DNA Strand Displacement Technology Research Articles

Backstepping synchronization control for four-dimensional chaotic system based on DNA strand displacement

Backstepping control is an important nonlinear control design method, which realizes the control of complex systems by constructing control law step by step, and has significant advantages for dealing with complex nonlinear systems. This article proposes a synchronization technique for four-dimensional chaotic systems using a combination of backstepping control method and DNA strand displacement technology. By relying on theoretical knowledge of DNA molecules, five basic chemical reaction modules such as trigger reaction, reference reaction, catalytic reaction, annihilation reaction and degradation reaction are given to construct a four-dimensional DNA chaotic system. On the basis of the relevant theory of chaotic dynamics, the constructed system is analyzed by Lyapunov exponent diagram and spectral entropy complexity algorithm, and the results come to the conclusion that the system reveals extremely complex and varied dynamic behaviors. Combining DNA strand displacement technology with backstepping control method, four controllers are developed to ensure that the trajectories of two homogeneous chaotic systems are synchronized. The numerical simulation results validate the feasibility and applicability of the proposed method. The method proposed in this paper may provide some references in the field of DNA molecular chaos synchronization control.

Design of Multi-Competitors Winner-Take-All Neural Networks Based on DNA Strand Displacement for Molecular Pattern Recognition

DNA strand displacement technology (DSDT) provides flexible and powerful technical support for DNA molecular computing. DNA-based neural networks with Winner-Take-All (WTA) strategy has a great potential for nonlinear calculation. However, so far it has been limited to achieving the simultaneous competition of two competitors. Optimizing the calculation model and reducing system response time to recognize complex and functional molecular patterns remains a huge challenge. Here a novel neural network with WTA strategy based on DSDT was constructed, which allowed three competitors to participate in the competition at the same time. Firstly, the feasibility of the three-competitor WTA neural network was proved by 9-bit pattern recognition. Then the three-competitors WTA neural network was further extended to larger scale pattern recognition, which successfully recognized 64-bit letters A, B, and C and 100-bit handwritten digits 0, 2, and 4, respectively. Simulations showed that when recognizing the same target patterns with same number bits, compared with two-competitors WTA neural network, the three-competitors WTA network only used down to two-thirds DNA strands, and the system response time was reduced by more than ten times. This paper demonstrated the efficient recognition ability of the three-competitor WTA neural network, which is expected to be used to identify more complex information.

Three-input logic gate based on DNA strand displacement reaction

In this paper, three kinds of three-input logic gates are designed based on DNA strand displacement reaction, which are three-input OR logic gate, three-input AND logic gate, and three-input MAJORITY logic gate. The logic gates designed in this paper takes different DNA strands as input and fluorescence signals as output. The biochemical experimental results verify my designs. The results show that DNA strand displacement technology has important application value in DNA computing, especially in the construction of DNA molecular logic gates.

Massively Parallel DNA Computing Based on Domino DNA Strand Displacement Logic Gates.

DNA computing has gained considerable attention due to the characteristics of high-density information storage and high parallel computing for solving computational problems. Building addressable logic gates with biomolecules is the basis for establishing biological computers. In the current calculation model, the multiinput AND operation often needs to be realized through a multilevel cascade between logic gates. Through experiments, it was found that the multilevel cascade causes signal leakage and affects the stability of the system. Using DNA strand displacement technology, we constructed a domino-like multiinput AND gate computing system instead of a cascade of operations, realizing multiinput AND computing on one logic gate and abandoning the traditional multilevel cascade of operations. Fluorescence experiments demonstrated that our methods significantly reduce system construction costs and improve the stability and robustness of the system. Finally, we proved stability and robustness of the domino AND gate by simulating the tic-tac-toe process with a massively parallel computing strategy.

Molecular Logic Gate Based on DNA Strand Displacement Reaction

In this paper, I construct an XOR logic gate based on DNA strand displacement reaction, and verify our design through corresponding biochemical experiment. I designed several different DNA strands. Based on two basic DNA strand displacement reaction mechanisms, by adding different input strands and taking the signal of FAM fluorescent group as the output, the XOR logic gate is realized. The result shows that DNA strand displacement technology has important application value in DNA computing, especially in the construction of DNA molecular logic gates.

