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A computer graphics study of sequence-directed bending in DNA.

S D Levene1, D M Crothers

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

Journal of Biomolecular Structure & Dynamics
|October 1, 1983
PubMed
Summary
This summary is machine-generated.

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A DNA fragment from Leishmania tarentolae exhibits unusual physical properties due to its ApA sequence. This periodic dinucleotide causes systematic DNA bending, impacting its behavior in gels.

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • A specific DNA fragment from Leishmania tarentolae kinetoplast displays anomalous physical characteristics.
  • These include reduced electrophoretic mobility and a shorter rotational relaxation time compared to control DNA fragments of similar molecular weight.

Purpose of the Study:

  • To provide theoretical explanations for the observed unusual physical properties of the DNA fragment.
  • To investigate the role of the adenine-adenine (ApA) dinucleotide sequence in DNA structure and behavior.

Main Methods:

  • Theoretical analysis of DNA structure and properties.
  • Computer graphics modeling of DNA chain trajectories.
  • Evaluation of existing DNA structural models, including Calladine's model.

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Main Results:

  • The anomalies are attributed to a highly periodic distribution of the ApA dinucleotide.
  • Repeated local bends at ApA sites, synchronized with the helical periodicity, induce systematic DNA bending.
  • Calladine's crystallographic model fails to predict this systematic bending in solution.

Conclusions:

  • The periodic ApA sequence is a key determinant of the DNA fragment's unusual physical properties.
  • Systematic DNA bending, influenced by local structural features, plays a significant role in DNA behavior.
  • Current crystallographic models may not fully capture DNA conformational dynamics in solution.