Multi-level logic gate operation based on amplified aptasensor performance

Single-Molecule Resettable DNA Computing via Magnetic Tweezers

DNA-based Boolean logic computing has emerged as a leading technique in biosensing, diagnosis, and therapeutics. Due to the development of the biological and chemical methods, especially the toehold-mediated DNA strand displacement (TMSD) reaction, different logic gates as well as circuits can be performed. However, most of these methods have been conducted at the bulk level, which may lead to missing information and be less controllable. Herein, we engineered single-molecule DNA computing controlled by stretching forces using magnetic tweezers. By tracking the real-time signals of the DNA extension, the output can be determined at a single base-pair resolution. A kinetics-controllable TMSD reaction was realized in the range of a ∼19-fold change of the reaction rate by different stretching forces. OR, AND, and NOT gates were also achieved. In addition, resettable DNA computing using force stretching cycles has been further exemplified. Overall, such a real-time, label-free, and force-controlled single-molecule DNA computing system provided new insight into molecular computing.

Multifunctional Carbon Nanocomposites as Nanoneurons from Multimode and Multianalyte Sensing to Molecular Logic Computing, Steganography, and Cryptography

Inspired by information exchange and logic functions of life based on molecular recognition and interaction networks, ongoing efforts are directed toward development of molecular or nanosystems for multiplexed chem/biosensing and advanced information processing. However, because of their preparation shortcomings, poor functionality, and limited paradigms, it is still a big challenge to develop advanced nanomaterials-based systems and comprehensively realize neuron-like functions from multimode sensing to molecular information processing and safety. Herein, using fish scales derived carbon nanoparticles (FSCN) as a reducing agent and stabilizer, a simple one-step synthesis method of multifunctional silver-carbon nanocomposites (AgNPs-FSCN) is developed. The prepared AgNPs-FSCN own wide antibacterial and multisignal response abilities in five channels (including color, Tyndall, absorption and fluorescence intensities, and absorption wavelength) for quantitative colorimetric and fluorescence sensing of H₂ O₂ , ascorbic acid, and dopamine. Benefiting from its multicoding stimuli-responsive ability, molecular concealment, and programmability, AgNPs-FSCN can be abstracted as nanoneurons for implementing batch and parallel molecular logic computing, steganography, and cryptography. This research will promote the preparation of advanced multifunctional nanocomposites and the development of their multipurpose applications, including the multireadout-guided multianalyte intelligent sensing and sophisticated molecular computing, communication, and security.

Highly selective and sensitive detection of glutamate by an electrochemical aptasensor

An electrochemical aptamer-based sensor was developed for glutamate, the major excitatory neurotransmitter in the central nervous system. Determining glutamic acid release and glutamic acid levels is crucial for studying signal transmission and for diagnosing pathological conditions in the brain. Glutamic acid-selective oligonucleotides were isolated from an ssDNA library using the Capture-SELEX protocol in complex medium. The selection permitted the isolation of an aptamer 1d04 with a dissociation constant of 12 µM. The aptamer sequence was further used in the development of an electrochemical aptamer sensor. For this purpose, a truncated aptamer sequence named glu1 was labelled with a ferrocene redox tag at the 3'-end and immobilized on a gold electrode surface via Au-thiol bonds. Using 6-mercapto-1-hexanol as the backfill, the sensor performance was characterized by alternating current voltammetry. The glu1 aptasensor showed a limit of detection of 0.0013 pM, a wide detection range between 0.01 pM and 1 nM, and good selectivity for glutamate in tenfold diluted human serum. With this enzyme-free aptasensor, the highly selective and sensitive detection of glutamate was demonstrated, which possesses great potential for implementation in microelectrodes and for in vitro as well as in vivo monitoring of neurotransmitter release.

DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations

A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.

Scalable Logic Circuits with Multiple Outputs and an Automatic Reset Function Based on DNAzyme-Mediated Branch Migration

A scalable logic platform made up of multilayer DNA circuits was constructed using Pb²⁺, Cu²⁺, and Zn²⁺ as the three inputs and three different fluorescent signals as the outputs. DNAzyme-guided cyclic cleavage reactions and DNA toehold-mediated strand branch migration were utilized to organize and connect nucleic acid probes for building the high-level logic architecture. The sequence communications between each circuit enable the logic network to work as a keypad lock, which is an information protection model at the molecular level. The multi-output mode was used to monitor the gradual unlocking process of the security system, from which one can determine which password is correct or not immediately. The autocatalytic cleavage of DNAzyme makes the biocomputing circuit feasible to realize the reset function automatically without external stimuli. Importantly, the logic platform is robust and can work effectively even in complex environmental samples.

