Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions

It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule‐modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA‐based logic gates. The enzyme‐based Fredkin gate with three input and three output signals was connected to the DNA‐based Feynman gate with two input and two output signals—both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input‐controlled signal‐routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing.     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

DNA‐Based Adaptive Plasmonic Logic Gates

Self‐assembled plasmonic logic gates that read DNA molecules as input and return plasmonic chiroptical signals as outputs are reported. Such logic gates are achieved on a DNA‐based platform that logically regulate the conformation of a chiral plasmonic nanostructure, upon specific input DNA strands and internal computing units. With systematical designs, a complete set of Boolean logical gates are realized. Intriguingly, the logic gates could be endowed with adaptiveness, so they can autonomously alter their logics when the environment changes. As a demonstration, a logic gate that performs AND function at body temperature while OR function at cold storage temperature is constructed. In addition, the plasmonic chiroptical output has three distinctive states, which makes a three‐state molecular logic gate readily achievable on this platform. Such DNA‐based plasmonic logic gates are envisioned to execute more complex tasks giving these unique characteristics.     

Chemiluminescent Logic Gates Based on Functionalized Gold Nanoparticles/Graphene Oxide Nanocomposites

Label‐free logic gates (AND, OR, and INHIBIT) based on chemiluminescence (CL) as new optical readout signal have been developed by taking advantage of the unique CL activity of luminol‐ and lucigenin‐functionalized gold nanoparticles/graphene oxide (luminol‐lucigenin/AuNPs/GO) nanocomposites. It was found that Fe²⁺ ions could induce the CL emission of luminol‐lucigenin/AuNPs/GO nanocomposites in alkaline solution. On this basis, by using Fe²⁺ ions and NaOH as the inputs and the CL signal as the output, an AND logic gate was fabricated. When the initial reaction system contained luminol‐lucigenin/AuNPs/GO nanocomposites and NaOH, either Fe²⁺ ions or Ag⁺ ions could react with the luminol‐lucigenin/AuNPs/GO nanocomposites to produce a strong CL emission. This result was used to design an OR logic gate using Fe²⁺ ions and Ag⁺ ions as the inputs and CL signal as the output. Moreover, two INHIBIT logic gates for Fe²⁺ and Ag⁺ were also developed using by NaClO and L ‐cysteine as their CL inhibitors, respectively. Furthermore, the proposed logic gates were successfully used to detect Fe²⁺, Ag⁺, and L ‐cysteine, respectively. The developed logic gates may find future applications in sensing, clinical diagnostics, and environmental monitoring.     

INHIBIT‐Inspired Two‐Output DNA Logic Gates Based on Surface‐Enhanced Raman Scattering

Herein, we presented a novel logic gate based on an INHIBITION gate that performs parallel readouts. Logic gates performing INHIBITION and YES/OR were constructed using surface‐enhanced Raman scattering as optical outputs for the first time. The strategy allowed for simultaneous reading of outputs in one tube. The applicability of this strategy has been successfully exemplified in the construction of half‐adder using the two‐output logic gates as reporting gates. This reporting strategy provides additional design flexibility for dynamic DNA devices.     

Reversible Logic Gates Based on Enzyme‐Biocatalyzed Reactions and Realized in Flow Cells: A Modular Approach

Reversible logic gates, such as the double Feynman gate, Toffoli gate and Peres gate, with 3‐input/3‐output channels are realized using reactions biocatalyzed with enzymes and performed in flow systems. The flow devices are constructed using a modular approach, where each flow cell is modified with one enzyme that biocatalyzes one chemical reaction. The multi‐step processes mimicking the reversible logic gates are organized by combining the biocatalytic cells in different networks. This work emphasizes logical but not physical reversibility of the constructed systems. Their advantages and disadvantages are discussed and potential use in biosensing systems, rather than in computing devices, is suggested.     

