Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing

Nanoclusters with specific DNA overhangs: modifying configurability, engineering contrary logic pairs and the parity generator/checker for error detection

The most promising alternative for next-generation molecular computers is biocomputing, which uses DNAs as its primary building blocks to perform a Boolean operation. DNA nanoclusters (NCs) have emerged as promising candidates for biosensing applications due to their unique self-assembly properties and programmability. It has been demonstrated that adding DNA overhangs to DNA NCs improves their adaptability in identifying specific biomolecular interactions. A recent proposal in DNA computing is the concept of "contrary logic pairs (CLPs)" executed by employing a DNA hybrid architecture as a universal platform. We have designed thymine overhang-modified DNA-templated NCs (T-Au/Ag NCs). These NCs serve as a chemosensing ensemble platform, where the presence of HgII ions mediates the formation of M-Au/Ag NCs. The resulting NCs exhibit the capability to drive elementary CLPs (YES, NOT, OR, NOR, INH and IMP) as well as complex logic operations (XOR and XNOR). Additionally, they can be utilized for advanced non-arithmetic DNA logic devices like a parity generator (pG) and a parity checker (pC) for "error detection". Bit errors are an unavoidable and common occurrence during any computing. A cascade of XOR operations was used to evaluate these errors by introducing the pG and pC at the transmitting (TX) and receiving (RX) ends in binary transmission, respectively, which has devastating implications for reliable logic circuits, especially in advanced logic computation. Moreover, an even/odd natural number from 0 to 9 distinguishable pC was designed based on a dual-source responsive computing platform. This work offers inspiring avenues for a cost-effective strategy to construct highly-intelligent DNA computing devices by enhancing the multi-input responsive single DNA platform concept.

Terbium-based metal-organic frameworks through energy transfer modulation for visual logical sensing zinc and fluorine ions

Zinc is the second most abundant trace element in the human central nervous system, which is closely related to various physiological activities in the human body. Fluoride ion is one of the most harmful elements in drinking water. Excessive intake of F^- may cause dental fluorosis, renal failure, or DNA damage. Therefore, it is urgent to develop sensors with high sensitivity and selectivity for the detection of Zn²⁺ and F^- ions at the same time. In this work, a series of mixed lanthanide metal-organic frameworks (Ln-MOFs) probes are synthesized using a simple method of in situ doping. The luminous color can be finely modulated by changing the molar ratio of Tb³⁺ and Eu³⁺ during synthesis. Benefiting from the unique energy transfer modulation mechanism, the probe has the continuous detection capability of zinc ions and fluoride ions. The detection of Zn²⁺ and F^- in a real environment shows that the probe has a good practical application prospect. The as-designed sensor at 262 nm excitation can sequentially detect Zn²⁺ concentrations ranging from 10^-8 to 10^-3 M (LOD = 4.2 nM) and F^- levels ranging from 10^-5 to 10^-3 M (LOD = 3.6 μM) with high selectivity. Based on different output signals, a simple Boolean logic gate device is constructed to realize intelligent visualization of Zn²⁺ and F^- monitoring.

DNA circuits compatible encoder and demultiplexer based on a single biomolecular platform with DNA strands as outputs

A series of multiple logic circuits based on a single biomolecular platform is constructed to perform nonarithmetic and arithmetic functions, including 4-to-2 encoder, 1-to-2 demultiplexer, 1-to-4 demultiplexer, and multi-input OR gate. The encoder to a DNA circuit is the equivalent of a sensory receptor to a reflex arc. They all function to encode information from outside the pathway (DNA circuit or reflex arc) into a form that subsequent pathways can recognize and utilize. Current molecular encoders are based on optical or electrical signals as outputs, while DNA circuits are based on DNA strands as transmission signals. The output of existing encoders cannot be recognized by subsequent DNA circuits. It is the first time the DNA-based encoder with DNA strands as outputs can be truly applied to the DNA circuit, enabling the application of DNA circuits in non-binary biological environments. Another novel feature of the designed system is that the developed nanodevices all have a simple structure, low leakage and low crosstalk, which allows them to implement higher-level encoders and demultiplexers easily. Our work is based on the idea of complex functionality in a simple form, which will also provide a new route for developing advanced molecular logic circuits.