Triphenyl-imidazole based reversible coloro/fluorimetric sensing and electrochemical removal of Cu2+ ions using capacitive deionization and molecular logic gates

A simple hydroxyl-substituted triphenyl-imidazole based receptor (HTPI) which selectively detects Cu²⁺ ion by colorimetric and fluorimetric methods was developed. HTPI detects the Cu²⁺ ions with the absorption enhancement and fluorescence quenching by the possible ligand to metal charge transfer (LMCT) and the chelation-enhanced quenching (CHEQ) approaches, respectively. HTPI showed high selectivity and sensitivity for Cu²⁺ ions detection over other interfering and competing metal ions. Interestingly, HTPI detects Cu²⁺ ion (LOD) at nanomolar concentrations (19 × 10^-9 M (UV-vis) & 27 × 10^-9 M (fluorescence), respectively), which is lower than the permissible level of Cu²⁺ ion reported by World Health Organization (WHO). Furthermore, HTPI was applied to the molecular logic gate function by using chemical inputs, and Cu²⁺ ion was potentially removed (95%) via Capacitive Deionization technique.

Construction of a simple and intelligent DNA-based computing system for multiplexing logic operations

Over the past few decades, DNA-based computing technology has become a rapidly developing technology and shown remarkable capabilities in handling complex computational problems. However, most of the logical operations that DNA computer can achieve are still very basic or using large-scale operations to realize complex functions, especially in mathematics. Graphene oxide (GO) is an ideal nanomaterial for biological computing, which has been used in our previous work to perform basic logic operations. Here, we utilize GO to implement far more complex and large-scale logical computing. For the first time, in this work, we utilize the unique interaction between GO and a variety of classified single-stranded DNAs as the reaction platform, by segmenting and encoding the DNA sequences, and programming the interactions between inputs and between the inputs and reaction platform, two relative large-scale logic operations, 6-bit square-root and 9-bit cube-root logical circuits are realized. This study provides a simple but efficient method for advanced and large-scale logical mathematic operations in biotechnology, opening a new horizon for building biocomputer-based innovative functional devices.

Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications

DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials

Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.

Electrochemical dual-aptamer biosensors based on nanostructured multielectrode arrays for the detection of neuronal biomarkers

Multielectrode arrays (MEAs) have been increasingly used for the development of biosensors due to their capability to record signals from multiple channels, fast mass transfer rates, and high spatial resolution. Alzheimer's disease (AD) is often associated with mitochondrial dysfunction, which is closely related to reduced levels of adenosine triphosphate (ATP). Therefore, simultaneous detection of ATP together with amyloid-β oligomers (AβO), a reliable biomarker for AD, can potentially advance the early detection of Alzheimer's disease. In this work, a dual-aptamer modified MEA chip was developed that consists of microelectrodes modified with electrodeposited 3D nanostructures (3D-GMEs). Electrodeposition methods, deposition potential, and deposition time were systematically altered and the active surface areas as well as the electrode morphologies were characterized by cyclic voltammetry and scanning electron microscopy. The nanostructured microelectrodes were sequentially modified with AβO and ATP specific aptamer receptors. To achieve the modification of different aptamer receptors at different 3D-GMEs of the same MEA chip, electrochemical cleaning was applied to individual 3D-GMEs. Ferrocene labels were attached to the aptamer receptors to enable amperometric signaling after target-aptamer binding. The developed aptasensor showed a linear detection range from 1 pM to 200 nM for the detection of AβO and from 0.01 nM to 1000 nM for the detection of ATP. Finally, ATP and AβO were detected simultaneously in the same analyte solution by the same sensor chip, which could support the early detection of AD, provide comprehensive information about the health status of the patient, and be helpful for pathological studies of neurodegenerative diseases.

Four-in-One: Advanced Copper Nanocomposites for Multianalyte Assays and Multicoding Logic Gates

The usage of non-noble-metal nanomaterials for nanoprobes or functional modules is still a big challenge because of their poor stability, functionality, and surface plasmon resonance property. In this work, copper ion, mercaptosuccinic acid, and nanocrystalline cellulose are combined for facile one-step synthesis and self-assembly of ultrasmall copper nanoparticles to produce supercolloidal particles (NCC@MSA-Cu SPs). Cu SPs show advanced multifunctionality for fast point-of-care tests (POCTs) of four metal ions (Hg²⁺, Pb²⁺, Ag⁺, and Zr⁴⁺). These selective recognitions integrate four different chemical reaction mechanisms (ion etching, core-shell deposition, templated synthesis, and precipitation) to produce four distinct readout signals. The multisignal mode-guided multianalyte sensing strategy can effectively avoid interference that affects single signal mode-based sensing. Benefiting from the creative multi-input and multireadout abilities, the visual multicoding logic gates of OR, NOR, AND, and INHIBIT are built based on optical responses of Cu SPs.

