A molecular device: A DNA molecular lock driven by the nicking enzymes

Implementation of Digital Computing by Colloidal Crystal Engineering with DNA

Toehold-mediated strand displacement (TMSD) provides a versatile toolbox for developing DNA digital computing systems. Although different logic circuits with diverse functions have achieved good performance in terms of complexity and scalability, most previous DNA logic circuits perform information processing only at the molecular level, and nonspecific signal leakages are often difficult to avoid. Here, we demonstrate the feasibility of constructing leakless digital computing systems in three-dimensionally ordered colloidal supercrystals. These systems possess a unique signal leakage resistance by integrating different TMSD-based logic gates with the catalytic assembly of DNA-functionalized gold colloids. A complete set of basic Boolean logic gates and different cascaded logic circuits is constructed on the basis of the catalytic assembly strategy enabled by a facilely designed catassembler, where the output signals are recognized by determining whether specific colloidal supercrystals are formed or not. In addition, a half adder is built through a combination of XOR and AND logic gates with two distinct crystal types as readouts. Finally, a leakless two-digit DNA keypad lock for information security protection is demonstrated. The combination of TMSD-based logic circuits with the universal nanoparticle catalytic assembly offers the possibility to develop highly complicated and leakage-free digital computing systems and promotes macroscopic colloidal superlattice materials with programmable logic functions.

Biomolecule-Driven Two-Factor Authentication Strategy for Access Control of Molecular Devices

The rise of DNA nanotechnology is promoting the development of molecular security devices and marking an essential change in information security technology, to one that can resist the threats resulting from the increase in computing power, brute force attempts, and quantum computing. However, developing a secure and reliable access control strategy to guarantee the confidentiality of molecular security devices is still a challenge. Here, a biomolecule-driven two-factor authentication strategy for access control of molecular devices is developed. Importantly, the two-factor is realized by applying the specificity and nicking properties of the nicking enzyme and the programmable design of the DNA sequence, endowing it with the characteristic of a one-time password. To demonstrate the feasibility of this strategy, an access control module is designed and integrated to further construct a role-based molecular access control device. By constructing a command library composed of three commands (Ca, Cb, Ca and Cb), the authorized access of three roles in the molecular device is realized, in which the command Ca corresponds to the authorization of role A, Cb corresponds to the authorization of role B, and Ca and Cb corresponds to the authorization of role C. In this way, when users access the device, they not only need the correct factor but also need to apply for role authorization in advance to obtain secret information. This strategy provides a highly robust method for the research on access control of molecular devices and lays the foundation for research on the next generation of information security.

Temporal logic circuits implementation using a dual cross-inhibition mechanism based on DNA strand displacement

Molecular circuits crafted from DNA molecules harness the inherent programmability and biocompatibility of DNA to intelligently steer molecular machines in the execution of microscopic tasks. In comparison to combinational circuits, DNA-based temporal circuits boast supplementary capabilities, allowing them to proficiently handle the omnipresent temporal information within biochemical systems and life sciences. However, the lack of temporal mechanisms and components proficient in comprehending and processing temporal information presents challenges in advancing DNA circuits that excel in complex tasks requiring temporal control and time perception. In this study, we engineered temporal logic circuits through the design and implementation of a dual cross-inhibition mechanism, which enables the acceptance and processing of temporal information, serving as a fundamental building block for constructing temporal circuits. By incorporating the dual cross-inhibition mechanism, the temporal logic gates are endowed with cascading capabilities, significantly enhancing the inhibitory effect compared to a cross-inhibitor. Furthermore, we have introduced the annihilation mechanism into the circuit to further augment the inhibition effect. As a result, the circuit demonstrates sensitive time response characteristics, leading to a fundamental improvement in circuit performance. This architecture provides a means to efficiently process temporal signals in DNA strand displacement circuits. We anticipate that our findings will contribute to the design of complex temporal logic circuits and the advancement of molecular programming.