Controlled Logic Gates—Switch Gate and Fredkin Gate Based on Enzyme‐Biocatalyzed Reactions Realized in Flow Cells

Controlled logic gates, where the logic operations on the Data inputs are performed in the way determined by the Control signal, were designed in a chemical fashion. Specifically, the systems where the Data output signals directed to various output channels depending on the logic value of the Control input signal have been designed based on enzyme biocatalyzed reactions performed in a multi‐cell flow system. In the Switch gate one Data signal was directed to one of two possible output channels depending on the logic value of the Control input signal. In the reversible Fredkin gate the routing of two Data signals between two output channels is controlled by the third Control signal. The flow devices were created using a network of flow cells, each modified with one enzyme that biocatalyzed one chemical reaction. The enzymatic cascade was realized by moving the solution from one reacting cell to another which were organized in a specific network. The modular design of the enzyme‐based systems realized in the flow device allowed easy reconfiguration of the logic system, thus allowing simple extension of the logic operation from the 2‐input/3‐output channels in the Switch gate to the 3‐input/3‐output channels in the Fredkin gate. Further increase of the system complexity for realization of various logic processes is feasible with the use of the flow cell modular design.     

Implication and Inhibition Boolean Logic Gates Mimicked with Enzyme Reactions

The enzyme system mimicking Implication (IMPLY) and Inhibition (INHIB) Boolean logic gates has been designed. The same enzyme system was used to operate as the IMPLY or INHIB gate simply by reformulating the input signals. The optical analysis of the logic operation confirmed the output generation as expected for the studied logic gates. The conceptual approach to the IMPLY and INHIB logic gates allows their construction with many other enzymes operating in a similar way.     

Multi‐Level Logic Gate Operation Based on Amplified Aptasensor Performance

Conventional electronic circuits can perform multi‐level logic operations; however, this capability is rarely realized by biological logic gates. In addition, the question of how to close the gap between biomolecular computation and silicon‐based electrical circuitry is still a key issue in the bioelectronics field. Here we explore a novel split aptamer‐based multi‐level logic gate built from INHIBIT and AND gates that performs a net XOR analysis, with electrochemical signal as output. Based on the aptamer–target interaction and a novel concept of electrochemical rectification, a relayed charge transfer occurs upon target binding between aptamer‐linked redox probes and solution‐phase probes, which amplifies the sensor signal and facilitates a straightforward and reliable diagnosis. This work reveals a new route for the design of bioelectronic logic circuits that can realize multi‐level logic operation, which has the potential to simplify an otherwise complex diagnosis to a “yes” or “no” decision.     

DNA-Based Adaptive Plasmonic Logic Gates

Self-assembled plasmonic logic gates that read DNA molecules as input and return plasmonic chiroptical signals as outputs are reported. Such logic gates are achieved on a DNA-based platform that logically regulate the conformation of a chiral plasmonic nanostructure, upon specific input DNA strands and internal computing units. With systematical designs, a complete set of Boolean logical gates are realized. Intriguingly, the logic gates could be endowed with adaptiveness, so they can autonomously alter their logics when the environment changes. As a demonstration, a logic gate that performs AND function at body temperature while OR function at cold storage temperature is constructed. In addition, the plasmonic chiroptical output has three distinctive states, which makes a three-state molecular logic gate readily achievable on this platform. Such DNA-based plasmonic logic gates are envisioned to execute more complex tasks giving these unique characteristics.     

Fluorescent Logic Gates Chemically Attached to Silicon Nanowires

I′m in the mood for dansyl : A chemically controlled fluorescent logic gate was formed by grafting a dansyl unit onto silicon nanowires (SiNWs; see picture). The logic gate was operated by utilizing pH changes, Hg^II, and Cl^? or Br^? ions as inputs and the fluorescence of the modified SiNWs as output. The modified SiNWs could perform as a three‐input logic gate that combines the YES and INH operations.

     

Interfacing Synthetic DNA Logic Operations with Protein Outputs

DNA logic gates are devices composed entirely of DNA that perform Boolean logic operations on one or more oligonucleotide inputs. Typical outputs of DNA logic gates are oligonucleotides or fluorescent signals. Direct activation of protein function has not been engineered as an output of a DNA‐based computational circuit. Explicit control of protein activation enables the immediate triggering of enzyme function and could yield DNA computation outputs that are otherwise difficult to generate. By using zinc‐finger proteins, AND, OR, and NOR logic gates were created that respond to short oligonucleotide inputs and lead to the activation or deactivation of a split‐luciferase enzyme. The gate designs are simple and modular, thus enabling integration with larger multigate circuits, and the modular structure gives flexibility in the choice of protein output. The gates were also modified with translator circuits to provide protein activation in response to microRNA inputs as potential cellular cancer markers.     

