Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase

Hua Bai, Mingxuan Sun, Pallavi Ghosh, Graham F. Hatfull, Nigel D.F. Grindley, John F. Marko

Research output: Contribution to journalArticlepeer-review

51 Scopus citations


Structural and topological data suggest that serine site-specific DNA recombinases exchange duplex DNAs by rigid-body relative rotation of the two halves of the synapse, mediated by a flat protein-protein interaction surface. We present evidence for this rotational motion for a simple serine recombinase, the Bxb1 phage integrase, from a single-DNA-based supercoil-release assay that allows us to follow crossover site cleavage, rotation, religation, and product release in real time. We have also used a two-DNA braiding-relaxation experiment to observe the effect of synapse rotation in reactions on two long molecules. Relaxation and unbraiding are rapid (averaging 54 and 70 turns/s, respectively) and complete, with no discernible pauses. Nevertheless, the molecular friction associated with rotation is larger than that of type-I topoisomerases in a similar assay. Surprisingly we find that the synapse can stay rotationally "open" for many minutes.

Original languageEnglish (US)
Pages (from-to)7419-7424
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number18
StatePublished - May 3 2011


  • DNA topology
  • Protein-DNA interactions
  • Single-DNA biophysics
  • Site-specific recombination

ASJC Scopus subject areas

  • General


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