DNA-sequence asymmetry directs the alignment of recombination sites in the FLP synaptic complex

J Mol Biol. 1999 Feb 12;286(1):1-13. doi: 10.1006/jmbi.1998.2468.


The FLP recombinase promotes site-specific recombination in the 2 micrometer circle of Saccharomyces cerevisiae. FLP recognizes a 48 bp target site (FLP recombination target, or FRT) consisting of three 13 bp protein binding sites, or symmetry elements, flanking an 8 bp spacer region. Efficient recombination also occurs with DNA substrates that have minimal FRT sites, consisting only of the spacer and two surrounding 13 bp symmetry elements arranged in inverse orientation; thus, the wild-type spacer sequence is the main asymmetric feature of the minimal recombination site. FLP carries out recombination with many minimal target sites bearing symmetric or asymmetric mutant spacer sequences; however, the overall directionality of recombination defined in terms of inversion or excision of a DNA domain is determined by spacer-sequence asymmetry. In order to evaluate the potential influence of spacer-sequence asymmetry on structures formed during early steps in recombination, we used electron microscopy to investigate the structure of the FLP synaptic complex, which is the intermediate protein-DNA complex involved in site pairing and strand exchange. Using linear substrate DNAs that have minimal FRTs with wild-type spacer sequences, we find that 85 to 90% of the FLP synaptic complexes examined contain the two FRTs aligned in parallel. This strong preference for parallel site alignment stands in contrast with prevailing models for lambda integrase-class recombination systems, which postulate antiparallel site alignment, and results from biophysical studies on synthetic, immobile four-way DNA junctions. Our results show that the strong preference for parallel alignment can be attributed to conformational preferences of Holliday junctions present in the synaptosome.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • DNA Nucleotidyltransferases / chemistry*
  • DNA Nucleotidyltransferases / metabolism
  • DNA Nucleotidyltransferases / ultrastructure
  • DNA, Fungal / chemistry*
  • DNA, Fungal / metabolism
  • DNA, Fungal / ultrastructure
  • Fungal Proteins / chemistry
  • Fungal Proteins / metabolism
  • Nucleic Acid Conformation
  • Protein Conformation
  • Recombination, Genetic*
  • Saccharomyces cerevisiae


  • DNA, Fungal
  • Fungal Proteins
  • DNA Nucleotidyltransferases
  • FLP recombinase