poly(dT) has fast large-amplitude local internal motions (.+-. 20-25.degree.) in solution and that the amplitudes of the base and sugar motions are similar. The motion of the bases in poly(dA) .cntdot. poly(dT) is also similar to that previously reported for poly(dA-dT) and poly(dG-DC) .cntdot. poly(dG-dC) [Assa-Munt, N., Granot, J., Behling, R. W., and Kearns, D. R. (1984) Biochemistry 23, 944-955; Mirau, P. A., Behling, R. W., and Kearns, D. R. (1985) Biochemistry 24, 6200-6211].