Sequential-Dependent Synthesis of Bimetallic Silver-Chromium Nanoparticles for Multichannel Sensing, Logic Computing, and 3 in 1 Information Protection

Bimetallic nanomaterials (BNMs) have been used in sensing, biomedicine, and environmental remediation, but their multipurpose and comprehensive applications in molecular logic computing and information security protection have received little attention. Herein, This synthesis method is achieved by sequentially adding reactants under ice bath conditions. Interestingly, Ag-Cr NPs can dynamically selectively sense anions and reductants in multiple channels. Especially, ClO^- can be quantitatively detected by oxidizing Ag-Cr NPs with detection limits of 98.37 nM (at 270 nm) and 31.83 nM (at 394 nm). Based on sequential-dependent synthesis process of Ag-Cr NPs, Boolean logic gates and customizable molecular keypad locks are constructed by setting the reactants as the inputs, the states of the resulting solutions as the outputs. Furthermore, dynamically selective response patterns of the Ag-Cr NPs can be converted into binary strings to exploit molecular crypto-steganography to encode, store, and hide information. By integrating the three dimensions of authorization, encryption, and steganography, 3 in 1 advanced information protection based on Ag-Cr nanosensing system can be achieved, which can enhance the anti-cracking ability of information. This research will promote the development and application of nanocomposites in the field of information security and deepen the connection between molecular sensing and the information world.

Programming DNA Reaction Networks Using Allosteric DNA Hairpins

The construction of DNA reaction networks with complex functions using various methods has been an important research topic in recent years. Whether the DNA reaction network can perform complex tasks and be recycled directly affects the performance of the reaction network. Therefore, it is very important to design and implement a DNA reaction network capable of multiple tasks and reversible regulation. In this paper, the hairpin allosteric method was used to complete the assembly task of different functional nucleic acids. In addition, information conversion of the network was realized. In this network, multiple hairpins were assembled into nucleic acid structures with different functions to achieve different output information through the cyclic use of trigger strands. A method of single-input dual-output information conversion was proposed. Finally, the network with signal amplification and reversible regulation was constructed. In this study, the reversible regulation of different functional nucleic acids in the same network was realized, which shows the potential of this network in terms of programmability and provides new ideas for constructing complex and multifunctional DNA reaction networks.

Reconfigurable DNA triplex structure for pH responsive logic gates†

The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C⁺ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks.

We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.

Molecular Visual Sensing, Boolean Logic Computing, and Data Security Using a Droplet-Based Superwetting Paradigm

Inspired by information processing and logic operations of life, many artificial biochemical systems have been designed for applications in molecular information processing. However, encoding the binary synergism between matter, energy, and information in a superwetting system remains challenging. Herein, a superwetting paradigm was proposed for multifunctional applications including molecular visual sensing and data security on a superhydrophobic surface. A Triton X-100-encapsulated gelatin (TeG) hydrogel was prepared and selectively decomposed by trypsin, releasing the surfactant to decrease the surface tension of a droplet. Integrating the droplet with the superhydrophobic surface, the superwetting behavior was utilized for visual detection and information encoding. Interestingly, the proposed TeG hydrogel can function as an artificial gelneuron for molecular-level logic computing, where the combination of matters (superhydrophobic surface, trypsin, and leupeptin) acts as inputs to interact with energy (liquid surface tension and solid surface energy) and information (binary character), resulting in superwettability transitions (droplet surface tension, contact angle, rolling angle, and bounce) as outputs. Impressively, the TeG gelneuron can be further developed as molecular-level double cryptographic steganography to encode, encrypt, and hide specific information (including the maze escape route and content of the classical literature) due to its programmability, stimuli responsive ability, and droplet concealment. This study will encourage the development of advanced molecular paradigms and their applications, such as superwetting visual sensing, molecular computing, interaction, and data security.