Highly sensitive and specific detection of tumor cells based on a split aptamer-triggered dual hybridization chain reaction

Highly sensitive and specific detection of rare tumor cells is urgently needed for early tumor diagnosis. Herein, a split aptamer-based dual hybridization chain reaction (dual-HCR) strategy with flow cytometry analysis was developed to meet this purpose. With the split aptamer pair as the recognition unit and HCR as the signal amplification technique, this strategy achieved an improved detection limit as low as 20 cells in 200 μL binding buffer. Meanwhile, this method was highly specific with distinct recognition of the target cells from the control cell and mixed cell samples. Furthermore, we succeeded in the specific detection of the target cells in 50% human serum, demonstrating that this method has great potential in clinical applications. In theory, this strategy can be used to detect different target cells by using different split aptamers. Therefore, this general, sensitive and specific tumor cell detection method may be helpful for early clinical diagnosis and cancer research.

Light-Controlled, Toehold-Mediated Logic Circuit for Assembly of DNA Tiles

Inspired by cytoskeletal structures that respond sensitively to environmental changes and chemical inputs, we report a strategy to trigger and finely control the assembly of stimulus-responsive DNA nanostructures with light under isothermal conditions. The strategy is achieved via integrating an upstream light-controlled, toehold-mediated DNA strand displacement circuit with a downstream DNA tile self-assembly process. By rationally designing an upstream DNA strand module, we further transform the upstream DNA strand displacement circuit to an "AND gate" circuit to control the assembly of DNA nanostructures. This example represents the demonstration of the spatial and temporal assembly of DNA nanostructures using a noninvasive chemical input. Such a light-controlled DNA logic circuit not only adds a new element to the tool box of DNA nanotechnology but also inspires us to assemble complex and responsive nanostructures.

Ten-Input Cube Root Logic Computation with Rational Designed DNA Nanoswitches Coupled with DNA Strand Displacement Process

The predictability of Watson-Crick base-pairing provides a unique structural programmability to DNAs, promoting a facile design of bimolecular reactions that perform computation. However, most of the current architectures could only implement limited logical circuits and are incapable of handling more complex mathematical operations, thus limiting computing devices from advancing to the next-stage functional complexity. Here, by designing a multifunctional DNA-based reaction platform coupled with multiple fluorescent substrates as output reporters, we construct, for the first time, a logic circuit that can compute the cube root of a 10-bit binary number (within the decimal number 1000). This relatively large-scale logic system with 10 inputs and four outputs showcases the power of DNAs in the field of biological computing and will potentially open up a new horizon for designing novel functional devices and complex computing circuits and bringing breakthroughs in biocomputing.

Amperometric Aptasensor for Amyloid-β Oligomer Detection by Optimized Stem-Loop Structures with an Adjustable Detection Range

Amyloid-β oligomers (AβO) have become representative biomarkers for early diagnosis of Alzheimer's disease. Here, we report on an aptasensor based on stem-loop probes for sensitive and specific detection of AβO by an amperometric transducer principle using alternating current voltammetry (ACV). Stem-loop probes with redox-active moieties are immobilized on a gold substrate as a receptor element. The signal transduction mechanism relies on redox ferrocene (Fc) reporting via charge transfer on a molecular recognition event involving a conformational change of the molecular beacon. The stem-loop structures were optimized by considering the aptamers' stem length, spacer, and different ferrocene terminals. In addition, the sensor assembly and signal recording including aptamer concentration and ACV frequency dependence are discussed. Using the optimized stem-loop probe (B-3' Fc), the aptasensor showed a decrease of the Fc peak current induced by AβO binding within the broad concentration range spanning 6 orders of magnitude. Furthermore, the detection limit of the sensor can be further decreased by optimizing the ACV frequency, however at the cost of a narrowed detection range. In this work, a label-free electrochemical aptasensor is demonstrated, which facilitates the quantification of the concentration of AβO with high selectivity and subpicomolar sensitivity, which may be conducive to improving the diagnosis and pharmacology studies of Alzheimer's disease.

