Strategies for Constructing and Operating DNA Origami Linear Actuators

Abstract

Linear actuators are ubiquitous components at all scales of engineering. DNA nanotechnology offers a unique opportunity for bottom‐up assembly at the molecular scale, providing nanoscale precision with multiple methods for constructing and operating devices. In this paper, DNA origami linear actuators with up to 200 nm travel, based on a rail threading a topologically locked slider, are demonstrated. Two strategies, one‐ and two‐pot assembly, are demonstrated whereby the two components are folded from one or two DNA scaffold strands, respectively. In order to control the position of the slider on the rail, the rail and the inside of the slider are decorated with single‐stranded oligonucleotides with distinct sequences. Two positioning strategies, based on diffusion and capture of signaling strands, are used to link the slider reversibly to determined positions on the rail with high yield and precision. These machine components provide a basis for applications in molecular machinery and nanoscale manufacture including programmed chemical synthesis.

Molecular Cybernetics: Challenges toward Cellular Chemical Artificial Intelligence

“…Several systems with other modes of motion have been reported. [156][157][158][159] Ketterer et al [156] and Kopperger et al [157] independently developed sophisticated rotary systems for rotary DNA origami devices by assembling multiple origami units or simply from a single unit, respectively. In contrast, Benson et al [158] developed a linear actuation system by applying ≈200 nm long DNA origami rotaxane structure.…”

“…[156][157][158][159] Ketterer et al [156] and Kopperger et al [157] independently developed sophisticated rotary systems for rotary DNA origami devices by assembling multiple origami units or simply from a single unit, respectively. In contrast, Benson et al [158] developed a linear actuation system by applying ≈200 nm long DNA origami rotaxane structure. Stömmer et al [159] also prepared a linear DNA origami actuation system by trapping a piston in a long DNA origami tube, which successfully realized linear transport up to 3 µm in length.…”

A DNA molecular printer capable of programmable positioning and patterning in two dimensions

“…Specifically, DNA origami, where a long DNA strand of (usually) biological origin is folded by hybridization to hundreds of short, synthetic oligonucleotides, can be used to create complex nanoscale objects with high resolution and yield (7). The origami technique has been used to produce a number of mechanical modules: mechanically interlocked slider rails (8)(9)(10)(11), rotary arms (12,13), hinges (14), and closable containers (15). DNA nanostructures have been engineered to respond to external stimuli including signaling oligonucleotides by means of strand-exchange reactions (15,16); light (17), electric (12), and magnetic fields (18); changes in chemical environment (19,20); and the specific binding of target molecules (21,22).…”

DNA Origami‐Based Protein Manipulation Systems: From Function Regulation to Biological Application

“…[17] DNA origami, usually prepared from a long scaffold single strand of 7000-8000 nucleotides matched with dozens of short staple strands, is able to fabricate complex architectures with nanoscale precision. [18][19][20] On account of programmability and addressability of DNA molecules, proteins could be immobilize at the predefined sites of DNA origami template with accurately directed angle. With the advance of DNA nanotechnology, the template of DNA origami-based protein manipulation systems (PMSs) gradually evolved from simple two-dimensional (2D) plane to complex three-dimensional (3D) manipulation nanoplatform, as well as the functions progressed from monomer protein cognition to multi-protein regulation, tackling the difficulty in investigating and managing complex physiological responses.…”

“…DNA origami, usually prepared from a long scaffold single strand of 7000–8000 nucleotides matched with dozens of short staple strands, is able to fabricate complex architectures with nanoscale precision [18–20] . On account of programmability and addressability of DNA molecules, proteins could be immobilize at the predefined sites of DNA origami template with accurately directed angle.…”