Field‐Effect Nanoparticle‐Based Glucose Sensor on a Chip: Amplification Effect of Coimmobilized Redox Species

A capacitive EIS (electrolyte‐insulator‐semiconductor) structure was modified with gold nanoparticles together with glucose oxidase and used as field‐effect‐based glucose biosensor using the constant capacitance mode. Co‐immobilization of ferrocene redox species resulted in a two‐fold increase of the biosensor sensitivity. The effect was explained by the hydrogen peroxide‐mediated oxidation of ferrocene resulting in a pool of charged species at the interface increasing the sensor response towards glucose. The studied approach was suggested as a general means to amplify signals from Si chip‐based field‐effect enzyme biosensors.     

Anion Sensors as Logic Gates: A Close Encounter?

Computers have become smarter, smaller, and more efficient due to the downscaling of silicon‐based components. Top‐down miniaturisation of silicon‐based computer components is fast reaching its limitations because of physical constraints and economical non‐feasibility. Therefore, the possibility of a bottom‐up approach that uses molecules to build nano‐sized devices has been initiated. As a result, molecular logic gates based on chemical inputs and measurable optical outputs have captured significant attention very recently. In addition, it would be interesting if such molecular logic gates could be developed by making use of ion sensors, which can give significantly sensitive output information. This review provides a brief introduction to anion receptors, molecular logic gates, a comprehensive review on describing recent advances and progress on development of ion receptors for molecular logic gates, and a brief idea about the application of molecular logic gates.     

Fluorescent Molecular Logic Gates and Pourbaix Sensors in Polyacrylamide Hydrogels

Polyacrylamide hydrogels formed by free radical polymerisation were formed by entrapping anthracene and 4-amino-1,8-naphthalimide fluorescent logic gates based on photoinduced electron transfer (PET) and/or internal charge transfer (ICT). The non-covalent immobilisation of the molecules in the hydrogels resulted in semi-solid YES, NOT, and AND logic gates. Two molecular AND gates, examples of Pourbaix sensors, were tested in acidic aqueous methanol with ammonium persulfate, a strong oxidant, and displayed greater fluorescence quantum yields than previously reported. The logic hydrogels were exposed to aqueous solutions with chemical inputs, and the fluorescence output response was viewed under 365 nm UV light. All of the molecular logic gates diffuse out of the hydrogels to some extent when placed in solution, particularly those with secondary basic amines. The study exemplifies an effort of taking molecular logic gates from homogeneous solutions into the realm of solid-solution environments. We demonstrate the use of Pourbaix sensors as pE-pH indicators for monitoring oxidative and acidic conditions, notably for excess ammonium persulfate, a reagent used in the polymerisation of SDS-polyacrylamide gels.     

Tunable Molecular Logic Gates Designed for Imaging Released Neurotransmitters

Tunable dual‐analyte fluorescent molecular logic gates (ExoSensors) were designed for the purpose of imaging select vesicular primary‐amine neurotransmitters that are released from secretory vesicles upon exocytosis. ExoSensors are based on the coumarin‐3‐aldehyde scaffold and rely on both neurotransmitter binding and the change in environmental pH associated with exocytosis to afford a unique turn‐on fluorescence output. A pH‐functionality was directly integrated into the fluorophore π‐system of the scaffold, thereby allowing for an enhanced fluorescence output upon the release of labeled neurotransmitters. By altering the pH‐sensitive unit with various electron‐donating and ‐withdrawing sulfonamide substituents, we identified a correlation between the pK_a of the pH‐sensitive group and the fluorescence output from the activated fluorophore. In doing so, we achieved a twelvefold fluorescence enhancement upon evaluating the ExoSensors under conditions that mimic exocytosis. ExoSensors are aptly suited to serve as molecular imaging tools that allow for the direct visualization of only the neurotransmitters that are released from secretory vesicles upon exocytosis.     