Ionic Strength Gated Redox Current Rectification by Ferrocene Grafted in Silica Nanochannels

In this work, a silica nanochannel membrane (SNM) consisting of a high density of vertically aligned channels on an indium tin oxide (ITO) electrode surface was used as a stencil to confine the grafting of ferrocene (Fc) via electrochemical reduction of diazonium cations. The grafting selectively occurs on the underlying ITO surface (namely, the bottom of silica nanochannels) instead of on the nanochannel walls. Thus, the obtained electrode, designated as Fc@SNM/ITO, is composed of an array of silica nanochannels with redox activity on the bottom. Immobilized Fc molecules are able to rectify the electron transfer between the underlying ITO electrode and soluble redox species. In other words, they can promote the electron transfer in one direction while suppressing that in the opposite direction. Anodic and cathodic redox rectification was observed for Fe(CN)₆^4- and IrCl₆^2-, respectively, with the magnitude of current rectification directly proportional to the concentration of redox species. Moreover, because of strong permselectivity of silica nanochannels arising from their ultrasmall size (2-3 nm in diameter) and negatively charged surface (due to deprotonation of surface silanol groups), the access of Fe(CN)₆^4- and IrCl₆^2- to nanochannels strongly depends on the ionic strength of electrolyte solution. A higher ionic strength favors the access of anionic redox species, thus leading to a larger redox current rectification. The redox current rectification phenomenon not only proves the permselective nature of silica nanochannels but also holds potential for the development of electrochemical current rectification-based sensors.

Amplification of aptamer sensor signals by four orders of magnitude via interdigitated organic electrochemical transistors

Electrochemical aptamer receptor/transducer systems are key elements of emerging E-AB sensors (aptasensor) used for the detection of various kinds of targets. However, the performance of these amperometric sensors is often limited by the low density of receptors attached to the sensor surface and high background signals. In the present work, interdigitated organic electrochemical transistors (iOECT) were used as a transducer to enhance the sensitivity and dynamic detection range of aptasensors. Therefore, the electrode of an amperometric sensor was utilized as gate electrode to operate the iOECT. This device was used to detect the low weight target molecule adenosine triphosphate (ATP), a common biomarker, which plays an important role for cardiovascular, neurodegenerative, and immune deficiency diseases. The novel aptasensor can selectively detect ATP with ultrahigh sensitivity down to the concentration of 10 pM, which is four orders of magnitude lower than the detection limit of the same aptasensor using an amperometric transducer principle (limit-of-detection of 106 nM) and most other previously reported electrochemical sensors. Furthermore, sensor regeneration was demonstrated, which facilitates reusability of OECT aptasensors. The small device size in combination with high transconductances paves the way for the development of highly sensitive integrated micro-biosensors for point-of-care applications.

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.

Enhanced Signal Amplification in a Toll-like Receptor-4 Biosensor Utilizing Ferrocene-Terminated Mixed Monolayers

A major challenge in effectively treating infections is to provide timely diagnosis of a bacterial or viral agent. Current cell culture methods require >24 h to identify the cause of infection. The Toll-like Receptor (TLR) family of proteins can identify classes of pathogens and has been shown to work well in an impedance-based biosensor, where the protein is attached to an electrode via a self-assembled monolayer (SAM). While the sensitivity of these sensors has been good, they contain a high resistance (>1 kΩ) SAM, generating relatively small signals and requiring longer data collection, which is ill-suited to implementation outside of a laboratory. Here, we describe a novel approach to increase the signal magnitude and decrease the measurement time of a TLR-4 biosensor by inserting a redox-active ferrocenyl-terminated alkanethiol into a mixed SAM containing hydroxyl- and carboxyl-terminated alkanethiols. The SAM formation and modification was confirmed via contact angle and X-ray photoelectron spectroscopy measurements, with TLR-4 immobilization demonstrated through a modified immunosorbent assay. It is shown that these TLR-4 biosensors respond selectively to their intended target, Gram-negative bacteria at levels between 1 and 10⁵ lysed cells/mL, while remaining insensitive to Gram-positive bacteria or viral particles at up to 10⁵ particles/mL. Furthermore, the signal enhancement due to the addition of ferrocene decreased the measurement time to less than 1 min and has enabled this sensor to be used with an inexpensive, portable, hand-held potentiostat that could be easily implemented in field settings.