PID Control of Biochemical Reaction Networks

Principles of feedback control have been shown to naturally arise in biological systems and have been applied with success to build synthetic circuits. Here, we present an implementation of a proportional&#x2013;integral&#x2013;derivative (PID) controller as a chemical reaction network with mass-action kinetics. This makes the controller synthesizable <i>in vitro</i> using DNA strand displacement technology, owing to its demonstrated capability of realizing arbitrary reaction-network designs as interacting DNA molecules. Previous related work has studied biological PID architectures using linearizations of nonlinear dynamics arising in both the controller components and in the plant. In this article, we present a proof of correctness of our nonlinear design in closed loop using arguments from singular perturbation theory. As an application to show the effectiveness of our controller, we provide numerical simulations on a genetic model to perform PID feedback control of protein expression.

Double Synchronization Based on DNA Strand Displacement Reaction

As an important part of biological computing, DNA strand displacement technology is used to construct complex biochemical circuits. Reversible molecular chemical reactions are basic chemical reactions. In this study, based on DNA strand displacement and reversible molecular chemical reactions, catalysis, degradation, annihilation and synchronization reaction modules were proposed. These chemical reaction modules were extended to the molecular level by DNA strand displacement. The function of these modules was confirmed, and the relationship between reaction rate and reaction concentration was also analyzed. Applying these modules to the six-input buffered oscillator, the input-output synchronization of the oscillator can be realized.

Four-Input Multi-Layer Majority Logic Circuit Based on DNA Strand Displacement Computing

Biomolecules have the advantage of high performance parallel computing and large information capacity. The use of biochemical circuits to solve computational problems has been studied by many researchers. In this paper, we use DNA strand displacement technology to construct complex molecular circuits as logic gates. The experimental process is demonstrated by a series of strand displacement reactions, and the feasibility of the design is verified by the strand displacement simulation platform Visual DSD. The key feature of this logic gate design is that when two inputs of the same signal are controlled, the remaining two different input signals implement AND and OR function to determine the output. Based on this feature, a four-input multi-layer logic circuit is designed and implemented. The calculation mode of the other three inputs AND and OR combinations is implemented by controlling each logic gate input.

Pattern Recognition of 2 × 2 Matrices Based on DNA Strand Displacement

Biochemical circuits have been transformed from simple logic circuits to large-scale complex circuits, benefitting from the maturity of DNA strand displacement technology. Pattern recognition is a process of analyzing perceptual signals and identifying and interpreting objects. In this study, pattern recognition of 2 × 2 matrices based on DNA strand displacement was designed, including dual-rail circuits and seesaw circuits. The effective results were obtained by simulation in Visual DSD software, simultaneously, the pattern recognition and DNA strand displacement technology were perfectly combined.

Solving probability reasoning based on DNA strand displacement and probability modules

In computation biology, DNA strand displacement technology is used to simulate the computation process and has shown strong computing ability. Most researchers use it to solve logic problems, but it is only rarely used in probabilistic reasoning. To process probabilistic reasoning, a conditional probability derivation model and total probability model based on DNA strand displacement were established in this paper. The models were assessed through the game “read your mind.” It has been shown to enable the application of probabilistic reasoning in genetic diagnosis.

Fluorescence Resonance Energy Transfer-Based Photonic Circuits Using Single-Stranded Tile Self-Assembly and DNA Strand Displacement.

Structural DNA nanotechnology has great potential in the fabrication of complicated nanostructures and devices capable of bio-sensing and logic function. A variety of nanostructures with desired shapes have been created in the past few decades. But the application of nanostructures remains to be fully studied. Here, we present a novel biological information processing system constructed on a self-assembled, spatially addressable single-stranded tile (SST) nanostructure as DNA nano-manipulation platform that created by SST self-assembly technology. Utilizing DNA strand displacement technology, the fluorescent dye that is pre-assembled in the nano-manipulation platform is transferred from the original position to the destination, which can achieve photonic logic circuits by FRET signal cascades, including logic AND, OR, and NOT gates. And this transfer process is successfully validated by visual DSD software. The transfer process proposed in this study may provide a novel method to design complicated biological information processing system constructed on a SST nanostructure, and can be further used to develop intelligent delivery of drug molecules in vivo.

A novel bio-sensor based on DNA strand displacement.

DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called “DNA neurons” are achieved, in which a “smart” way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The “DNA neuron” is bistable, that is, it can sense DNA molecules as input signals, and release “negative” or “positive” signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized “DNA neurons”, which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement) software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.