Programmable DNA-Based Boolean Logic Microfluidic Processing Unit

Sea Anemone-like Nanomachine Based on DNA Strand Displacement Composed of Three Boolean Logic Gates: Diversified Input for Intracellular Multitarget Detection

Efficient and accurate acquisition of cellular biomolecular information is crucial for exploring cell fate, achieving early diagnosis, and the effective treatment of various diseases. However, current DNA biosensors are mostly limited to single-target detection, with few complex logic circuits for comprehensive analysis of three or more targets. Herein, we designed a sea anemone-like DNA nanomachine based on DNA strand displacement composed of three logic gates (YES-AND-YES) and delivered into the cells using gold nano bipyramid carriers. The AND gate activation depends on the trigger chain released by upstream DNA strand displacement reactions, while the output signal relies on the downstream DNAzyme structure. Under the influence of diverse inputs (including enzymes, miRNA, and metal ions), the interconnected logic gates simultaneously perform logical analysis on multiple targets, generating a unique output signal in the YES/NO format. This sensor can successfully distinguish healthy cells from tumor cells and can be further used for the diagnosis of different tumor cells, providing a promising platform for accurate cell-type identification.

DNA as a universal chemical substrate for computing and data storage

DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.

Processing DNA Storage through Programmable Assembly in a Droplet-Based Fluidics System

DNA can be used to store digital data, and synthetic short-sequence DNA pools are developed to store high quantities of digital data. However, synthetic DNA data cannot be actively processed in DNA pools. An active DNA data editing process is developed using splint ligation in a droplet-controlled fluidics (DCF) system. DNA fragments of discrete sizes (100-500 bps) are synthesized for droplet assembly, and programmed sequence information exchange occurred. The encoded DNA sequences are processed in series and parallel to synthesize the determined DNA pools, enabling random access using polymerase chain reaction amplification. The sequencing results of the assembled DNA data pools can be orderly aligned for decoding and have high fidelity through address primer scanning. Furthermore, eight 90 bps DNA pools with pixel information (png: 0.27-0.28 kB), encoded by codons, are synthesized to create eight 270 bps DNA pools with an animation movie chip file (mp4: 12 kB) in the DCF system.

Programming DNA Circuits for Controlled Immunostimulation through CpG Oligodeoxynucleotide Delivery

Herein, we present a DNA circuit programmed for the delivery of CpG oligodeoxynucleotides (CpG ODNs) with the pharmacological immunostimulation function. The circuit employs a complementary DNA (cDNA) strand to deactivate the biological function of CpG ODNs via hybridization, while T7 exonuclease mediates the activation by hydrolyzing the cDNA and releasing the CpG ODN as an active moiety. We investigated the influence of several factors on the kinetic profile and temporal behavior of the circuit. These include the design of the cDNA strand, the concentration of the DNA duplex, and the concentration of T7 exonuclease. The DNA circuit's in vitro activation resulted in toll-like receptor 9 stimulation in the HEK-engineered cell line, as well as tumor necrosis factor-alpha release by J774A.1 macrophages. By programming the DNA circuit to control the release of the CpG ODN, we achieved an altered pharmacological profile with acute and potent immunostimulation, in comparison to a system without controlled CpG ODN release, which exhibited a slow and delayed response. Our findings demonstrate the potential of DNA circuits in controlling the pharmacological activity of DNA strands for controlled drug delivery.

Construction of DNA-based molecular circuits using normally open and normally closed switches driven by lambda exonuclease

Building synthetic molecular circuits is an important way to realize ion detection, information processing, and molecular computing. However, it is still challenging to implement the NOT logic controlled by a single molecule input in synthetic molecular circuits wherein the presence or absence of the molecule represents the ON or OFF state of the input. Here, based on lambda exonuclease (λ exo), for the first time, we propose the normally open (NO) and normally closed (NC) switching strategy with a unified signal transmission mechanism to build molecular circuits. Specifically, the opposite logic can be output with or without a single signal, and the state of the switch can be adjusted by the addition order and time interval of the upstream signal and switch signal, which endows the switch with time-responsive characteristics. In addition, a time-delay relay with the function of delayed disconnection is developed to realize quantitative control of outputs, which has the potential to meet the automation control need of the system. Finally, digital square and square root circuits are constructed by cascading the NO and NC switches, which demonstrates the versatility of switches. Our design can be extended to time logic and complex digital computing circuits for use in information processing and nanomachines.

A survey on molecular-scale learning systems with relevance to DNA computing

DNA computing has emerged as a promising alternative to achieve programmable behaviors in chemistry by repurposing the nucleic acid molecules into chemical hardware upon which synthetic chemical programs can be executed. These chemical programs are capable of simulating diverse behaviors, including boolean logic computation, oscillations, and nanorobotics. Chemical environments such as the cell are marked by uncertainty and are prone to random fluctuations. For this reason, potential DNA-based molecular devices that aim to be deployed into such environments should be capable of adapting to the stochasticity inherent in them. In keeping with this goal, a new subfield has emerged within DNA computing, focusing on developing approaches that embed learning and inference into chemical reaction systems. If realized in biochemical contexts, such molecular machines can engender novel applications in fields such as biotechnology, synthetic biology, and medicine. Therefore, it would be beneficial to review how different ideas were conceived, how the progress has been so far, and what the emerging ideas are in this nascent field of 'molecular-scale learning'.

Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits

The construction of logic circuits is critical to DNA computing. Simple and effective scalability methods have been the focus of attention in various fields related to constructing logic circuits. We propose a double-stranded separation (DSS) strategy to facilitate the construction of complex circuits. The strategy combines toehold-mediated strand displacement with exonuclease III (Exo III), which is a multifunctional nuclease. Exo III can quickly recognize an apurinic/apyrimidinic (AP) site. DNA oligos with an AP site can generate an output signal by the strand displacement reaction. However, in contrast to traditional strand displacement reactions, the double-stranded waste from the strand displacement can be further hydrolysed by the endonuclease function of Exo III, thus generating an additional output signal. The DSS strategy allows for the effective scalability of molecular logic circuits, enabling multiple logic computing capabilities simultaneously. In addition, we succeeded in constructing a logic circuit with dual logic functions that provides foundations for more complex circuits in the future and has a broad scope for development in logic computing, biosensing, and nanomachines.

A light-operated dual-mode method for neuroblastoma diagnosis based on a Tb-MOF: from biometabolite detection to logic devices

Tb-DBA can not only serve as a light-operated dual-mechanism driven platform to detect VMA (an early pathological feature of neuroblastoma), but can also produce a different fluorescence response to epinephrine (EP, the metabolic precursor of VMA).

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.

Quadruple analyte responsive platform: Point-of-care testing and multi-coding logic computation based on metal ions recognition and selective response

While it is recognized that instrumentation techniques can provide precise and sensitive solutions to heavy metal ion monitoring, it remains challenging to transform laboratory testing into a convenient, on-site, and quantitative sensing platform for point-of-care testing (POCT) in a resource-constrained setting. To address these limitations, an affordable and user-friendly colorimetric POCT sensing system is proposed here for selectively monitoring four metal ions (Fe³⁺, Co²⁺, Pb²⁺, and Cd²⁺) based on the sulfur quantum dots (S dots). Quadruple distinct visual signals (green, brown, precipitation, and bright yellow) are presented on the fabricated paper-based analytical devices (PADs) when mixing S dots and metal ions. The high-quality photographs of the PADs are captured by a scanner, while a smartphone App converts visual signals to HSV values. The quantitative analysis relies on the digital colorimetric reading, and the limits of detection are 0.59, 0.47, 0.82, and 0.53 μM for Fe³⁺, Co²⁺, Cd²⁺, and Pb²⁺, respectively. This metal ions-responsive platform is engineered as a smart strategy for multiple logic operations (YES, NOT, AND, INHIBIT, and NOR) by integrating multi-responsive blocks into the S dots with encoded patterns, which improves the computing capability. Accordingly, this strategy demonstrates its potential for on-site environmental testing and sophisticated molecular computation.

From Theoretical Network to Bedside: Translational Application of Brain-Inspired Computing in Clinical Medicine

Advances in the brain-inspired computing space are growing at a rapid rate, and many of these emerging strategies are in the field of neuromorphic control, robotics, and sensor development, just to name a few. These innovations are disruptive in their own right and have numerous, multi-dimensional medical applications within precision medicine, telematics, device development, and informed clinical decision making. For this discussion, I will define brain-inspired computing in the scope of simulating the architecture of the brain and discuss the realization of integrating hardware and other technologies with the applications of medicine, along with the considerations for the regulatory pathway for approval and evaluating the risk/consequences of failure modes. This perspective is a call for continued discussion of the development of a pathway for translating these technologies into medical treatment and diagnostic strategies. The aim is to align with global regulatory bodies and ensure that regulation does not limit the capacity of these emerging innovations while ensuring patient safety and clinical efficacy. It is my perspective that it is and will continue to be critical that these technologies are correctly perceived and understood in the lens of multiple disciplines in order to reach their full potential for medical applications.

Design and Realization of Triple dsDNA Nanocomputing Circuits in Microfluidic Chips

DNA logic gates, nanocomputing circuits, have already implemented basic computations and shown great signal potential for nano logic material application. However, the reaction temperature and computing speed still limit its development. Performing complicated computations requires a more stable component and a better computing platform. We proposed a more stable design of logic gates based on a triple, double-stranded, DNA (T-dsDNA) structure. We demonstrated a half adder and a full adder using these DNA nanocircuits and performed the computations in a microfluidic chip device at room temperature. When the solutions were mixed in the device, we obtained the expected results in real time, which suggested that the T-dsDNA combined microfluidic chip provides a concise strategy for large DNA nanocircuits.