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.     

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.     

Sugar‐based Molecular Computing by Material Implication

A method to integrate an (in principle) unlimited number of molecular logic gates to construct complex circuits is presented. Logic circuits, such as half‐ or full‐adders, can be reinterpreted by using the functional completeness of the implication function (IMP) and the trivial FALSE operation. The molecular gate IMP is represented by a fluorescent boronic acid sugar probe. An external wiring algorithm translates the fluorescent output from one gate into a chemical input for the next gate on microtiter plates. This process is demonstrated on a four‐bit full adder.     

Modular multi-level circuits from immobilized DNA-based logic gates

One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals.     

Rational Design and Application of a Redox‐Active,Photoresponsive, Discrete Metallogelator

A photoresponsive discrete metallogelator was rationally designed by incorporating a photochromic azobenzene subunit in the structure of a redox‐active ferrocene–peptide conjugate. The target molecule was purposefully equipped with a dipeptide unit capable of self‐assembly in response to sonication. The designed molecule was shown to undergo supramolecular self‐assembly and achieve organogelation in response to ultrasound, light, heat, and redox signals. The sol–gel phase transition of the designed gelator was found to be sensitive to a plethora of input stimuli, allowing the application of the sol–gel transition behavior in basic logic gate operations. A gel‐based NOT logic gate operation was realized when the redox‐active property of the organogel was examined by using different oxidizing agents. The smart response of the gelator was further exploited in designing XOR operations under oxidizing or non‐oxidizing conditions.     

以DNA为模板的银纳米簇荧光检测及逻辑门的构建

以DNA为模板, 合成了具有荧光性质的银纳米簇(DNA-Ag NCs), 利用荧光光谱、 紫外光谱和红外光谱等手段对其进行了表征. 基于DNA-Ag NCs与离子相互作用时产生的荧光变化可实现对离子浓度的检测. 实验结果表明, 在最佳实验条件下, Ni ²⁺及Hg ²⁺的浓度与DNA-Ag NCs荧光强度呈线性关系; 并验证了该荧光探针用于检测自来水样品中汞离子和镍离子的实用性. 由于以DNA为模板的DNA-Ag NCs能够响应多种刺激, 如Ni ²⁺, S ^2-, Hg ²⁺和pH等, 利用相应的荧光强度可构建多输入的DNA-Ag NCs逻辑门及其组合逻辑门. 当荧光输出强度(I_output)>初始荧光强度(I_origin)时, 设定输出为1, 采用各种刺激及其组合作为输入, 构建了YES, INH和组合的NOR与INH逻辑门. 而只有当I_output≥I_origin时定义为输出为1, 可建立NOT, NOR, 组合的IMP加上NOR与AND逻辑门. 基于DNA-Ag NCs可以构建响应多元输入的复杂逻辑门, 实现化学信息的转变和传输, 在构建新的分子器件方面有较大应用前景.     

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.     

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.     

Two coupled enzymes perform in parallel the 'AND' and 'InhibAND' logic gate operations

The coupled activation of two enzymes: glucose dehydrogenase (GDH) and horseradish peroxidase (HRP), is used to construct the parallel-operating AND and InhibAND logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated NADH and gluconic acid provide the output signals that follow the operations of the gates. The two gates are generated in the same vial, thus allowing the logic operations to take place in parallel, and the simultaneous readout of the functions of the gates.     

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.     

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.     

Not-XOR (NXOR) Logic Gate Realized with Enzyme-Catalyzed Reactions: Optical and Electrochemical Signal Transduction

