Paper Origami‐Inspired Design and Actuation of DNA Nanomachines with Complex Motions

Abstract

Significant progress in DNA nanotechnology has accelerated development of molecular machines with functions like macroscale machines. However, the mobility of DNA self-assembled nanorobots are still dramatically limited due to challenges with designing and controlling nanoscale systems with many degrees of freedom. Here, an origami-inspired method to design transformable DNA nanomachines is presented. This approach integrates stiff panels formed by bundles of double-stranded DNA (dsDNA) connected with foldable creases formed by single-stranded DNA (ssDNA). To demonstrate the method, we have constructed a DNA version of the paper origami mechanism called a waterbomb base (WBB) consisting of six panels connected by six joints. This nanoscale WBB can follow four distinct This article is protected by copyright. All rights reserved. 2 motion paths to transform between five distinct configurations including a flat square, two triangle, a rectangle, and a fully compacted trapezoidal shape. To achieve this, the sequence specificity of DNA base-pairing is leveraged for the selective actuation of joints and the ionsensitivity of base-stacking interactions is employed for the flattening of joints. In addition, higher-order assembly of DNA waterbomb bases (WBBs) into reconfigurable arrays is achieved. This work establishes a foundation for origami-inspired design for next generation synthetic molecular robots and reconfigurable nanomaterials enabling more complex and controllable motion.

Coarse-grained modelling of the structural properties of DNA origami

“…Our comparison to the 3D origami of (24), together with other recent studies of DNA origami using oxDNA (38,63–65,68,69), confirms the suitability of the oxDNA model for structural characterization of DNA origami. Structures that have been carefully characterised experimentally will give further opportunities to test and refine the structural predictions of the model, while for DNA origami that have only been visualized using low-resolution methods, oxDNA has the potential to provide more detailed structural insights, as has already been done for a number of examples (63,64,68,69). The model could also be used to pre-screen the properties of putative origami designs prior to experimental realization to aid the design process.…”

“…OxDNA has previously been used to characterize a number of specific DNA origami nanostructures with good success (38,63–65,68,69). Here, our aim is to provide a detailed structural analysis of some of the basic features of DNA origami and to test the reliability of the oxDNA model by comparing to the most structurally detailed available experimental data.…”

Programmable low-cost DNA-based platform for viral RNA detection

“…The functionality of our DNA nanoswitches is largely enabled by DNA nanotechnology, which has become a well-established field that uses DNA as a functional material to fabricate nanostructures ( 38 ). Biosensing is a particularly promising application of DNA nanotechnology ( 39 ), and reconfigurable DNA devices ( 40 ) have been demonstrated for the detection of DNA ( 40 ), RNA ( 41 ), proteins ( 42 ), and pH ( 43 ). However, most designs are complex and require laborious readout with advanced microscopy that reduces their practicality.…”

Programmable low-cost DNA-based platform for viral RNA detection

“…The functionality of our DNA nanoswitches is largely enabled by DNA nanotechnology, which has become a well-established field that uses DNA as a functional material to fabricate nanostructures. 43,44 Biosensing is a particularly promising application of DNA nanotechnology, 45 and reconfigurable DNA devices 46 have been demonstrated for the detection of DNA, 46 RNA, 47,48 proteins, 49 and pH. 50 However, most designs are complex and require laborious readout with advanced microscopy that reduces their practicality.…”