Folding and cutting DNA into reconfigurable topological nanostructures

Abstract

Topology is the mathematical study of the spatial properties that are preserved through the deformation, twisting and stretching of objects. Topological architectures are common in nature and can be seen, for example, in DNA molecules that condense and relax during cellular events. Synthetic topological nanostructures, such as catenanes and rotaxanes, have been engineered using supramolecular chemistry, but the fabrication of complex and reconfigurable structures remains challenging. Here, we show that DNA origami can be used to assemble a Möbius strip, a topological ribbon-like structure that has only one side. In addition, we show that the DNA Möbius strip can be reconfigured through strand displacement to create topological objects such as supercoiled ring and catenane structures. This DNA fold-and-cut strategy, analogous to Japanese kirigami, may be used to create and reconfigure programmable topological structures that are unprecedented in molecular engineering.

Figure 1. Design of a Möbius DNA strip

a, Three-dimensional illustration of the Möbius DNA strip. Each coloured band represents a different DNA double helix. b, A fraction of the Möbius strip in a is illustrated in the DNA helical model. The whole Möbius strip is composed of 20.5 of these units. c, Generalized folding path of a unit in the Möbius strip with the scaffold strand (blue) running through the entire structure and staple strands (black) helping to fold it into the designed structure. d, Design used in the experiment for one of the 20 units. The scaffold strand crosses over between helices 3 and 4. e, DNA helical strand model for the unit shown in d.

Figure 2. Visualization of the Möbius DNA strips with AFM and TEM imaging

a,b, Zoom-out and zoom-in AFM images of the Möbius DNA strip. c,TEM images of the Möbius DNA strip negatively stained with uranyl formate. The two images on the left have a right-handed chirality, and the two images on the right have a left-handed chirality. d, AFM amplitude images with the tip scanning in trace and retrace directions indicating the co-existence of both left-handed and right-handed chiral structures in the sample. Schematics are shown to illustrate the chirality of the Möbius strip.

Figure 3. DNA kirigami to achieve reconfigurable topologies from the Möbius strip

a–d, DNA kirigami-ring structure: design schematics (a,b), AFM height images (c)and TEMimages (d). e–h, The DNA kirigami-catenane structure: design schematics (e,f), AFM height (g, upper panels) and amplitude (g, lower panels) images, and TEM images (h).