Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure

Yosuke Takeuchi, Masayuki Endo, Yuki Suzuki, Kumi Hidaka, Guillaume Durand, Eric Dausse, Jean Jacques Toulmé, Hiroshi Sugiyama

Research output: Contribution to journalArticlepeer-review

20 Citations (Scopus)


RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.

Original languageEnglish
Pages (from-to)130-135
Number of pages6
JournalBiomaterials Science
Issue number1
Publication statusPublished - 2016 Jan
Externally publishedYes

ASJC Scopus subject areas

  • Biomedical Engineering
  • Materials Science(all)


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