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Related Experiment Videos

Solution formation of Holliday junctions in inverted-repeat DNA sequences.

Franklin A Hays1, Virgil Schirf, P Shing Ho

  • 1Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Oregon State University, Corvallis, Oregon 97331-7305, USA.

Biochemistry
|February 24, 2006
PubMed
Summary

Holliday junctions form four-stranded structures in solution, dependent on DNA and cation concentrations. The ACC trinucleotide core stabilizes these crucial recombination intermediates.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Holliday junctions are key intermediates in homologous recombination.
  • Previous studies characterized junction structures using X-ray crystallography, primarily with symmetric DNA sequences.
  • Questions remain about whether these structures form in solution or are crystallization artifacts.

Purpose of the Study:

  • To investigate the solution behavior of DNA sequences known to form Holliday junctions in crystals.
  • To determine if Holliday junction formation is sequence-dependent in solution.
  • To elucidate the role of specific DNA sequences and ion concentrations in junction stability.

Main Methods:

  • Analytical ultracentrifugation was employed to study DNA structures in solution.

Related Experiment Videos

  • Two specific DNA sequences, d(CCGGTACCGG) and d(CCGCTAGCGG), were analyzed.
  • The influence of DNA and cation concentrations on structural transitions was assessed.

    • Main Results:

    • The sequence d(CCGGTACCGG) forms four-stranded Holliday junctions in solution, with formation dependent on DNA and cation concentrations.
    • An equilibrium between junction and duplex forms was observed for d(CCGGTACCGG) at 100-200 microM DNA duplex.
    • The sequence d(CCGCTAGCGG) exclusively adopted a double-helical form under all tested conditions.
    • The ACC trinucleotide core was identified as critical for Holliday junction formation and stability.

    Conclusions:

    • Holliday junction formation is sequence-dependent and occurs in solution, not solely an artifact of crystallization.
    • The ACC trinucleotide core significantly stabilizes Holliday junctions, contributing approximately -4 kcal/mol.
    • These findings have implications for understanding homologous recombination and related cellular processes.