DNA Logic Circuits for Cancer Theranostics

Cancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self-assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor-specific markers and the TME through logic operations and signal amplification, to generate detectable signals or to release anti-cancer agents. In this review, the fundamental concepts of DNA logic circuits are clarified, the basic modules in the circuit are summarized, and how this advanced nano-assembly circuit responds to tumor-related molecules, how to perform logic operations, to realize signal amplification, and selectively release drugs through discussing over 30 application examples, are demonstrated. This review shows that DNA logic circuits have powerful logic judgment and signal amplification functions in improving the specificity and sensitivity of cancer diagnosis and making cancer treatment controllable. In the future, researchers are expected to overcome the existing shortcomings of DNA logic circuits and design smarter DNA devices with better biocompatibility and stability, which will further promote the development of cancer theranostics.

Construction of Multiple Logic Circuits Based on Allosteric DNAzymes

In DNA computing, the implementation of complex and stable logic operations in a universal system is a critical challenge. It is necessary to develop a system with complex logic functions based on a simple mechanism. Here, the strategy to control the secondary structure of assembled DNAzymes’ conserved domain is adopted to regulate the activity of DNAzymes and avoid the generation of four-way junctions, and makes it possible to implement basic logic gates and their cascade circuits in the same system. In addition, the purpose of threshold control achieved by the allosteric secondary structure implements a three-input DNA voter with one-vote veto function. The scalability of the system can be remarkably improved by adjusting the threshold to implement a DNA voter with 2n + 1 inputs. The proposed strategy provides a feasible idea for constructing more complex DNA circuits and a highly integrated computing system.

DNA tile self-assembly driven by antibody-mediated four-way branch migration

The antibody-mediated four-way branch migration mechanism provides a novel idea for realizing the assembly of nanostructures, simply by attaching structures such as tiles, proteins, quantum dots, etc. to the ends of the four-way branches.

A novel strategy for programmable DNA tile self-assembly with a DNAzyme-mediated DNA cross circuit

The proposed strategy promotes the controllability and modularization of trigger elements, realizes programmable molecular self-assembly, and has broad applications for the construction of DNA nanodevices.

Constructing DNA logic circuits based on the toehold preemption mechanism

Strand displacement technology and ribozyme digestion technology have enriched the intelligent toolbox of molecular computing and provided more methods for the construction of DNA logic circuits. In recent years, DNA logic circuits have developed rapidly, and their scalability and accuracy in molecular computing and information processing have been fully demonstrated. However, existing DNA logic circuits still have some problems such as high complexity of DNA strands (number of DNA strands) hindering the expansion of practical computing tasks. In view of the above problems, we presented a toehold preemption mechanism and applied it to construct DNA logic circuits using E6-type DNAzymes, such as half adder circuit, half subtractor circuit, and 4-bit square root logic circuit. Different from the dual-track logic expressions, all the signals in the circuits of this study were monorail which substantially reduced the number of DNA strands in the DNA logic circuits. The presented preemption mechanism provides a way to simplify the implementation of large and complex DNA integrated circuits.

Enhancing Physical and Thermodynamic Properties of DNA Storage Sets with End-constraint

With the explosion of data, DNA is considered as an ideal carrier for storage due to its high storage density. However, low-quality DNA sets hamper the widespread use of DNA storage. This work proposes a new method to design high-quality DNA storage sets. Firstly, random switch and double-weight offspring strategies are introduced in Double-strategy Black Widow Optimization Algorithm (DBWO). Experimental results of 26 benchmark functions show that the exploration and exploitation abilities of DBWO are greatly improved from previous work. Secondly, DBWO is applied in designing DNA storage sets, and compared with previous work, the lower bounds of storage sets are boosted by 9%-37%. Finally, to improve the poor stabilities of sequences, the End-constraint is proposed in designing DNA storage sets. By measuring the number of hairpin structures, melting temperature, and minimum free energy, it is evaluated that with our innovative constraint, DBWO can construct not only a larger number of storage sets, but also enhance physical and thermodynamic properties of DNA storage sets.