Functional nucleic acids as modular components against SARS-CoV-2: From diagnosis to therapeutics

Coronavirus Disease 2019 (COVID-19), which poses an extremely serious global impact on human public healthcare, represents a high transmission and disease-causing viral infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is expanding at a rapid pace. Therefore, it is urgent for researchers to establish effective platforms for the assay and treatment of SARS-CoV-2. Functional nucleic acids (FNAs), comprising aptamers and nucleases, are of primary concern within the biological and medical communities owing of the distinctive properties of their target recognition and catalysis. This review will concentrate on the essential aspects of insights regarding FNAs and their technological expertise for the diagnostic and therapeutic utilization against COVID-19. We first offer a historical perspective of the COVID-19 pandemics, its clinical characteristics and potential biomarkers. Then, we briefly discuss the current diagnostic and therapeutic methodology towards COVID-19, highlighting the superiorities and existing shortcomings. After that, we introduce the key features of FNAs, and summarize recent progress of in vitro selection of FNAs for SARS-CoV-2 specific proteins and RNAs, followed by highlighting the general concept of translating FNAs into functional probes for diagnostic and therapeutic purposes. Then, we critically review the emerging FNAs-based diagnostic and therapeutic strategies that are fast, precise, efficient, and highly specific to fight COVID-19. Finally, we identify remaining challenges and offer future outlook of this emerging field.

Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes

Recently, a Na+-binding aptamer was reported to be embedded in a few RNA-cleaving DNAzymes, including NaA43, Ce13d, and NaH1. The Na+ aptamer consists of multiple GG stretches, which is a prerequisite for the formation of G-quadruplex (G4) structures. These DNAzymes require Na+ for activity but show no activity in the presence of K+ or other metal ions. Given that DNA can selectively bind K+ by forming a G4 structure, this work aims to answer whether this Na+ aptamer also uses a G4 to bind Na+. Through comparative ThT fluorescence spectrometry studies, while a control G4 DNA exhibited notable fluorescence enhancement up to 5 mM K+ with a Kd of 0.28 ± 0.06 mM, the Ce13d DNAzyme fluorescence was negligibly perturbed with similar concentrations of K+. Opposed to this, Ce13d displayed specific remarkable fluorescence decrease with low millimolar concentrations of Na+. NMR experiments at two different pH values suggest that Ce13d adopts a significantly different conformation or equilibrium of conformations in the presence of Na+ versus K+ and has a more stable structure in the presence of Na+. Additionally, absence of characteristic G4 peaks in one-dimensional 1H NMR suggest that G4 is not responsible for the Na+ binding. This hypothesis is confirmed by the absence of characteristic peaks in the CD spectra of this sequence. Therefore, we concluded that the aptamer must be selective for Na+ and that it binds Na+ using a structural element that does not contain G4.

Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes

Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.

Constructing a Facile Biocomputing Platform Based on Smart Supramolecular Hydrogel Film Electrodes with Immobilized Enzymes and Gold Nanoclusters

Herein, fluorescent gold nanoclusters (AuNCs) and horseradish peroxidase (HRP) were simultaneously embedded into self-assembled dipeptide supramolecular films of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-FF) on the surface of ITO electrodes (Fmoc-FF/AuNCs/HRP) by using a simple single-step process. In the films, both the fluorescence property of AuNCs and the bioelectrocatalytic property of HRP were well maintained and could be reversibly regulated by pH-sensitive structural changes in the Fmoc-FF hydrogel films. Cu(II)/EDTA in the solution could lead to the aggregation/disaggregation of AuNCs and further quenching/dequenching the fluorescence signal from the films. Meanwhile, the blue complexes formed by Cu(II) and EDTA could produce a UV-vis signal in the solution. In addition, the coordinated Cu(II) in the films enhanced the electrocatalytic capacity toward the reduction of H₂O₂ and could switch the current signal. A biomolecular logic circuit was built based on the smart film electrode system by using pH, the concentrations of EDTA, Cu(II) and H₂O₂ as inputs, while the fluorescence intensity (FL), current (I) and UV-vis extinction (E) of the solution as outputs. Various logic devices were fabricated using the uniform platform, consisting of an encoder/decoder, demultiplexer, dual-transfer gate, keypad lock, digital comparator, half adder, and controlled NOT (CNOT) gate. Specifically, an electronic three-value logic gate, gullibility (ANY) gate, was first mimicked in this biocomputing system. This work not only demonstrated the construction of a new type of multivalued logic gate by using a dipeptide micromolecular matrix but also provided a new approach for designing sophisticated biologic functions, establishing smart multianalyte biosensing or fabricating biology information processing through the use of a simple film system.

