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Single base-pair precision and structural rigidity in a small IHF-induced DNA loop

S E Nunes-Düby1, L I Smith-Mungo, A Landy

  • 1Division of Biology & Medicine, Brown University, Providence, RI 02912, USA.

Journal of Molecular Biology
|October 20, 1995
PubMed
Summary
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The integration host factor (IHF) precisely bends DNA within Lambda att sites, crucial for recombination. Misplaced DNA bends or insertions within the loop disrupt this process, impacting protein-DNA interactions and recombination efficiency.

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Prokaryotic integration host factor (IHF) is a DNA-bending protein that binds DNA as a heterodimer.
  • Previous studies identified asymmetric protein-DNA contacts by individual IHF subunits.

Purpose of the Study:

  • To identify a symmetry element of IHF binding within Lambda attachment (att) sites.
  • To localize the functional DNA bend center within the H' site of Lambda att sites.
  • To investigate the impact of DNA bend positioning and insertions on recombination.

Main Methods:

  • Exploiting the sequence and positional context of the H' IHF binding site in Lambda att sites.
  • Analyzing recombination efficiency in response to altered DNA bend centers and insertions within the loop formed with Lambda integrase (Int).

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Main Results:

  • A symmetry element of IHF binding was identified, localizing the functional bend center to the center of this symmetry.
  • Shifting the H' bend center by a single base pair significantly reduced recombination.
  • Ten base-pair insertions within the loop affected recombination in a position-dependent manner: distal insertions abolished it, while proximal or double insertions were tolerated.

Conclusions:

  • Precise positioning of the DNA bend by IHF is critical for att site recombination.
  • The length and phasing of DNA loops formed by IHF and Int are sensitive to bend center location and insertions.
  • IHF's role in DNA bending is essential for the correct spatial arrangement of proteins and DNA during recombination.