Combinatorial constraint coding based on the EORS algorithm in DNA storage

The development of information technology has produced massive amounts of data, which has brought severe challenges to information storage. Traditional electronic storage media cannot keep up with the ever-increasing demand for data storage, but in its place DNA has emerged as a feasible storage medium with high density, large storage capacity and strong durability. In DNA data storage, many different approaches can be used to encode data into codewords. DNA coding is a key step in DNA storage and can directly affect storage performance and data integrity. However, since errors are prone to occur in DNA synthesis and sequencing, and non-specific hybridization is prone to occur in the solution, how to effectively encode DNA has become an urgent problem to be solved. In this article, we propose a DNA storage coding method based on the equilibrium optimization random search (EORS) algorithm, which meets the Hamming distance, GC content and no-runlength constraints and can reduce the error rate in storage. Simulation experiments have shown that the size of the DNA storage code set constructed by the EORS algorithm that meets the combination constraints has increased by an average of 11% compared with previous work. The increase in the code set means that shorter DNA chains can be used to store more data.

DNA strand displacement reactions to accomplish a two-degree-of-freedom PID controller and its application in subtraction gate

Synthesis control circuits can be used to effectively control biochemical molecule processes. In the controller design based on chemical reaction networks (CRNs), generally only the tracking set-point is considered. However, the influence of disturbances, which are frequently encountered in biochemical systems, is often neglected, thus weakening the control effect of the system. In this article, tracking set-point input and suppressing disturbance input are considered in the control effect. Firstly, CRNs are adopted to construct a two-degree-of-freedom PID controller by combining a one-degree-of-freedom PID controller with a feedforward controller for the first time. Then, CRN expressions of the two input functions (step function and ramp function) used as input signals are defined. Furthermore, the two-degree-of-freedom PID controller is founded by DNA strand displacement (DSD) reaction networks, because DNA is an ideal engineering material to constitute molecular devices based on CRNs. The overshoot of the two-degree-of-freedom PID control system is significantly reduced compared to the one-degree-of-freedom PID control system. Finally, a leak reaction is treated as an extraneous disturbance input to a subtraction gate. The influence of external disturbance is solved by the two-degree-of-freedom PID controller. It is worth noting that the two-degree-of-freedom subtraction gate control system better restrains the impact of a disturbance input (leak reaction).

Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint

DNA computing is a new method based on molecular biotechnology to solve complex problems. The design of DNA sequences is a multi-objective optimization problem in DNA computing, whose objective is to obtain optimized sequences that satisfy multiple constraints to improve the quality of the sequences. However, the previous optimized DNA sequences reacted with each other, which reduced the number of DNA sequences that could be used for molecular hybridization in the solution and thus reduced the accuracy of DNA computing. In addition, a DNA sequence and its complement follow the principle of complementary pairing, and the sequence of base GC at both ends is more stable. To optimize the above problems, the constraints of Pairing Sequences Constraint (PSC) and Close-ending along with the Improved Chaos Whale (ICW) optimization algorithm were proposed to construct a DNA sequence set that satisfies the combination of constraints. The ICW optimization algorithm is added to a new predator–prey strategy and sine and cosine functions under the action of chaos. Compared with other algorithms, among the 23 benchmark functions, the new algorithm obtained the minimum value for one-third of the functions and two-thirds of the current minimum value. The DNA sequences satisfying the constraint combination obtained the minimum of fitness values and had stable and usable structures.

CLGBO: An Algorithm for Constructing Highly Robust Coding Sets for DNA Storage

In the era of big data, new storage media are urgently needed because the storage capacity for global data cannot meet the exponential growth of information. Deoxyribonucleic acid (DNA) storage, where primer and address sequences play a crucial role, is one of the most promising storage media because of its high density, large capacity and durability. In this study, we describe an enhanced gradient-based optimizer that includes the Cauchy and Levy mutation strategy (CLGBO) to construct DNA coding sets, which are used as primer and address libraries. Our experimental results show that the lower bounds of DNA storage coding sets obtained using the CLGBO algorithm are increased by 4.3–13.5% compared with previous work. The non-adjacent subsequence constraint was introduced to reduce the error rate in the storage process. This helps to resolve the problem that arises when consecutive repetitive subsequences in the sequence cause errors in DNA storage. We made use of the CLGBO algorithm and the non-adjacent subsequence constraint to construct larger and more highly robust coding sets.

