Pseudorotaxane formation via the slippage process with chemically cyclized oligonucleotides

Nucleic Acids Res. 2017 May 19;45(9):5036-5047. doi: 10.1093/nar/gkx265.


Circular nucleic acids have been utilized for versatile applications by taking advantage of the unique characteristic of their circular structure. In our previous study, we found that the chemically-cyclized ODN (cyODN) with double-tailed parts formed a pseudorotaxane structure with the target via the slippage process. We now report the investigation of the slippage properties and the mechanism of the slippage process using six different cyODNs. Our results indicate that the formation efficiency significantly depend on the temperature, the ring size, the target length and the mismatched position of the target. The kinetic studies also showed that this pseudorotaxane formation would proceed via a non-threaded structure which hybridizes with the target at the double-tailed parts. In addition, the resulting pseudorotaxanes showed interesting characteristics unlike the canonical duplex such as the hysteresis loop in the Tm measurements and the kinetic stabilization by lengthening the target. This information will be fundamentally important for finding new functions of circular nucleic acids and elucidating the threading mechanism regarding other synthetic small molecules and biopolymers.

MeSH terms

  • Nucleic Acid Conformation
  • Oligonucleotides / chemistry*
  • Rotaxanes / chemical synthesis*


  • Oligonucleotides
  • Rotaxanes