DNA Sequential Logic Gate Using Two-Ring DNA

The Amplified DNA Logic Gates Based on Aptamer-Receptor Recognition for Cell Detection and Bioimaging

A powerful and accurate method for identifying and isolating cells would be of great importance due to its sensitivity, gentleness and effectiveness. Here, we designed a receptor-based DNA logic device that allows Boolean logic analysis of multiple cells. For ease of expression, the molecules on the cell surface that can bind to the aptamer are referred to as "receptors". This DNA logic device sends signals based on cell surface sgc8c and sgc4f receptor expression by performing NOT, NOR, AND and OR logic operations, and amplifies and evaluates the signals using HCR. Meanwhile, the release of ICG from the endopore of HMSNs is controlled by affecting structural changes in the DNA logic device. This approach can accurately identify and treat multiple cells on demand based on the presence or absence of cell-specific receptors, facilitating the development of personalized medicine.

An amplified logic gate driven by in situ synthesis of silver nanoclusters for identification of biomarkers

An amplified DNA logic sensor was constructed for the identification of multiple biomarkers, in which the inputs of targets triggered the disassembly of a V-shaped probe (VSP) structure by a strand displacement reaction, leading to the synthesis of silver nanoclusters (AgNCs) for electrocatalytic reduction of H₂O₂. The sensing platform achieved sensitive detection of methylated DNA and microRNA 122 with detection limits down to 3.4 and 4.1 fM, respectively, and can be used for the assay of clinical serum samples from healthy volunteers and liver injury patients with satisfactory results. The DNA logic sensor exhibited the advantages of convenience, low cost, and versatility without the involvement of electroactive label modification, which is helpful for disease diagnosis as well as the fundamental investigation of interfacial electrochemistry and molecular biology.

Mapping Temporally Ordered Inputs to Binary Message Outputs with a DNA Temporal Logic Circuit

Molecular circuits and devices with temporal signal processing capability are of great significance for the analysis of complex biological processes. Mapping temporal inputs to binary messages is a process of history-dependent signal responses, which can help understand the signal-processing behavior of organisms. Here, we propose a DNA temporal logic circuit based on DNA strand displacement reactions, which can map temporally ordered inputs to corresponding binary message outputs. The presence or absence of the output signal is determined by the type of substrate reaction with the input so that different orders of inputs correspond to different binary outputs. We demonstrate that a circuit can be generalized to more complex temporal logic circuits by increasing or decreasing the number of substrates or inputs. We also show that our circuit had excellent responsiveness to temporally ordered inputs, flexibility, and expansibility in the case of symmetrically encrypted communications. We envision that our scheme can provide some new ideas for future molecular encryption, information processing, and neural networks.

Membrane Protein and Extracellular Acid Heterogeneity-Driven Amplified DNA Logic Gate Enables Accurate and Sensitive Identification of Cancer Cells

DNA logic gates, as a class of smart molecular devices with excellent biocompatibility and convenient information processing mode, have been widely used for identification of cancer cells based on logic analysis of cancer biomarkers. However, most of the developed DNA logic gates for identification of cancer cells are mainly driven by homogeneous biomarkers such as membrane proteins or RNAs, which may suffer from insufficient accuracy. Herein, we reported a membrane protein and extracellular acid heterogeneity-driven amplified DNA logic gate (HDLG) for accurate and sensitive identification of cancer cells by combining the superior signal amplification characteristics of the hybridization chain reaction (HCR) and the precise computation ability of the logic operation. In this strategy, a DNA aptamer was employed for membrane protein recognition, and a split i-motif was used for the response of the extracellular acid. Only when the two heterogeneous biomarkers existed simultaneously, the DNA logic gate could be driven to perform the "AND" logic operation and induce the formation of an intact trigger to initiate a HCR process on the cell surface, generating an amplified "ON" fluorescence signal. Benefiting from the design of heterogeneity-driven and signal amplification, this DNA logic gate could not only autonomously perform high-resolution fluorescence imaging on the surface of target cancer cells, but also perform sensitive analysis of target cancer cells with a cell number of 70 detected in 200 μL of buffer and desirable accuracy in differentiating target cancer cells from complicated cell mixtures. We anticipate that this novel HDLG is expected to be applied in precise disease diagnosis.