Information processing using an integrated DNA reaction network

Living organisms use interconnected chemical reaction networks (CRNs) to exchange information with the surrounding environment and respond to diverse external stimuli. Inspired by nature, numerous artificial CRNs with a complex information processing function have been recently introduced, with DNA as one of the most attractive engineering materials. Although much progress has been made in DNA-based CRNs in terms of controllable reaction dynamics and molecular computation, the effective integration of signal translation with information processing in a single CRN remains to be difficult. In this work, we introduced a stimuli-responsive DNA reaction network capable of integrated information translation and processing in a stepwise manner. This network is designed to integrate sensing, translation, and decision-making operations by independent modules, in which various logic units capable of performing different functions were realized, including information identification (YES and OR gates), integration (AND and AND-AND gates), integration-filtration (AND-AND-NOT gate), comparison (Comparator), and map-to-map analysis (Feynman gate). Benefitting from the modular and programmable design, continuous and parallel processing operations are also possible. With the innovative functions, we show that the DNA network is a highly useful addition to the current DNA-based CRNs by offering a bottom-up strategy to design devices capable of cascaded information processing with high efficiency.

Leveraging autocatalytic reactions for chemical domain image classification

Autocatalysis is fundamental to many biological processes, and kinetic models of autocatalytic reactions have mathematical forms similar to activation functions used in artificial neural networks. Inspired by these similarities, we use an autocatalytic reaction, the copper-catalyzed azide-alkyne cycloaddition, to perform digital image recognition tasks. Images are encoded in the concentration of a catalyst across an array of liquid samples, and the classification is performed with a sequence of automated fluid transfers. The outputs of the operations are monitored using UV-vis spectroscopy. The growing interest in molecular information storage suggests that methods for computing in chemistry will become increasingly important for querying and manipulating molecular memory.

Dual recognition element-controlled logic DNA circuit for COVID-19 detection based on exonuclease III and DNAzyme

Two fragments of the COVID-19 genome (specific and homologous) were used as two inputs to construct an AND logic gate for COVID-19 detection based on exonuclease III and DNAzyme. The detection sensitivity of the assay can reach fM levels. Satisfactory recovery values were obtained in real sample analysis.

A versatile molecular logic system based on Eu(III) coordination polymer film electrodes combined with multiple properties of NADH

Herein, a new type of lanthanide coordination polymer film made up of europium (Eu(iii)) and poly(N-methacryloylglycine) (Eu(iii)-PMAG) was prepared on an ITO electrode surface driven by the coordination between N-methacryloylglycine (MAG) and Eu(iii) through a single-step polymerization process. The fluorescence signal of Eu(iii)-PMAG films at 617 nm originating from Eu(iii) could be well retained in the buffer solution but was regulated by the concentration of Cu(ii) and the complexing agent EDTA. The switching of fluorescence by Cu(ii) was attributed to the inhibition of the "antenna effect" between Eu(iii) and the MAG ligand in the films. The coexistence of reduced β-nicotinamide adenine dinucleotide (NADH) in the solution can apparently quench the fluorescence of Eu(iii)-PMAG films through the internal filtration effect of UV absorbance overlapping the excitation wavelength, but itself exhibiting a fluorescence emission at 468 nm. In addition, the electrocatalytic oxidation of NADH with the help of the ferrocenedicarboxylic acid (FcDA) probe demonstrated a cyclic voltammetry (CV) signal at 0.45 V (vs. SCE). Based on various reversible stimulus-responsive behaviours, a 4-input/10-output logic network was built using Cu(ii), EDTA, NADH and FcDA as inputs and the signals of fluorescence from Eu(iii)-PMAG (617 nm) and NADH (468 nm), the CV response from FcDA and the UV-vis absorbance from the Cu(ii)-EDTA complex as outputs. Meanwhile, 6 different functional logic devices were constructed based on the same versatile platform, including a 2-to-1 encoder, a 1-to-2 decoder, a 1-to-2 demultiplexer, a parity checker, a transfer gate and a reprogrammable 3-input/2-output keypad lock. Combined with the new type of lanthanide coordination polymer film, NADH played central roles in designing sophisticated computing systems with its fluorescence, UV and electrocatalytic properties. This work might provide a novel avenue to develop intelligent multi-analyte sensing and information processing at the molecular level based on one single platform.

Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA-Templated Silver Nanoclusters as Universal Dual-Output Generators

Exquisite administration of a new type of hairpin DNA-templated silver nanoclusters (H-AgNCs) as universal dual-output generators in DNA-based logic systems is reported. Diverse concomitant contrary logic gates (CCLGs) with opposite functions (YES^{^} NOT, OR^{^} NOR, INHIBIT^{^} IMPLICATION, XOR^{^} XNOR, and MAJORITY^{^} MINORITY) and extended concatenated logic circuits are presented and some of them perform specific functions, such as parity generators and checkers. The introduction of H-AgNCs as noncovalent signal reporters avoids tedious and high-cost labeling procedures. Of note, the concomitant feature of CCLGs attributed to the dual-emitter AgNCs conduces to reducing the time and cost to devise multiple logic gates. As compared to previous ones, this design eliminates numerous substances (e.g., organic dyes) and unstable components (hydrogen peroxide), which not only decreases the complexity of logic performs and improves repeatability of operation, but also makes it convenient to connect distinct DNA-based logic gates. It is worthy to anticipate that the cost-effective strategy will inspire researchers to develop much more complex logic systems and contribute to the field of molecular computing.

Indicator Displacement Assay Inside Dye-Functionalized Covalent Organic Frameworks for Ultrasensitive Monitoring of Sialic Acid, an Ovarian Cancer Biomarker

Identifying biomolecules for disease diagnosis requires simple, accurate, and reliable analytical techniques. Multiple signal transduction pathways have promoted the development of various biological analysis systems. However, most systems are largely limited by a single mechanism or model analysis, which can easily lead to false-positive/negative results. Herein, we report a covalent organic framework (COF) (TpPa-1) functionalized with a dye (fluorescein sodium) and design this hybrid material (TpPa-1@Dye) to fabricate hydrogels for subsequent analysis with the indicator displacement assay (IDA) method. Selecting a suitable metal cation (Cr³⁺) for the preparation of hydrogels can reduce the background fluorescence, improve the detection sensitivity, and increase the corresponding sensing selectivity. The TpPa-1@Dye functions as an indicator in the IDA-in-COF system, and Cr³⁺ is a receptor of the analyte (sialic acid (SA), a biomarker for ovarian cancer diagnosis). Based on the above studies, the integrative logic operations (AND + IMP) are further established, it helps in elucidating the design rules of the IDA-in-COF approach. This work represents the first effort in designing IDA-in-COF luminescent sensors with an On-Off-On mechanism to determine biomarkers and provides a new approach for developing hybrid COF luminescent materials as analysis platforms for human health monitoring.

DNA logic circuits based on FokI enzyme regulation

A series of DNA logic devices was constructed based on the allosteric strategy of the enzyme-assisted cleavage regulation system, which are simple in scale, modular, and work efficiently.

A biocomputing platform with electrochemical and fluorescent signal outputs based on multi-sensitive copolymer film electrodes with entrapped Au nanoclusters and tetraphenylethene and electrocatalysis of NADH

In this work, poly(N,N'-dimethylaminoethylmethacrylate-co-N-isopropylacrylamide) copolymer films were polymerized on the surface of Au electrodes with a facile one-step method, and Au nanoclusters (AuNCs) and tetraphenylethene (TPE) were synchronously embedded in the films, designated as P(DMA-co-NIPA)/AuNCs/TPE. Ferrocene dicarboxylic acid (FDA), an electroactive probe in solution displayed inverse pH- and SO42--sensitive on-off cyclic voltammetric (CV) behaviors at the film electrodes. The electrocatalytic oxidation of nicotinamide adenine dinucleotide (NADH) mediated by FDA in solution could substantially amplify the CV response difference between the on and off states. Moreover, the two fluorescence emission (FL) signals from the TPE constituent at 450 nm and AuNCs component at 660 nm in the films also demonstrated SO42-- and pH-sensitive behaviors. Based on the aforementioned results, a 4-input/9-output biomolecular logic circuit was constructed with pH, Na2SO4, FDA and NADH as the inputs, and the CV signals and the FL responses at 450 and 660 nm at different levels as the outputs. Additionally, some functional non-Boolean devices were elaborately designed on an identical platform, including a 1-to-2 decoder, a 2-to-1 encoder, a 1-to-2 demultiplexer and different types of keypad locks. This work combines copolymer films, bioelectrocatalysis, and fluorescence together so that more complicated biocomputing systems could be established. This work may pave a new way to develop advanced and sophisticated biocomputing logic circuits and functional devices in the future.

