Interconverting conformations of slipped-DNA junctions formed by trinucleotide repeats affect repair outcome

Biochemistry. 2013 Feb 5;52(5):773-85. doi: 10.1021/bi301369b. Epub 2013 Jan 22.


Expansions of (CTG)·(CAG) repeated DNAs are the mutagenic cause of 14 neurological diseases, likely arising through the formation and processing of slipped-strand DNAs. These transient intermediates of repeat length mutations are formed by out-of-register mispairing of repeat units on complementary strands. The three-way slipped-DNA junction, at which the excess repeats slip out from the duplex, is a poorly understood feature common to these mutagenic intermediates. Here, we reveal that slipped junctions can assume a surprising number of interconverting conformations where the strand opposite the slip-out either is fully base paired or has one or two unpaired nucleotides. These unpaired nucleotides can also arise opposite either of the nonslipped junction arms. Junction conformation can affect binding by various structure-specific DNA repair proteins and can also alter correct nick-directed repair levels. Junctions that have the potential to contain unpaired nucleotides are repaired with a significantly higher efficiency than constrained fully paired junctions. Surprisingly, certain junction conformations are aberrantly repaired to expansion mutations: misdirection of repair to the non-nicked strand opposite the slip-out leads to integration of the excess slipped-out repeats rather than their excision. Thus, slipped-junction structure can determine whether repair attempts lead to correction or expansion mutations.

Publication types

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

MeSH terms

  • Base Pairing
  • Base Sequence
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism*
  • DNA Repair*
  • DNA-Binding Proteins / metabolism
  • Endonucleases / metabolism
  • HMGB1 Protein / metabolism
  • HeLa Cells
  • Humans
  • Molecular Sequence Data
  • MutS DNA Mismatch-Binding Protein / metabolism
  • Nuclear Proteins / metabolism
  • Nucleic Acid Conformation
  • Oligonucleotides / chemistry
  • Oligonucleotides / genetics
  • Oligonucleotides / metabolism
  • Protein Binding
  • Transcription Factors / metabolism
  • Trinucleotide Repeats*


  • DNA excision repair protein ERCC-5
  • DNA-Binding Proteins
  • HMGB1 Protein
  • Nuclear Proteins
  • Oligonucleotides
  • Transcription Factors
  • xeroderma pigmentosum group F protein
  • DNA
  • ERCC1 protein, human
  • Endonucleases
  • MutS DNA Mismatch-Binding Protein