Logic Gates Based on Magnetic Nanoparticles Functionalized with a Bioelectrocatalytic System

Magneto‐controlled OR, AND and INHIB logic gates were designed using cobalt ferrite magnetic nanoparticles (CoFe₂O₄, saturated magnetization ca. 70 emu g^?1, 17±2 nm diameter) functionalized with microperoxidase‐11. Tunable magnetic field generated by three external permanent magnets (NdFeB) upon moving them below the electrochemical cell resulted in translocation of the biofunctionalized magnetic nanoparticles between conductive and nonconductive domains of a solid plate. This resulted in electrochemically readable output signals with the Boolean logic controlled by the magnetic input signals. The current corresponding to the reversible redox process of the heme measured at ?0.4 V (vs. SCE) was considered as “1” output signal, while a small background current obtained from the conducting interface in the absence of the magnetic nanoparticles was considered as “0” output signal. Addition of H₂O₂ to the solution resulted in the generation of a cathodic catalytic current when the microperoxidase‐11‐functionalized magnetic nanoparticles are associated with the conductive domain of the support. This resulted in the amplification of “1” output signal and the increased difference between “1” and “0” signals generated by the cell, thus reducing the possibility of errors in the Boolean logic operations.     

An Elaborate Supramolecular Assembly for a Smart Nanodevice for Ratiometric Molecular Recognition and Logic Gates

Ingenious approaches to supramolecular assembly for fabricating smart nanodevices is one of the more significant topics in nanomaterials research. Herein, by using surface quaternized cationic carbon dots (CDots) as the assembly and fluorescence platform, anionic sulfonatocalix[4]arene with modifiable lower and upper rims as a connector, as well as in situ coordination of Tb³⁺ ions, we propose an elaborate supramolecular assembly strategy for the facile fabrication of a multifunctional nanodevice. The dynamic equilibrium characteristics of the supramolecular interaction can eventually endow this nanodevice with functions of fluorescent ratiometric molecular recognition and as a nano‐logic gate with two output channels.     

Manufacturing Reusable NAND Logic Gates and Their Initial Circuits for DNA Nanoprocessors

DNA-based computers can potentially analyze complex sets of biological markers, thereby advancing diagnostics and the treatment of diseases. Despite extensive efforts, DNA processors have not yet been developed due, in part, to limitations in the ability to integrate available logic gates into circuits. We have designed a NAND gate, which is one of the functionally complete set of logic connectives. The gate's design avoids stem-loop-folded DNA fragments, and is capable of reusable operations in RNase H-containing buffer. The output of the gate can be translated into RNA-cleaving activity or a fluorescent signal produced either by a deoxyribozyme or a molecular beacon probe. Furthermore, three NAND-gate-forming DNA strands were crosslinked by click chemistry and purified in a simple procedure that allowed ≈10¹³ gates to be manufactured in 16 h, with a hands-on time of about 30 min. Two NAND gates can be joined into one association that performs a new logic function simply by adding a DNA linker strand. Approaches developed in this work could contribute to the development of biocompatible DNA logic circuits for biotechnological and medical applications.     

Metal‐Ion‐Triggered Exonuclease III Activity for the Construction of DNA Colorimetric Logic Gates

The logic system is obtained by using a series of double‐stranded (ds) DNA templates with mismatched base pairs (T–T or C–C) and ion‐modulated exonuclease III (Exo III) activity, in which the Exo III cofactors, Hg²⁺ and Ag⁺ ions, are used as inputs for the activation of the respective scission of Exo III based on the formation of T–Hg²⁺–T or C–Ag⁺–C base pairs. Additionally, two kinds of signal probes are utilized to transduce the logic operations. One is the two split G‐rich DNA strands that are used to design the OR, AND, INHIBIT, and XOR gates, whereas the other is the self‐assembled split G‐quadruplex structure to construct NOR, NAND, IMPLICATION, and XNOR operations based on DNA hybridization and strand displacement. In the presence of hemin, the split G‐quadruplex biocatalyzes the formation of a colored product, which is an output signal for the different logic gates. Thus, we have constructed a complete set of colorimetric DNA logic gates based on the Exo III and split G‐quadruplex for the first time. In addition, we are able to effortlessly recognize the logic output signals by the naked eye and their simplicity and cost‐effective design is the most apparent feature for the logic gates developed in this work.