The studied enzyme-based biocatalytic system mimics NXOR Boolean logic gate, which is a logical operator that corresponds to equality in Boolean algebra. It gives the functional value true ( 1 ) if both functional arguments (input signals) have the same logical value ( 0 , 0 or 1 , 1 ), and false ( 0 ) if they are different ( 0 , 1 or 1 , 0 ). The output signal producing reaction is catalyzed by pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH), which is inhibited at acidic and basic pH values. Two other reactions catalyzed by esterase and urease produce acetic acid and ammonium hydroxide, respectively, shifting solution pH from the optimum pH for PQQ-GDH to acidic and basic values ( 1 , 0 and 0 , 1 input combinations, respectively), thus switching the enzyme activity off (output 0 ). When the input signals are not applied ( 0 , 0 combination) or both applied compensating each other ( 1 , 1 combination) the optimum pH is preserved, thus keeping PQQ-GDH running at the high rate (output 1 ). The biocatalytic cascade mimicking the NXOR gate was characterized optically and electrochemically. In the electrochemical experiments the PQQ-GDH enzyme communicated electronically with a conducting electrode support, thus resulting in the electrocatalytic current when signal combinations 0 , 0 and 1 , 1 were applied. The logic gate operation, when it was realized electrochemically, was also extended to the biomolecular release controlled by the gate. The release system included two electrodes, one performing the NXOR gate and another one activated for the release upon electrochemically stimulated alginate hydrogel dissolution. The studied system represents a general approach to the biocatalytic realization of the NXOR logic gate, which can be included in different catalytic cascades mimicking operation of concatenated gates in sophisticated logic circuitries.     

Effective PET and ICT switching of boradiazaindacene emission: a unimolecular, emission-mode, molecular half-subtractor with reconfigurable logic gates

[reaction, structure: see text] We report a unimolecular system functioning as a combinatorial logic circuit for half-subtractor. The emission characteristics can be modulated by chemical inputs, and when followed at two different wavelengths, two functionally integrated logic gates XOR and INHIBIT are obtained. Both logic gates function in the emission mode, and with very large differences in the signal intensity allowing unequivocal assignment of logic-0 and logic-1.     

Semibiological molecular machine with an implemented "AND" logic gate for regulation of protein folding

A semibiological molecular machine with an implemented "AND" logic gate was developed, which was capable of controlling the folding process of proteins in response to ATP and light as input stimuli. The molecular design made use of a genetically engineered chaperonin GroEL bearing, at both entrance parts of its cylindrical cavity, cysteine residues, which were functionalized by an azobenzene derivative to construct photoresponsive mechanical gates (azo-GroEL). This engineered chaperonin trapped denatured green fluorescent protein (GFP(denat)) and prohibited its refolding. However, when hosting azo-GroEL detected ATP (input stimulus 1) and UV light (input stimulus 2) at the same time, it quickly released GFP(denat) to allow its refolding. In contrast, reception of either input stimulus 1 or 2 resulted in only very slow or no substantial refolding of GFP(denat). Implementation of such "AND" logic gate mechanisms in mechanically driven biomolecular systems is an important step toward the design of secured drug delivery systems.     

Digital logic circuit based on a single molecular system of salicylidene Schiff base

The salicylidene Schiff base N-3,5-dichloro-salicylidene-(S)-alpha-phenylethylamine (SPEA) has been synthesized and characterized. Stimulated by one optical input (UV light) and two chemical inputs (OH(-) and Zn(2+)), SPEA undergoes reactions of photochemistry, deprotonation, and complexation. Tailing these reactions by means of the UV-vis absorption spectra and fluorescence spectra, two obvious optical outputs, an absorption band at 323 nm and a fluorescent emission peak at 460 nm, have been obtained. On the basis of encoding binary digits in these inputs and outputs applying positive logic conventions, one monomolecular circuit, which integrates one OR, two NOT, and four AND gates, has been achieved.     

Deoxyribozyme-based logic gates

We report herein a set of deoxyribozyme-based logic gates capable of generating any Boolean function. We construct basic NOT and AND gates, followed by the more complex XOR gate. These gates were constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxyribozymes. Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in solution. The operation of these gates is conveniently connected to a fluorescent readout.     

DNA computation: a photochemically controlled AND gate

DNA computation is an emerging field that enables the assembly of complex circuits based on defined DNA logic gates. DNA-based logic gates have previously been operated through purely chemical means, controlling logic operations through DNA strands or other biomolecules. Although gates can operate through this manner, it limits temporal and spatial control of DNA-based logic operations. A photochemically controlled AND gate was developed through the incorporation of caged thymidine nucleotides into a DNA-based logic gate. By using light as the logic inputs, both spatial control and temporal control were achieved. In addition, design rules for light-regulated DNA logic gates were derived. A step-response, which can be found in a controller, was demonstrated. Photochemical inputs close the gap between DNA computation and silicon-based electrical circuitry, since light waves can be directly converted into electrical output signals and vice versa. This connection is important for the further development of an interface between DNA logic gates and electronic devices, enabling the connection of biological systems with electrical circuits.     

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.