An Exonuclease I-Aided Turn-Off Fluorescent Strategy for Alkaline Phosphatase Assay Based on Terminal Protection and Copper Nanoparticles

As an important DNA 3'-phosphatase, alkaline phosphatase can repair damaged DNA caused by replication and recombination. It is essential to measure the level of alkaline phosphatase to indicate some potential diseases, such as cancer, related to alkaline phosphatase. Here, we designed a simple and fast method to detect alkaline phosphatase quantitively. When alkaline phosphatase is present, the resulting poly T-DNA with a 3'-hydroxyl end was cleaved by exonuclease I, prohibiting the formation of fluorescent copper nanoparticles. However, the fluorescent copper nanoparticles can be monitored with the absence of alkaline phosphatase. Hence, we can detect alkaline phosphatase with this turn-off strategy. The proposed method is able to quantify the concentration of alkaline phosphatase with the LOD of 0.0098 U/L. Furthermore, we utilized this method to measure the effects of inhibitor Na₃VO₄ on alkaline phosphatase. In addition, it was successfully applied to quantify the level of alkaline phosphatase in human serum. The proposed strategy is sensitive, selective, cost effective, and timesaving, having a great potential to detect alkaline phosphatase quantitatively in clinical diagnosis.

Minimum Free Energy Coding for DNA Storage

With the development of information technology, huge amounts of data are produced at the same time. How to store data efficiently and at low cost has become an urgent problem. DNA is a high-density and persistent medium, making DNA storage a viable solution. In a DNA data storage system, the first consideration is how to encode the data effectively into code words. However, DNA strands are prone to non-specific hybridization during the hybridization reaction process and are prone to errors during synthesis and sequencing. In order to reduce the error rate, a thermodynamic minimum free energy (MFE) constraint is proposed and applied to the construction of coding sets for DNA storage. The Brownian multi-verse optimizer (BMVO) algorithm, based on the Multi-verse optimizer (MVO) algorithm, incorporates the idea of Brownian motion and Nelder-Mead method, and it is used to design a better DNA storage coding set. In addition, compared with previous works, the coding set has been increasing by 4%-50% in size and has better thermodynamic properties. With the improvement of the quality of the DNA coding set, the accuracy of reading and writing and the robustness of the DNA storage system are also enhanced.

Development of a neuron model based on DNAzyme regulation

Neural networks based on DNA molecular circuits play an important role in molecular information processing and artificial intelligence systems. In fact, some DNA molecular systems can become dynamic units with the assistance of DNAzymes. The complex DNA circuits can spontaneously induce corresponding feedback behaviors when their inputs changed. However, most of the reported DNA neural networks have been implemented by the toehold-mediated strand displacement (TMSD) method. Therefore, it was important to develop a method to build a neural network utilizing the TMSD mechanism and adding a mechanism to account for modulation by DNAzymes. In this study, we designed a model of a DNA neuron controlled by DNAzymes. We proposed an approach based on the DNAzyme modulation of neuronal function, combing two reaction mechanisms: DNAzyme digestion and TMSD. Using the DNAzyme adjustment, each component simulating the characteristics of neurons was constructed. By altering the input and weight of the neuron model, we verified the correctness of the computational function of the neurons. Furthermore, in order to verify the application potential of the neurons in specific functions, a voting machine was successfully implemented. The proposed neuron model regulated by DNAzymes was simple to construct and possesses strong scalability, having great potential for use in the construction of large neural networks.