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Sequence elements responsible for DNA curvature

T E Haran1, J D Kahn, D M Crothers

  • 1Department of Chemistry, Yale University, New Haven, CT 06511.

Journal of Molecular Biology
|November 25, 1994
PubMed
Summary
This summary is machine-generated.

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DNA bending, crucial for DNA transactions, is influenced by sequences between A-tracts. This study shows minimal sequence-dependent modulation of DNA curvature, supporting models of intrinsic DNA structure.

Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • Intrinsic DNA bending is vital for DNA transactions.
  • Homopolymeric dA.dT runs (A-tracts) cause significant DNA curvature when phased.
  • The influence of intervening sequences on A-tract-induced curvature is not fully understood.

Purpose of the Study:

  • To investigate how the 5 bp DNA sequence between A-tracts modulates DNA bending.
  • To assess the contribution of intervening sequences to overall DNA curvature.
  • To validate assumptions about DNA curvature arising from A-tracts in generic B-DNA.

Main Methods:

  • Electrophoretic mobility modulation was used to measure DNA bending.
  • Molecules of the form (A5-6N5)n were analyzed, where N represents variable 5 bp sequences.

Related Experiment Videos

  • Curvature was quantified by analyzing the electrophoretic mobility of DNA fragments.

    • Main Results:

    • A-tract-induced DNA curvature is modulated by intervening sequences, but only slightly (+/- 10%).
    • This minor modulation suggests that the helical axis deflection of 5 bp B-DNA segments is largely sequence-independent.
    • Published wedge angle parameters could predict curvature direction and magnitude for a specific non-A-tract sequence.

    Conclusions:

    • The assumption that DNA curvature primarily results from A-tracts inserted into generic B-DNA is largely validated.
    • The findings support models where B-DNA segments have a general roll of approximately 6 degrees, or models dominated by A-tract negative roll.
    • Ambiguity between roll in A-tracts versus intervening B-DNA segments persists and cannot be resolved by current methods.