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Related Experiment Videos

A-Tract bending: insights into experimental structures by computational models.

D Strahs1, T Schlick

  • 1Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, NY 10012, USA.

Journal of Molecular Biology
|September 1, 2000
PubMed
Summary
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Molecular dynamics simulations reveal that adenine tract (A-tract) DNA structures exhibit negative global roll, consistent with minor-groove bending. Local changes in DNA structure stabilize this bending, influencing DNA flexibility and protein binding.

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Adenine tract (A-tract) oligomers exhibit unique bending, with solution structures suggesting minor-groove bending (negative global roll).
  • Crystallographic data for A-tracts share features like propeller twisting and narrow minor grooves but lack unambiguous bend direction characterization.
  • Understanding A-tract bending is crucial for DNA-protein interactions, such as TATA-binding protein (TBP) binding.

Purpose of the Study:

  • To investigate the origin of DNA bending in A-tracts using molecular dynamics (MD) simulations.
  • To reconcile findings from crystallographic and solution structures of A-tracts.
  • To analyze the role of local DNA structural features in stabilizing global DNA bending.

Main Methods:

Related Experiment Videos

  • Analysis of molecular dynamics trajectories for two solvated A-tract dodecamers (1D89 and 1D98).
  • Application of a novel general global bending framework for bent DNA and DNA/protein complexes.
  • Comparison with a control DNA sequence (1BNA) with a different sequence composition.

    • Main Results:

    • MD simulations converted initial dissimilar A-tract structures to similar bend directions, exhibiting negative global roll with average helical-axis bends of 10.5–14.1 degrees.
    • The largest bend occurred as positive roll on the 5' side of the A-tracts, supported by gradual curvature at each base-pair step.
    • A-tract dodecamers showed stabilized bending due to propeller twisting, deoxyribose puckering differences, narrow minor grooves, and water spines, features also present in crystallographic structures.

    Conclusions:

    • Small local changes in DNA structure, accumulated across flexible moieties, are sufficient to induce negative global roll in A-tracts.
    • Sequence outside the A-tract significantly influences the overall bending path, explaining differences between experimental and theoretical findings.
    • The study provides insights into sequence-dependent DNA flexibility and its implications for DNA-protein interactions, including TBP binding.