DNA topology and geometry in Flp and Cre recombination

J Mol Biol. 2006 Apr 7;357(4):1089-104. doi: 10.1016/j.jmb.2006.01.037. Epub 2006 Jan 30.


The Flp recombinase of yeast and the Cre recombinase of bacteriophage P1 both belong to the lambda-integrase (Int) family of site-specific recombinases. These recombination systems recognize recombination-target sequences that consist of two 13bp inverted repeats flanking a 6 or 8bp spacer sequence. Recombination reactions involve particular geometric and topological relationships between DNA target sites at synapsis, which we investigate using nicked-circular DNA molecules. Examination of the tertiary structure of synaptic complexes formed on nicked plasmid DNAs by atomic-force microscopy, in conjunction with detailed topological analysis using the mathematics of tangles, shows that only a limited number of recombination-site topologies are consistent with the global structures of plasmids bearing directly and inversely repeated sites. The tangle solutions imply that there is significant distortion of the Holliday-junction intermediate relative to the planar structure of the four-way DNA junction present in the Flp and Cre co-crystal structures. Based on simulations of nucleoprotein structures that connect the two-dimensional tangle solutions with three-dimensional models of the complexes, we propose a recombination mechanism in which the synaptic intermediate is characterized by a non-planar, possibly near-tetrahedral, Holliday-junction intermediate. Only modest conformational changes within this structure are needed to form the symmetric, planar DNA junction, which may be characteristic of shorter-lived intermediates along the recombination pathway.

Publication types

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

MeSH terms

  • Base Sequence
  • DNA / chemistry*
  • DNA Nucleotidyltransferases / chemistry*
  • DNA Nucleotidyltransferases / metabolism
  • Integrases / chemistry*
  • Integrases / metabolism
  • Macromolecular Substances
  • Mathematics
  • Microscopy, Atomic Force
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Plasmids / genetics
  • Protein Conformation
  • Recombination, Genetic
  • Viral Proteins / chemistry*
  • Viral Proteins / metabolism


  • Macromolecular Substances
  • Viral Proteins
  • DNA
  • Cre recombinase
  • DNA Nucleotidyltransferases
  • FLP recombinase
  • Integrases