Partial reconstitution of DNA large loop repair with purified proteins from Saccharomyces cerevisiae

Nucleic Acids Res. 2008 Aug;36(14):4699-707. doi: 10.1093/nar/gkn446. Epub 2008 Jul 15.


Small looped mispairs are corrected by DNA mismatch repair. In addition, a distinct process called large loop repair (LLR) corrects heteroduplexes up to several hundred nucleotides in bacteria, yeast and human cells, and in cell-free extracts. Only some LLR protein components are known, however. Previous studies with neutralizing antibodies suggested a role for yeast DNA polymerase delta (Pol delta), RFC and PCNA in LLR repair synthesis. In the current study, biochemical fractionation studies identified FEN1 (Rad27) as another required LLR component. In the presence of purified FEN1, Pol delta, RFC and PCNA, repair occurred on heteroduplexes with loops ranging from 8 to 216 nt. Repair utilized a 5' nick, with correction directed to the nicked strand, irrespective of which strand contained the loop. In contrast, repair of a G/T mismatch occurred at low levels, suggesting specificity of the reconstituted system for looped mispairs. The presence of RPA enhanced reactivity on some looped substrates, but RPA was not required for activity. Although additional LLR factors remain to be identified, the excision and resynthesis steps of LLR from a 5' nick can be reconstituted in a purified system with FEN1 and Pol delta, together with PCNA and its loader RFC.

Publication types

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

MeSH terms

  • Cell Extracts
  • Cell Nucleus / metabolism
  • DNA Polymerase III / metabolism
  • DNA Repair*
  • Flap Endonucleases / analysis
  • Flap Endonucleases / isolation & purification
  • Flap Endonucleases / metabolism*
  • Nucleic Acid Heteroduplexes / metabolism
  • Proliferating Cell Nuclear Antigen / metabolism
  • Replication Protein C / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / analysis
  • Saccharomyces cerevisiae Proteins / isolation & purification
  • Saccharomyces cerevisiae Proteins / metabolism*


  • Cell Extracts
  • Nucleic Acid Heteroduplexes
  • Proliferating Cell Nuclear Antigen
  • Saccharomyces cerevisiae Proteins
  • DNA Polymerase III
  • Flap Endonucleases
  • RAD27 protein, S cerevisiae
  • Replication Protein C