Reconfigurable Bioinspired Framework Nucleic Acid Nanoplatform Dynamically Manipulated in Living Cells for Subcellular Imaging

In nature, the formation of spider silk fibers begins with dimerizing the pH-sensitive N-terminal domains of silk proteins (spidroins) upon lowering pH, and provides a natural masterpiece for programmable assembly. Inspired by the similarity of pH-dependent dimerization behaviors, introduced here is an i-motif-guided model to mimic the initial step of spidroin assembly at the subcellular level. A framework nucleic acid (FNA) nanoplatform is designed using two tetrahedral DNA nanostructures (TDNs) with different branched vertexes carrying a bimolecular i-motif and a split ATP aptamer. Once TDNs enter acidic lysosomes within living cells, they assemble into a heterodimeric architecture, thereby enabling the formation of a larger-size framework and meanwhile subcellular imaging in response to endogenous ATP, which can be dynamically manipulated by adjusting intracellular pH and ATP levels with external drug stimuli.

Water-Soluble Perylene Diimide for Highly Sensitive and Repeatable Metal Ion Detection with Novel Logic Gate Operation

In this paper, we report a synthesised water soluble perylene derivative, N,N′-di(2-aspartic acid)-perylene-3,4,9,10-tetracarboxylic diimide (PASP), for highly sensitive and repeatable detection of copper (Cu2+) and aluminium ions (Al3+) and novel logic gate operation. In the presence of metal ions, a dramatic decrease in PASP optical intensity was induced based on the strong interaction between terminal carboxy groups and the metal ions. Detection limits of 0.22 and 0.24μM were respectively obtained at physiological pH. The signals could be recovered upon the addition of ethylenediaminetetraacetate (EDTA) and P2O74−, which competed for Cu2+ and Al3+ in the PASP-CuII and PASP-AlIII systems and induced their dissociation as secondary sensors for anions. At least four detection cycles were performed with a high recovery efficiency. Based on these phenomena, a novel three-level logic gate (OR-IMP-OR) was performed for smart signal readout with metal ions (Cu2+ and Al3+) and anions (EDTA and P2O74−) as input signals, and the relative change of optical intensity of PASP as output signal. Furthermore, the prepared PASP molecule also responded sensitively to Cu2+ and Al3+ in 10% diluted serum medium.

Logic circuit controlled multi-responsive branched DNA scaffolds

A logic circuit controlled multi-responsive sensing platform built on a three-way DNA junction (TWJ) is reported. It enabled the construction of novel fluorescent sensing platforms responsive to any target out of HIV gene, ATP and pH value, and furthermore were logically regulated by two other targets and then behaved as different logic circuits, which consist of two tandem AND gates or cascaded NAND and INH gates by varying the positions of the fluorescent tags.

Reactive Blue 4 as a Single Colorimetric Chemosensor for Sequential Determination of Multiple Analytes with Different Optical Responses in Aqueous Media: Cu2+-Cysteine Using a Metal Ion Displacement and Cu2+-Arginine Through the Host-Guest Interaction

In the current study, we reported a novel label-free and facile colorimetric approach for the sequential detection of copper ion (Cu²⁺), L-arginine (Arg), and L-cysteine (Cys) in the H₂O (10.0 mmol L^-1 HEPES buffer solution, pH 7.0) using Reactive Blue 4 (RB4). First, the presence of Cu²⁺ led to a naked-eye color and spectral changes according to the binding site-signaling subunit approach. Then, the RB4-Cu²⁺ complex was successfully applied for Cys and Arg through different recognition pathways. The optical signals for Arg were observed due to its association involving the amino group, as well as the participation of the carboxylate group in a bidentate form to the complex, while selective behavior for Cys was explained by a metal displacement mechanism. The limits of detection for Cu²⁺, Arg, and Cys were calculated to be 1.96, 1.06, and 1.33 μmol L^-1, respectively. It could also be employed for the determination of three analytes in environmental, biological, and pharmaceutical samples. Importantly, the test strips based on RB4-Cu²⁺ complex could be used as a solid-state sensor for the detection of Cys and Arg. In addition, NAND and IMPLICATION molecular logic gates were obtained by using chemical inputs and UV-Vis absorbance signal as the output. Graphical Abstract.

A simple, label-free, electrochemical DNA parity generator/checker for error detection during data transmission based on "aptamer-nanoclaw"-modulated protein steric hindrance

The first electrochemical DNA parity generator/checker system for error detection during data transmission was constructed based on “aptamer-nanoclaw”-modulated protein steric hindrance.

