Powered motion for molecular robotic devices via chemical and photochemical reactions

Industrial production necessitates ever smaller parts requiring new, more precise manufacturing techniques. Multiple approaches are being researched and tested to reach the goal of Atomically Precise Manufacturing (APM), including Molecular Additive Manufacturing (MAM). The core concept of MAM relies on the build-up, atom by atom, molecule by molecule, of a material or component. The framework necessary for the controlled positioning of these elements needs to have great precision and may be as complex to develop as the product itself.
The robustness and ease of use provided by the DNA origami self-assembly technique can be used as a means for the design and production of these smart material synthesizers. As I will explore in this thesis, the development of such synthesizer requires exploration of different methods of actuation. I will present the development of a device based on a 2D printer capable of traversing a flat substrate on request via the introduction of commands.
Initially I work to develop a dynamic, 3D, DNA origami system capable of linear actuation, that is, 1-dimensional movement. I base its architecture on the rotaxane given its structural particularities, mechanically locked but freely diffusing components. I improve the production of this system through different iterations, originally based on existing examples in the literature before moving onto more original designs that suit better the intended scope of the project. Throughout, protocols of synthesis were tested and improved upon to reduce the amount of time necessary for the assembly of the whole system. I also explore in these initial steps the method of actuating the movement of the slider along the rail, particularly the presence of overhang sequences that interact with the sequences in the slider oligonucleotides. This depends mostly on a “chemical” actuation dependent on the introduction of specific staples that force the detachment / attachment cycle of the slider necessary to produce diffusive motion between two points in the rail via strand displacement reactions (SDRs). The structures and their effective actuation are characterized via agarose gels, TEM, and DNA-PAINT.
As the work progresses, the following step is to obtain motion in 2 dimensions so that a surface area can be covered. To achieve this I developed a polar positioning device reminiscent of a circle quadrant, with a radial arm able to move along the arc while pivoting from the centre of the circle. This arm, like that of an analogue clock, is in turn a rotaxane, with a slider moving up and down its length. That way I obtain a polar system of 2-dimensional motion that covers the area encompassed by one quarter of the circle.
Later in the thesis I explore an alternative method for driving motion of a DNA device by using a photochrome, azobenzene, to induce double-stranded DNA (dsDNA) to dissociate into individual strands by shining UV light onto the modified complexes. The actual versatility and feasibility of the photoactuation is tested in two different prototype systems, a tweezer, and an array of dsDNAs.

Keywords: DNA nanotechnology
DNA origami
dynamic structures
photochemistry
Advisor: Turberfield, A