MIL-61 and Eu3+@MIL-61 as Signal Transducers To Construct an Intelligent Boolean Logical Library Based on Visualized Luminescent Metal-Organic Frameworks

MIL-61 and its postsynthesis product (Eu³⁺@MIL-61) are employed as signal transducers to construct a series of basic logic gates (NOT, NAND, INHIBIT, and XNOR) on account of their simple synthetic process and fascinating luminescent properties. Also, a two-output combinational logic gate and a cascaded logic gate can be constructed on these two signal transducers by changing the inputs. In this logic gate library system, the fluorescence of MIL-61 (λ_395nm) or Eu³⁺@MIL-61 (λ_615nm) is used as outputs with a threshold of 0.5. The advantage of this boolean logical library is that the two signal transducers are readily available and cost effective. In addition, the luminescence change is visible to the naked eye under a UV lamp, which is more convenient in application. More importantly, it presents a new route for the design of a molecular logic gate library based on luminescent metal-organic frameworks. And for further application, we experimentally construct two logic devices (a 4-to-2 encoder and a parity checker) based on Eu³⁺@MIL-61 to perform nonarithmetic information.

Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits

DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.

DNA Quadruple Helices in Nanotechnology

DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.

A DNA arithmetic logic unit for implementing data backtracking operations

A data backtracking operation was successfully realized by adding redundant modules to the circuit, greatly improving the system reliability.

A resettable supramolecular platform for constructing scalable encoders

A supramolecular platform prototype for implementing resettable encoding functions was designed, which could be configured into a series of encoders, from 4-to-2 to 7-to-3, and even 14-to-4 ECs.

Target-inspired Zn2+-dependent DNAzyme for ultrasensitive impedimetric aptasensor based on polyacrylic acid nanogel as amplifier

In general, the traditional impedimetric aptasensor for detecting protein is based on its high molecular weight and low dielectric constant. Yet, the efficiency of these aptasensors is hindered by the slight resistance change in the trace concentration range because of the high initial resistance (the electrostatic repulsion between the compact negatively charged DNA on the electrode and [Fe(CN)₆]^3-/4-). To effectively and simply circumvent this issue and improve the detection sensitivity, we design an impedimetric aptasensor by reducing the substrate DNA's density on the electrode through the target-inspired recycling DNA cleavage. In order to enlarge the differences in resistance, the polyacrylic acid (PAA) nanogel is implemented as amplifier due to its poor conduction and negative charge that can hinder electron transfer and repulse the mediator [Fe(CN)₆]^3-/4-, respectively. Based on the target-inspired DNAzyme and PAA nanogel as amplifier, the ultrasensitive impedimetric aptasensor of carcinoembryonic antigen (CEA) in the buffer solution possesses a wide dynamic range of 10 fg mL^-1 to 10 ng mL^-1 and ultra-low detection limit of 7.9 fg mL^-1 (10-fold relative to equivalent aptasensors). When tested in human serum, the proposed aptasensor exhibits good performance with an ultra-low detection limit of 1.4 fg mL^-1, which is slightly higher than that in buffer solution.

Tuning the ring strain effect in acridine derivatives on binding affinity with G-quadruplex-DNA: A computational and experimental study

Search for inhibitors to stabilize the telomeric G-quadruplex in order to deter telomerase activity is an active area of research. Inhibitors play an important role to initiate the tumor cell mortalization process. This work reports for the first time of acridine derivative with four membered ammonium rings at the side chain to surpass the binding ability against BRACO-19 with G-quadruplex-DNA. It is known in the literature that acridine based molecule BRACO-19 can effectively bind with G-quadruplex-DNA. The computational study performed in this study revealed that the binding ability of acridine based molecule can be augmented with subtle variation in the molecular structure of the drug like candidates. Steered molecular dynamics (SMD) performed with the acridine derivatives and G-quadruplex DNA showed the importance of ring strain to the side chain of those ligand molecules. The rupture force analysis, hydrogen bonding interactions and the calculated free energies in MM-PBSA method suggest that ligand 3 is superior than that of BRACO-19. The synthesized ligand 3 and BRACO-19 showed the binding constants obtained from ITC measurements are 4 × 10⁶ mol^-1 and 2.6 × 10⁶, which corroborates the computational findings.

