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Length-dependent cruciform extrusion in d(GTAC)n sequences.

L H Naylor1, H A Yee, J H van de Sande

  • 1Department of Medical Biochemistry, University of Calgary, Alberta, Canada.

Journal of Biomolecular Structure & Dynamics
|February 1, 1988
PubMed
Summary

DNA inserts called d(GTAC)n.d(GTAC)n form specific structures called cruciforms. Longer inserts are more stable and form cruciforms more readily, influencing DNA

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • pBR322-derived plasmids were engineered with varying lengths of d(GTAC)n.d(GTAC)n inserts.
  • Investigating the impact of insert size on cruciform extrusion and B-Z transition is crucial for understanding DNA structural dynamics.

Purpose of the Study:

  • To determine how insert size affects cruciform extrusion in d(GTAC)n.d(GTAC)n sequences.
  • To analyze the influence of superhelical density on cruciform formation and stability.

Main Methods:

  • Construction of pBR322-derived plasmids with d(GTAC)n.d(GTAC)n inserts (n=4-12).
  • Assessing hypersensitivity to single-strand specific nucleases (S1 nuclease, Bal31 nuclease).
  • Site-selective cleavage using T7 endonuclease I to identify cruciform structures.

Main Results:

  • All inserts formed cruciform structures in negatively supercoiled plasmids.
  • Increased superhelical density induced cruciform formation, reducing torsional stress.
  • Cruciform stability increased with insert length (larger n), requiring lower superhelical density for formation.

Conclusions:

  • The cruciform geometry is the preferred conformation for d(GTAC)n.d(GTAC)n sequences under torsional stress.
  • Insert size directly correlates with cruciform stability and the conditions required for its formation.
  • These findings elucidate the relationship between DNA sequence, supercoiling, and structural transitions.

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