Mismatch repair factor MSH2-MSH3 binds and alters the conformation of branched DNA structures predicted to form during genetic recombination

J Mol Biol. 2006 Jul 14;360(3):523-36. doi: 10.1016/j.jmb.2006.05.032. Epub 2006 Jun 5.


Genetic studies in Saccharomyces cerevisiae predict that the mismatch repair (MMR) factor MSH2-MSH3 binds and stabilizes branched recombination intermediates that form during single strand annealing and gene conversion. To test this model, we constructed a series of DNA substrates that are predicted to form during these recombination events. We show in an electrophoretic mobility shift assay that S. cerevisiae MSH2-MSH3 specifically binds branched DNA substrates containing 3' single-stranded DNA and that ATP stimulates its release from these substrates. Chemical footprinting analyses indicate that MSH2-MSH3 specifically binds at the double-strand/single-strand junction of branched substrates, alters its conformation and opens up the junction. Therefore, MSH2-MSH3 binding to its substrates creates a unique nucleoprotein structure that may signal downstream steps in repair that include interactions with MMR and nucleotide excision repair factors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Base Sequence
  • DNA Repair / genetics*
  • DNA, Fungal / chemistry*
  • DNA, Fungal / genetics
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / metabolism
  • DNA-Binding Proteins / metabolism*
  • Fungal Proteins / metabolism*
  • Molecular Sequence Data
  • MutS Homolog 2 Protein / metabolism*
  • Nucleic Acid Conformation*
  • Protein Binding
  • Recombination, Genetic*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Substrate Specificity


  • DNA, Fungal
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • Fungal Proteins
  • Saccharomyces cerevisiae Proteins
  • Adenosine Triphosphate
  • MSH2 protein, S cerevisiae
  • MutS Homolog 2 Protein