Direct Observation of the Formation and Dissociation of Double-Stranded DNA Containing G-Quadruplex/i-Motif Sequences in the DNA Origami Frame Using High-Speed AFM

Abstract

We demonstrate the single-molecule operation and observation of the formation and resolution of double-stranded DNA (dsDNA) containing G-quadruplex (GQ)- and counterpart i-motif-forming sequences 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 the 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 under acidic conditions. The dissociation of the dsDNA under the GQ and i-motif formation conditions 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.