A domain-based DNA circuit for smart single-nucleotide variant identification

According to the differential information of four homologous oligonucleotides, two domain-based encoders have been constructed with the molecular information as the input. Based on the one-to-one correspondence between the input and output, SNVs can be identified and their sites can be located at the domain level.

Enzyme-Regulated DNA-Based Logic Device

Herein, we report a carbazole (Cz) ligand that displays distinct turn-on fluorescence signals upon interaction with human telomeric G-quadruplex ( h-TELO) and nuclease enzymes. Interestingly, Cz selectively binds and stabilizes the mixed hybrid topology of h-TELO G-quadruplex that withstands digestion by exonucleases and nuclease S1. The distinct fluorescence signatures of Cz-stabilized h-TELO with nucleases are used to design conceptually novel DNA devices for selectively detecting the enzymatic activity of DNase I as well as performing logic operations. An INHIBIT logic gate is constructed using h-TELO and DNase I as the inputs while the inputs of h-TELO and nuclease S1 form a YES logic gate. Furthermore, a two-input two-output reusable logic device with "multireset" function is developed by using h-TELO and DNase I as inputs. On the basis of this platform, combinatorial logic systems (INHIBIT-INHIBIT and NOR-OR) have been successfully installed using different combinations of nucleases as inputs. Moreover, this new strategy of using a synthetic dual emissive probe and enzyme/DNA inputs for constructing reusable logic device may find important applications in biological computing and information processing.

How to Construct DNA Hydrogels for Environmental Applications: Advanced Water Treatment and Environmental Analysis

With high binding affinity, porous structures, safety, green, programmability, etc., DNA hydrogels have gained increasing recognition in the environmental field, i.e., advanced treatment technology of water and analysis of specific pollutants. DNA hydrogels have been demonstrated as versatile potential adsorbents, immobilization carriers of bioactive molecules, catalysts, sensors, etc. Moreover, altering components or choosing appropriate functional DNA optimizes environment-oriented hydrogels. However, the lack of comprehensive information hinders the continued optimization. The principle used to fabricate the most suitable hydrogels in terms of the requirements is the focus of this Review. First, different fabrication strategies are introduced and the ideal characteristic for environmental applications is in focus. Subsequently, recent environmental applications and the development of diverse DNA hydrogels regarding their synthesis mechanism are summarized. Finally, the Review provides an insight into the remaining challenging and future perspectives in environmental applications.

Smart Sensing Based on DNA-Metal Interaction Enables a Label-Free and Resettable Security Model of Electrochemical Molecular Keypad Lock

Recently, molecular keypad locks have received increasing attention. As a new subgroup of smart biosensors, they show great potential for protecting information as a molecular security data processor, rather than merely molecular recognition and quantitation. Herein, label-free electrochemically transduced Ag⁺ and cysteine (Cys) sensors were developed. A molecular keypad lock model with reset function was successfully realized based on the balanced interaction of metal ion with its nucleic acid and chemical ligands. The correct input of "1-2-3" (i.e., "Ag⁺-Cys-cDNA") is the only password of such molecular keypad lock. Moreover, the resetting process of either correct or wrong input order could be easily made by Cys, buffer, and DI water treatment. Therefore, our system provides an even smarter system of molecular keypad lock, which could inhibit illegal access of unauthorized users, holding great promise in information protection at the molecular level.

Thiolated DNA-templated silver nanoclusters with strong fluorescence emission and a long shelf-life

Thiolated DNA (DNA-SH) was employed as a template in the synthesis and stabilization of AgNCs (DNA-SH-AgNCs). Resulting from the synergistic protective effect of specific Ag⁺-DNA interactions and Ag-S bonding, DNA-SH-AgNCs exhibited high quantum yields and resistance to oxidation.