Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions

Arivazhagan Rajendran, Kirankumar Krishnamurthy, Seojeong Park, Eiji Nakata, Youngjoo Kwon, Takashi Morii

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.

Original languageEnglish
Article numbere202200108
JournalChemistry - A European Journal
Issue number22
StatePublished - 19 Apr 2022

Bibliographical note

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© 2022 Wiley-VCH GmbH.


  • DNA catenane
  • DNA origami
  • DNA rotaxane
  • DNA-protein interactions
  • restriction reactions


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