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Related Experiment Videos

DNA bending and sequence-dependent backbone conformation NMR and computer experiments.

R P Ojha1, M M Dhingra, M H Sarma

  • 1Institute of Biomolecular Stereodynamics, Dept. of Chemistry, University at Albany, NY, USA.

European Journal of Biochemistry
|September 22, 1999
PubMed
Summary
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DNA A-tracts exhibit sequence-directed bending due to sugar phosphate conformation. This study reveals localized structural distortions, challenging existing models and suggesting proteins recognize these DNA deformations.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biophysics

Background:

  • DNA bending is critical for biological processes.
  • The link between sugar phosphate conformation and sequence-directed DNA bending is poorly understood.
  • A-tracts are known DNA sequences that exhibit significant bending.

Purpose of the Study:

  • To experimentally determine the relationship between sugar phosphate conformation and sequence-directed DNA bending in A-tracts.
  • To investigate the structural basis of DNA kinking and bending within A-tracts.
  • To compare experimental findings with existing DNA bending models.

Main Methods:

  • Two-dimensional Nuclear Magnetic Resonance (2D NMR) experiments were used to determine coupling constants.
  • Analysis of sugar pucker, torsional preferences, and conformational averaging about key bonds (C3'-O3', C4'-C5', C5'-O5') for each nucleotide.

Related Experiment Videos

  • Characterization of the equilibrium between canonical B-form and noncanonical B-form DNA within the A-tract.

    • Main Results:

    • The A-tract exists as an equilibrium of canonical and noncanonical B-form DNA.
    • A noncanonical B-form involves a trans conformation at the C4'-C5' bond, increasing interphosphate distance and causing local unwinding and base pair rolling.
    • Structural distortions are highly localized, with significant disagreement with the Crothers A-tract DNA bending model but agreement with Leroy et al.'s findings of local structural differences from B-DNA.

    Conclusions:

    • The study elucidates the specific sugar phosphate conformations responsible for DNA bending in A-tracts.
    • Localized structural distortions, rather than propagated changes, are key to A-tract bending.
    • These pre-existing DNA deformations are likely recognized by transcription factors for protein-DNA complex formation.