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.
DNA origami linear actuators are promising components of nanoscale machinery but remain difficult to assemble and control. This paper explores different routes for assembly and control, achieving a high device yield and reversible actuator positioning. Simulation shows that these devices are capable of few‐nanometer precision, opening up potential uses in molecular machinery and nanoscale manufacture.
Cancer is one of the main causes of death around the world, lacking efficient clinical treatments that generally present severe side effects. In recent years, various nanosystems have been explored ...to specifically target tumor tissues, enhancing the efficacy of cancer treatment and minimizing the side effects. In particular, bladder cancer is the ninth most common cancer worldwide and presents a high survival rate but serious recurrence levels, demanding an improvement in the existent therapies. Here, we present urease-powered nanomotors based on mesoporous silica nanoparticles that contain both polyethylene glycol and anti-FGFR3 antibody on their outer surface to target bladder cancer cells in the form of 3D spheroids. The autonomous motion is promoted by urea, which acts as fuel and is inherently present at high concentrations in the bladder. Antibody-modified nanomotors were able to swim in both simulated and real urine, showing a substrate-dependent enhanced diffusion. The internalization efficiency of the antibody-modified nanomotors into the spheroids in the presence of urea was significantly higher compared with antibody-modified passive particles or bare nanomotors. Furthermore, targeted nanomotors resulted in a higher suppression of spheroid proliferation compared with bare nanomotors, which could arise from the local ammonia production and the therapeutic effect of anti-FGFR3. These results hold significant potential for the development of improved targeted cancer therapy and diagnostics using biocompatible nanomotors.
The smallest grammar problem—namely, finding a smallest context-free grammar that generates exactly one sequence—is of practical and theoretical importance in fields such as Kolmogorov complexity, ...data compression and pattern discovery. We propose a new perspective on this problem by splitting it into two tasks: (1) choosing which words will be the constituents of the grammar and (2) searching for the smallest grammar given this set of constituents. We show how to solve the second task in polynomial time parsing longer constituent with smaller ones. We propose new algorithms based on classical practical algorithms that use this optimization to find small grammars. Our algorithms consistently find smaller grammars on a classical benchmark reducing the size in 10% in some cases. Moreover, our formulation allows us to define interesting bounds on the number of small grammars and to empirically compare different grammars of small size.
Nanoscale manipulation and patterning usually require costly and sensitive top-down techniques such as those used in scanning probe microscopies or in semiconductor lithography. DNA nanotechnology ...enables exploration of bottom-up fabrication and has previously been used to design self-assembling components capable of linear and rotary motion. In this work, we combine three independently controllable DNA origami linear actuators to create a nanoscale robotic printer. The two-axis positioning mechanism comprises a moveable gantry, running on parallel rails, threading a mobile sleeve. We show that the device is capable of reversibly positioning a write head over a canvas through the addition of signaling oligonucleotides. We demonstrate "write" functionality by using the head to catalyze a local DNA strand-exchange reaction, selectively modifying pixels on a canvas. This work demonstrates the power of DNA nanotechnology for creating nanoscale robotic components and could find application in surface manufacturing, biophysical studies, and templated chemistry.
Automated Machine Learning (AutoML) has become increasingly popular in recent years due to its ability to reduce the amount of time and expertise required to design and develop machine learning ...systems. This is very important for the practice of machine learning, as it allows building strong baselines quickly, improving the efficiency of the data scientists, and reducing the time to production. However, despite the advantages of AutoML, it faces several challenges, such as defining the solutions space and exploring it efficiently. Recently, some approaches have been shown to be able to do it using tree-based search algorithms and context-free grammars. In particular, GramML presents a model-free reinforcement learning approach that leverages pipeline configuration grammars and operates using Monte Carlo tree search. However, one of the limitations of GramML is that it uses default hyperparameters, limiting the search problem to finding optimal pipeline structures for the available data preprocessors and models. In this work, we propose an extension to GramML that supports larger search spaces including hyperparameter search. We evaluated the approach using an OpenML benchmark and found significant improvements compared to other state-of-the-art techniques.
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.
Motivated by the inference of the structure of genomic sequences, we address here the smallest grammar problem. In previous work, we introduced a new perspective on this problem, splitting the task ...into two different optimization problems: choosing which words will be considered constituents of the final grammar and finding a minimal parsing with these constituents. Here we focus on making these ideas applicable on large sequences. First, we improve the complexity of existing algorithms by using the concept of maximal repeats when choosing which substrings will be the constituents of the grammar. Then, we improve the size of the grammars by cautiously adding a minimal parsing optimization step. Together, these approaches enable us to propose new practical algorithms that return smaller grammars (up to 10%) in approximately the same amount of time than their competitors on a classical set of genomic sequences and on whole genomes of model organisms.
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