Versatile DNA logic devices have exhibited magical power in molecular-level computing and data processing. During any type of data transmission, the appearance of erroneous bits (which have severe impacts on normal computing) is unavoidable. Luckily, the erroneous bits can be detected via placing a parity generator (pG) at the sending module and a parity checker (pC) at the receiving module. However, all current DNA pG/pC systems use optical signals as outputs. In comparison, sensitive, facilely operated, electric-powered electrochemical outputs possess inherent advantages in terms of potential practicability and future integration with semiconductor transistors. Herein, taking an even pG/pC as a model device, we construct the first electrochemical DNA pG/pC system so far. Innovatively, a thrombin aptamer is integrated into the input-strand and it functions as a “nanoclaw” to selectively capture thrombin; the electrochemical impedance changes induced by the “nanoclaw/thrombin” complex are used as label-free outputs. Notably, this system is simple and can be operated within 2 h, which is comparable with previous fluorescent ones, but avoids the high-cost labeled-fluorophore and tedious nanoquencher. Moreover, taking non-interfering poly-T strands as additional inputs, a cascade logic circuit (OR-2 to 1 encoder) and a parity checker that could distinguish even/odd numbers from natural numbers (0 to 9) is also achieved based on the same system. This work not only opens up inspiring horizons for the design of novel electrochemical functional devices and complicated logic circuits, but also lays a solid foundation for potential logic-programmed target detection.

Remote Electronic Control of DNA-Based Reactions and Nanostructure Assembly

The use of synthetic DNA to design and build molecular machines and well-defined structures at the nanoscale has greatly impacted the field of nanotechnology. Here we expand the current toolkit in this field by demonstrating an efficient, quantitative, and versatile approach that allows us to remotely control DNA-based reactions and DNA nanostructure self-assembly using electronic inputs. To do so we have deposited onto the surface of disposable chips different DNA input strands that upon the application of a cathodic potential can be desorbed in a remote and controlled way and trigger DNA-based reactions and DNA nanostructure self-assembly. We demonstrate that this effect is specific and versatile and allows the orthogonal control of multiple reactions and multiple structures in the same solution. Moreover, the strategy is highly tunable and can be finely modulated by varying the cathodic potential, the period of applied potential, and the density of the DNA strand on the chip surface. Our approach thus represents a versatile way to remotely control DNA-based circuits and nanostructure assembly and can allow new possible applications of DNA-based nanotools.

Programmable DNA switches and their applications

DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.

Implementation of cascade logic gates and majority logic gate on a simple and universal molecular platform

Wiring a series of simple logic gates to process complex data is significantly important and a large challenge for untraditional molecular computing systems. The programmable property of DNA endows its powerful application in molecular computing. In our investigation, it was found that DNA exhibits excellent peroxidase-like activity in a colorimetric system of TMB/H₂O₂/Hemin (TMB, 3,3′, 5,5′-Tetramethylbenzidine) in the presence of K⁺ and Cu²⁺, which is significantly inhibited by the addition of an antioxidant. According to the modulated catalytic activity of this DNA-based catalyst, three cascade logic gates including AND-OR-INH (INHIBIT), AND-INH and OR-INH were successfully constructed. Interestingly, by only modulating the concentration of Cu²⁺, a majority logic gate with a single-vote veto function was realized following the same threshold value as that of the cascade logic gates. The strategy is quite straightforward and versatile and provides an instructive method for constructing multiple logic gates on a simple platform to implement complex molecular computing.

A label-free and enzyme-free platform with a visible output for constructing versatile logic gates using caged G-quadruplex as the signal transducer

A complete set of binary basic logic gates (OR, AND, NOR, NAND, INHIBT, IMPLICATION, XOR and XNOR) is realized on a label-free and enzyme-free sensing platform using caged G-quadruplex as the signal transducer. In the presence of an appropriate input, the temporarily blocked G-rich sequence in the hairpin DNA is released through cleavage by the synergetically-stabilized Mg²⁺-dependent DNAzyme which can be made to function via the input-guided cooperative conjunction of the DNAzyme subunits. In the presence of hemin, the unblocked G-quadruplex DNAzyme catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H₂O₂ to generate a colored readout signal which can be readily distinguished by the naked eye. This strategy is quite versatile and straightforward for logic operations. Two combinatorial gates (XOR + AND and XOR + NOR) are also successfully fabricated to demonstrate the modularity and scalability of the computing elements. The distinctive advantage of this logic system is that molecular events in aqueous solution could be translated into a color change which can be directly observed by the naked eye without resorting to any analytical instrumentation. Moreover, this work reveals a new route for the design of molecular logic gates that can be executed without any labeling and immobilization procedure or separation and washing step, which holds great promise for intelligent point-of-care diagnostics and in-field applications.

