Single-Molecule Manipulation of the Duplex Formation and Dissociation at the G-Quadruplex/i-Motif Site in the DNA Nanostructure

ACS Nano. 2015 Oct 27;9(10):9922-9. doi: 10.1021/acsnano.5b03413. Epub 2015 Sep 24.


We demonstrate the single-molecule operation and observation of the formation and resolution of double-stranded DNA (dsDNA) containing a G-quadruplex (GQ) forming and counterpart i-motif forming sequence in the DNA nanostructure. Sequential manipulation of DNA strands in the DNA frame was performed to prepare a topologically controlled GQ/i-motif dsDNA. Using strand displacement and the addition and removal of K(+), the topologically controlled GQ/i-motif dsDNA in the DNA frame was obtained in high yield. The dsDNA was resolved into the single-stranded DNA, GQ, and i-motif by the addition of K(+) and operation in acidic conditions. The dissociation of the dsDNA under the GQ and i-motif formation condition was monitored by high-speed atomic force microscopy. The results indicate that the dsDNA containing the GQ- and i-motif sequence is effectively dissolved when the duplex is helically loosened in the DNA nanoscaffold.

Keywords: DNA origami; G-quadruplex; high-speed AFM; i-motif; single-molecule observation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA / chemistry*
  • DNA, Single-Stranded / chemistry*
  • G-Quadruplexes*
  • Microscopy, Atomic Force
  • Nanostructures / chemistry*
  • Nanostructures / ultrastructure
  • Nanotechnology
  • Potassium / chemistry*


  • DNA, Single-Stranded
  • DNA
  • Potassium