DNA topology and geometry in Flp and Cre recombination

Alexandre A. Vetcher, Alexander Y. Lushnikov, Junalyn Navarra-Madsen, Robert G. Scharein, Yuri L Lyubchenko, Isabel K. Darcy, Stephen D. Levene

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

The Flp recombinase of yeast and the Cre recombinase of bacteriophage P1 both belong to the λ-integrase (Int) family of site-specific recombinases. These recombination systems recognize recombination-target sequences that consist of two 13 bp inverted repeats flanking a 6 or 8 bp 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.

Original languageEnglish (US)
Pages (from-to)1089-1104
Number of pages16
JournalJournal of Molecular Biology
Volume357
Issue number4
DOIs
StatePublished - Apr 7 2006

Fingerprint

Genetic Recombination
DNA
Cruciform DNA
Plasmids
Chromosome Pairing
Integrases
Circular DNA
Recombinases
Nucleoproteins
Mathematics
Atomic Force Microscopy
Yeasts

Keywords

  • DNA looping
  • DNA topology
  • Protein-DNA interactions
  • Site-specific recombination
  • Tangle analysis

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Vetcher, A. A., Lushnikov, A. Y., Navarra-Madsen, J., Scharein, R. G., Lyubchenko, Y. L., Darcy, I. K., & Levene, S. D. (2006). DNA topology and geometry in Flp and Cre recombination. Journal of Molecular Biology, 357(4), 1089-1104. https://doi.org/10.1016/j.jmb.2006.01.037

DNA topology and geometry in Flp and Cre recombination. / Vetcher, Alexandre A.; Lushnikov, Alexander Y.; Navarra-Madsen, Junalyn; Scharein, Robert G.; Lyubchenko, Yuri L; Darcy, Isabel K.; Levene, Stephen D.

In: Journal of Molecular Biology, Vol. 357, No. 4, 07.04.2006, p. 1089-1104.

Research output: Contribution to journalArticle

Vetcher, AA, Lushnikov, AY, Navarra-Madsen, J, Scharein, RG, Lyubchenko, YL, Darcy, IK & Levene, SD 2006, 'DNA topology and geometry in Flp and Cre recombination', Journal of Molecular Biology, vol. 357, no. 4, pp. 1089-1104. https://doi.org/10.1016/j.jmb.2006.01.037
Vetcher AA, Lushnikov AY, Navarra-Madsen J, Scharein RG, Lyubchenko YL, Darcy IK et al. DNA topology and geometry in Flp and Cre recombination. Journal of Molecular Biology. 2006 Apr 7;357(4):1089-1104. https://doi.org/10.1016/j.jmb.2006.01.037
Vetcher, Alexandre A. ; Lushnikov, Alexander Y. ; Navarra-Madsen, Junalyn ; Scharein, Robert G. ; Lyubchenko, Yuri L ; Darcy, Isabel K. ; Levene, Stephen D. / DNA topology and geometry in Flp and Cre recombination. In: Journal of Molecular Biology. 2006 ; Vol. 357, No. 4. pp. 1089-1104.
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