DNA origami based visualization system for studying site-specific recombination events

Yuki Suzuki, Masayuki Endo, Yousuke Katsuda, Keiyu Ou, Kumi Hidaka, Hiroshi Sugiyama

Research output: Contribution to journalArticlepeer-review

50 Citations (Scopus)


Site-specific recombination involves reciprocal exchange between defined DNA sites. The reaction initiates from the formation of a recombinase-DNA synaptic complex, in which two recombination sites arrange in an appropriate configuration. However, there is incomplete information about how the topological state of the substrate influences the synapsis and outcome of the reaction. Here, we show that Cre-mediated recombination can be regulated by controlling the orientation and topology of the loxP substrate in a DNA frame nanoscaffold. High-speed atomic force microscopy analyses revealed that the loxP-containing substrate strands in the antiparallel orientation can be recombined only through formation of synaptic complexes. By tethering Holliday junction (HJ) intermediates to DNA frames in different connection patterns and using them as a starting substrate, we found that the topological state of the HJ intermediates dictates the outcome of the resolution. Our approach should provide a new platform for structural-functional studies of various DNA targeting enzymes, especially which require formation of synaptic complexes.

Original languageEnglish
Pages (from-to)211-218
Number of pages8
JournalJournal of the American Chemical Society
Issue number1
Publication statusPublished - 2014 Jan 8
Externally publishedYes

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry


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