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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 h-1 nuclear magnetic-resonance spectra

Academic Article
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Overview

authors

  • Celda, B.
  • Widmer, H.
  • Leupin, W.
  • Chazin, Walter J.
  • Denny, W. A.
  • Wuthrich, Kurt

publication date

  • February 1989

journal

  • Biochemistry  Journal

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.

subject areas

  • Base Sequence
  • DNA
  • Hydrogen
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides
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Identity

International Standard Serial Number (ISSN)

  • 0006-2960

Digital Object Identifier (DOI)

  • 10.1021/bi00430a006

PubMed ID

  • 2719909
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Additional Document Info

start page

  • 1462

end page

  • 1471

volume

  • 28

issue

  • 4

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