I‑Motif-Programmed Functionalization of DNA Nanocircles

Abstract

The folding of various intra- and intermolecular i-motif DNAs is systematically studied to expand the toolbox for the control of mechanical operations in DNA nanoarchitectures. We analyzed i-motif DNAs with two C-tracts under acidic conditions by gel electrophoresis, circular dichroism, and thermal denaturation and show that their intra- versus intermolecular folding primarily depends on the length of the C-tracts. Two stretches of six or fewer C-residues favor the intermolecular folding of i-motifs, whereas longer C-tracts promote the formation of intramolecular i-motif structures with unusually high thermal stability. We then introduced intra- and intermolecular i-motifs formed by DNAs containing two C-tracts into single-stranded regions within otherwise double-stranded DNA nanocircles. By adjusting the length of C-tracts we can control the intra- and intermolecular folding of i-motif DNAs and achieve programmable functionalization of dsDNA nanocircles. Single-stranded gaps in the nanocircle that are functionalized with an intramolecular i-motif enable the reversible contraction and extension of the DNA circle, as monitored by fluorescence quenching. Thereby, the nanocircle behaves as a proton-fueled DNA prototype machine. In contrast, nanorings containing intermolecular i-motifs induce the assembly of defined multicomponent DNA architectures in response to proton-triggered predicted structural changes, such as dimerization, “kiss”, and cyclization. The resulting DNA nanostructures are verified by gel electrophoresis and visualized by atomic force microscopy, including different folding topologies of an intermolecular i-motif. The i-motif-functionalized DNA nanocircles may serve as a versatile tool for the formation of larger interlocked dsDNA nanostructures, like rotaxanes and catenanes, to achieve diverse mechanical operations