Periodic Reporting for period 1 - DNAMAKER (Molecular additive manufacturing through DNA nanotechnology)
Reporting period: 2019-10-01 to 2021-09-30
Today, objects and materials that are manipulated on the nano-scale form essential parts of our everyday life. One important example is electronics, powered by computer chips with miniscule features. Several techniques exist for manufacturing of such materials, most of which rely on top-down approaches. These techniques require careful control of clean-room conditions and are expensive and complicated to implement. In contrast, nature uses bottoms-up approaches to construct atomically precise materials like proteins with a low energy expenditure and extreme speed and precision. Drawing inspiration from the bottoms-up approaches found in nature, DNA nanotechnology use carefully programmed DNA strands to self-assemble complex structures and machines on the nanometre scale. In this project, we aimed at using DNA nanotechnology to produce tiny motors called linear actuators. The plan was to use external control strands to drive the position of the motors and then utilize the motors for nanoscale patterning through the addition of a write-head function.
We found that DNA nanotechnology, specifically through the technique DNA origami could create linear actuators through creating a two-component DNA origami structure consisting of a linear rail and a topologically locked slider structure. The slider was capable of diffusing freely along the rail, and when control strands were added, we could lock it at a programmed position. Importantly, this locking was reversible through the addition of invader strands releasing the slider to diffuse freely again along the rail. We were also able to connect multiple slider devices together to create a 2D gantry where a slider could be positioned in two dimensions over a surface. Finally, we were able to use the slider in the 2D gantry to pattern a canvas at programmed positions.
We found that DNA nanotechnology, specifically through the technique DNA origami could create linear actuators through creating a two-component DNA origami structure consisting of a linear rail and a topologically locked slider structure. The slider was capable of diffusing freely along the rail, and when control strands were added, we could lock it at a programmed position. Importantly, this locking was reversible through the addition of invader strands releasing the slider to diffuse freely again along the rail. We were also able to connect multiple slider devices together to create a 2D gantry where a slider could be positioned in two dimensions over a surface. Finally, we were able to use the slider in the 2D gantry to pattern a canvas at programmed positions.
We designed a linear actuator from a single DNA origami scaffold. In this design, both slider and rail were created from the same scaffold strand. The slider was designed to fold around the rail and we used the fact that the scaffold strand of natural origin feature sequences recognised by restriction enzymes to distribute the scaffold into a large region creating the rail and a small region creating the slider. After assembly, these were cut apart by the introduction of the restriction enzyme to allow the slider to move freely on the rail. We then used transmission electron microscopy (TEM) and DNA-PAINT super resolution microscopy to study the free diffusion of the slider on the rail. We then designed a track of unique address strands on the rail and two unique address strands protruding from slider. When we wanted to control the position of the slider we added linking strands that were partially complementary to the an address strand on the track and partially complementary to an address strand on the rail. This locked the freely diffusing slider in place on the rail, and we also found that this locking was reversible through the introduction of a toehold exchange invader strand. The result of this work was published in the journal small in 2021. Moving beyond this, we combined multiple such linear positioning elements to create a 2D gantry with two separate axes that are independently controllable with a address strand scheme similar to what we demonstrated in one dimension. Using this, we were able to reversibly control the position of the slider in two dimensions over the surface. Finally, we functionalized the bottom of the slider with a toehold catalyst to make it function as a write head. This writ head was capable of interaction with an array of ‘pixels’ on a target canvas an specifically pattern the canvas when it was in a correct position.
The main progresses beyond the state of the art begin with the design scheme used in the linear actuator. It was designed in a novel way where both components needed to create the rotaxane was constructed from the same scaffold but then separated using restriction enzymes after assembly. Secondly, our coupling of multiple linear positioning elements to create a 2D gantry is the first demonstration that independent DNA origami motors can be combined and independently controlled. It is also the first demonstration of programmed 2D motion in a DNA origami device. Finally, our patterning method is the first of its kind implemented in a DNA origami device. We believe that these types devices may form a new route to nanoscale manufacture that is cheaper, more scalable and more environmentally friendly than current techniques. We believe it could find applications in nanoscale surface manufacturing, templated chemistry and biophysical studies.