Developing a three-input cascade DNA logic gate based on the biological characteristics of metal ion-GO, combined with analysis and verification

Due to the limitation of technology, electronic computing is approaching the limit of technology, and new computing tools need to be developed. Here, we build a three-input cascade logic gate based on the advantages of biomolecules, particularly DNA, in the construction of computational logic systems, combined with metal ions and graphene oxide (GO). It is worth mentioning that this study uses a variety of research methods. In addition to the commonly used biological experiments, NUPACK and visual DSD simulation methods are used for analysis, and orthogonal, standardized and other statistical means are used to simplify the experimental process and make the results intuitive. Finally, the designed three-input logic gate is successfully constructed, and it is found that it may have the potential to realize complex computing.

Three-Variable Chaotic Oscillatory System Based on DNA Strand Displacement and Its Coupling Combination Synchronization

The synchronization control of two chaotic oscillatory systems is designed based on DNA strand displacement in the present work. Thus, combination synchronization of three 3-variable chaotic oscillatory systems is proposed based on DNA strand displacement. Firstly, five chemical reaction modules of double, displacement, adjustment, catalysis and degradation are designed. Based on these five modules, a 3-variable chaotic oscillatory system is designed. Secondly, based on the design principle of coupling terms and theory of stability, synchronization modules and coupling terms are added to three chaotic oscillatory systems to design combination synchronization of three 3-variable chaotic oscillatory systems based on DNA strand displacement. Modules and systems are implemented and tested using visual DSD and Matlab, and the simulation results are presented to demonstrate the effectiveness and correctness of the chemical reaction modules and systems. The combination synchronization of three 3-variable chaotic oscillatory systems is proposed based on DNA strand displacement, which may be extended to the reaction networks of DNA strand displacement and to the combination synchronization of multivariable chaotic oscillatory systems based on DNA strand displacement.

Constructing Controllable Logic Circuits Based on DNAzyme Activity

Recently, DNA molecules have been widely used to construct advanced logic devices due to their unique properties, such as a simple structure and predictable behavior. In fact, there are still many challenges in the process of building logic circuits. Among them, the scalability of the logic circuit and the elimination of the crosstalk of the cascade circuit have become the focus of research. Inspired by biological allosteric regulation, we developed a controllable molecular logic circuit strategy based on the activity of DNAzyme. The E6 DNAzyme sequence was temporarily blocked by hairpin DNA and activated under appropriate input trigger conditions. Using a substrate with ribonucleobase (rA) modification as the detection strand, a series of binary basic logic gates (YES, AND, and INHIBIT) were implemented on the computational component platform. At the same time, we demonstrate a parallel demultiplexer and two multi-level cascade circuits (YES-YES and YES-Three input AND (YES-TAND)). In addition, the leakage of the cascade process was reduced by exploring factors such as concentration and DNA structure. The proposed DNAzyme activity regulation strategy provides great potential for the expansion of logic circuits in the future.

Entropy-driven DNA logic circuits regulated by DNAzyme

The catalytic DNA circuits play a critical role in engineered biological systems and molecular information processing. Actually, some of the natural or synthetic DNA circuits were triggered by covalent modifications, where conformational changes were induced to facilitate complex DNA engineering functions and signal transmissions. However, most of the reported artificial catalytic DNA circuits were regulated by the toehold-mediated reaction. Therefore, it is significant to propose a strategy to regulate the catalytic DNA circuit not only by the toehold-mediated mechanism, but also by involving the conformational changes induced by the covalent modification. In this study, we developed the catalytic DNA logic circuits regulated by DNAzyme. Here, a regulation strategy based on the covalent modification was proposed to control the DNA circuit, combing two reaction mechanisms: DNAzyme digestion and entropy-driven strand displacement. The DNAzyme and DNA catalyst can participate into the reactions alternatively, thus realizing the cascading catalytic circuits. Using the DNAzyme regulation, a series of logic gates (YES, OR and AND) were constructed. In addition, a two-layer cascading circuit and a feedback self-catalysis circuit were also established. The proposed DNAzyme-regulated strategy shows great potentials as a reliable and feasible method for constructing more complex catalytic DNA circuits.

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis

Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers. However, those regulations required to change the sequences of whole DNAzyme, as separating parts and inserting extra DNA sequence. Inspired by the allosteric regulation of proteins in nature, a new allosteric strategy is proposed to regulate the activity of DNAzyme without DNA sequences changes. In this strategy, DNA strand displacement was used to regulate the DNAzyme structure, through which the activity of DNAzyme was well controlled. The strategy was applied to E6-type DNAzymes, and the operations of DNA logic circuit (YES, OR, AND, cascading and feedback) were established and simulated with the dynamic analyses. The allosteric regulation has potential to construct more complicated molecular systems, which can be applied to bio-sensing and detection.