A colorimetric sensor of cysteine based on self-assembly nanostructures of Fe3+-H2O2/Tetramethylbenzidine system with "On-Off" switching function

Many strategies have been explored for selectively and sensitively detecting cysteine in different samples. Here, a novel colorimetric sensor based on self-assembly nanostructures of Fe³⁺-H₂O₂/Tetramethylbenzidine system with dual-level logic gate function and colorimetric determination of cysteine were firstly explored. The proposed Fe³⁺-H₂O₂-TMB system provides a sensitive optical signal due to the selectively reductive ability of cysteine to the oxidized TMB and thus could be successfully applied to the construction of instant on-site visual detection method with a paper based test strip for cysteine determination in a sample solution as well as for a dual-level logic gate fabrication.

Introducing Ratiometric Fluorescence to MnO2 Nanosheet-Based Biosensing: A Simple, Label-Free Ratiometric Fluorescent Sensor Programmed by Cascade Logic Circuit for Ultrasensitive GSH Detection

Glutathione (GSH) plays crucial roles in various biological functions, the level alterations of which have been linked to varieties of diseases. Herein, we for the first time expanded the application of oxidase-like property of MnO₂ nanosheet (MnO₂ NS) to fluorescent substrates of peroxidase. Different from previously reported fluorescent quenching phenomena, we found that MnO₂ NS could not only largely quench the fluorescence of highly fluorescent Scopoletin (SC) but also surprisingly enhance that of nonfluorescent Amplex Red (AR) via oxidation reaction. If MnO₂ NS is premixed with GSH, it will be reduced to Mn²⁺ and lose the oxidase-like property, accompanied by subsequent increase in SC's fluorescence and decrease in AR's. On the basis of the above mechanism, we construct the first MnO₂ NS-based ratiometric fluorescent sensor for ultrasensitive and selective detection of GSH. Notably, this ratiometric sensor is programmed by the cascade logic circuit (an INHIBIT gate cascade with a 1 to 2 decoder). And a linear relationship between ratiometric fluorescent intensities of the two substrates and logarithmic values of GSH's concentrations is obtained. The detection limit of GSH is as low as 6.7 nM, which is much lower than previous ratiometric fluorescent sensors, and the lowest MnO₂ NS-based fluorescent GSH sensor reported so far. Furthermore, this sensor is simple, label-free, and low-cost; it also presents excellent applicability in human serum samples.

Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System

This paper describes an AND logic operation with amplification and transcription from DNA to RNA, using T7 RNA polymerase. All four operations, (0 0) to (1 1), with an enzyme reaction can be performed simultaneously, using four-droplet devices that are directly connected to a patch-clamp amplifier. The output RNA molecule is detected using a biological nanopore with single-molecule translocation. Channel current recordings can be obtained using the enzyme solution. The integration of DNA logic gates into electrochemical devices is necessary to obtain output information in a human-recognizable form. Our method will be useful for rapid and confined DNA computing applications, including the development of programmable diagnostic devices.

Serial DNA relay in DNA logic gates by electrical fusion and mechanical splitting of droplets

DNA logic circuits utilizing DNA hybridization and/or enzymatic reactions have drawn increasing attention for their potential applications in the diagnosis and treatment of cellular diseases. The compartmentalization of such a system into a microdroplet considerably helps to precisely regulate local interactions and reactions between molecules. In this study, we introduced a relay approach for enabling the transfer of DNA from one droplet to another to implement multi-step sequential logic operations. We proposed electrical fusion and mechanical splitting of droplets to facilitate the DNA flow at the inputs, logic operation, output, and serial connection between two logic gates. We developed Negative-OR operations integrated by a serial connection of the OR gate and NOT gate incorporated in a series of droplets. The four types of input defined by the presence/absence of DNA in the input droplet pair were correctly reflected in the readout at the Negative-OR gate. The proposed approach potentially allows for serial and parallel logic operations that could be used for complex diagnostic applications.

