title: 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 1H nuclear magnetic resonance spectra.
abstract: The conformation at 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 Overhauser 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 degrees. 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, with the pseudorotation phase angle P in the range 100-130 degrees, 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.
authors.affiliation: Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
authors.forename: B
authors.initials: B
authors.lastname: Celda
authors.forename: H
authors.initials: H
authors.lastname: Widmer
authors.forename: W
authors.initials: W
authors.lastname: Leupin
authors.forename: W J
authors.initials: WJ
authors.lastname: Chazin
authors.forename: W A
authors.initials: WA
authors.lastname: Denny
authors.forename: K
authors.initials: K
authors.lastname: Wüthrich
mesh_terms: D001483:Base Sequence; D004247:DNA; D006859:Hydrogen; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides
chemical_list: D009838:Oligodeoxyribonucleotides; D006859:Hydrogen; D004247:DNA