A label-free visual platform for self-correcting logic gate construction and sensitive biosensing based on enzyme-mimetic coordination polymer nanoparticles

In molecular logic gates, the occurrence of erroneous procedures is a frequently encountered and critical problem in data transmission, and thus it is highly desirable to develop novel logic systems with self-correction abilities. Herein, based on the horseradish peroxidase (HRP)-like activity of the novel metal coordination polymer nanoparticles formed between Cu²⁺ and guanosine monophosphate (GMP), denoted as Cu-GMP CPNs, a label-free visual platform was constructed and successfully utilized for both self-correcting logic gate construction and sensitive biosensing. The HRP-mimicking ability of Cu-GMP CPNs was verified and utilized for the sensitive detection of both H₂O₂ and glucose. More importantly, a set of logic gates (AND, OR, NOR, INHIBIT, and XNOR) were fabricated, in which two intermediate outputs, i.e., color change and precipitate formation, were combined in an "AND" mode to produce the final output, and thus the as-proposed logic system exhibited the self-correction ability to automatically correct the erroneous intermediate outputs induced by interfering substances such as HRP. Moreover, in addition to the unique feature of self-correction, the as-proposed logic system also exhibited the advantages of simple operation, rapid response and easy detection of the visual outputs by the naked eye, thus expanding its practical applications to a variety of fields. Therefore, the label-free visual platform we have proposed here offers a promising strategy for logic gate fabrication and may pave the way for the development of novel molecular computing with self-correction abilities.

DNA Domino-Based Nanoscale Logic Circuit: A Versatile Strategy for Ultrasensitive Multiplexed Analysis of Nucleic Acids

In recent years, the analytical application of logical nanodevices has attracted much attention for making accurate decisions on molecular diagnosis. Herein, a DNA domino-based nanoscale logic circuit has been constructed by integrating three logic gates (AND-AND-YES) for simultaneous analysis of multiple nucleic acid biomarkers. In the first AND gate, a chimeric target DNA comprising of four biomarkers was hybridized to three biomarker-specific oligonucleotides (TRs) via their 5'-end regions and to a capture probe-magnetic microparticle. After harvesting the complex, 3' overhang regions of the TRs were labeled with three distinct monolayer double-stranded (ds) DNA-gold nanoparticles (DNA-AuNPs). Upon gleaning the complex and addition of initiator oligonucleotide, a series of toehold-mediated strand displacement reactions, which are reminiscent of a domino chain, spontaneously occurred between the confined dsDNAs on the nanoparticles' surface in the second AND gate. The output of the second gate entered into the last gate and triggered an exponential hairpin assembly to form four-way junction nanostructures. The resulting nanostructures bear split parts of DNAzyme at each end of the four arms which, in the presence of hemin, form catalytic hemin/G-quadruplex DNAzymes with peroxidase activity. The smart biosensor has exhibited a turn-on signal when all biomarkers are present in the sample. In fact, should any of the biomarkers be nonexistent, the signal remains turned-off. The biosensor can detect the biomarkers with a LOD value of 100 aM and a noticeable capability to discriminate single-nucleotide substitutions.

Engineering chemical reaction modules via programming the assembly of DNA hairpins

The architect of enzyme-free chemical reaction modules, working as building blocks in implementing complex computing tasks, was achieved by modulating the assembly of DNA hairpins, including non-catalytic and catalytic systems. The performance of heterogeneous outputted sequences, which were programmed on different hairpins for triggering the downstream reaction, was asymmetric in the non-catalytic system, whereas symmetric in the catalytic system. Furthermore, complicated DNA-only chemical modules possessing controllable species of inputs or outputs were constructed based on our strategy. The kinetic studies revealed that the performance of the chemical modules was toehold length correlated; on the basis of which, a DNA concentration monitor was constructed.

A DNA-based parity generator/checker for error detection through data transmission with visual readout and an output-correction function

During any type of binary data transmission, the occurrence of bit errors is an inevitable and frequent problem suffered. These errors, which have fatal effects on the correct logic computation, especially in sophisticated logic circuits, can be checked through insertion of a parity generator (pG) at the transmitting end and a parity checker (pC) at the receiving end. Herein, taking even pG/pC as a model device, we constructed the first DNA-based molecular parity generator/checker (pG/pC) for error detection through data transmission, on a universal single-strand platform according to solely DNA hybridization. Compared with previous pG/pC systems, the distinct advantage of this one is that it can present not only fluorescence signals but also visual outputs, which can be directly recognized by the naked eye, using DNA inputs modulated split-G-quadruplex and its DNAzyme as signal reporters, thus greatly extending its potential practical applications. More importantly, an "Output-Correction" function was introduced into the pC for the first time, in which all of the erroneous outputs can be adequately corrected to their normal states, guaranteeing the regular operation of subsequent logic devices. Furthermore, through negative logic conversion towards the constructed even pG/pC, the odd pG/pC with equal functions was obtained. Furthermore, this system can also execute multi-input triggered concatenated logic computations with dual output-modes, which largely fulfilled the requirements of complicated computing.