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.     

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.     

An Enzyme‐Based Half‐Adder and Half‐Subtractor with a Modular Design

A half‐adder and a half‐subtractor have been realized using enzymatic reaction cascades performed in a flow cell device. The individual cells were modified with different enzymes and assembled in complex networks to perform logic operations and arithmetic functions. The modular design of the logic devices allowed for easy re‐configuration, enabling them to perform various functions. The final output signals, represented by redox species [Fe(CN)₆]^3?/4? or NADH/NAD⁺, were analyzed optically to derive the calculation results. These output signals might be applicable in the future for actuation processes, for example, substance release activated by logically processed signals.     

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.     

The Construction of DNA Logic Gates Restricted to Certain Live Cells Based on the Structure Programmability and Aptamer-Cell Affinity of G-Quadruplexes

DNA computation is considered a fascinating alternative to silicon-based computers; it has evoked substantial attention and made rapid advances. Besides realizing versatile functions, implementing spatiotemporal control of logic operations, especially at the cellular level, is also of great significance to the development of DNA computation. However, developing simple and efficient methods to restrict DNA logic gates performing in live cells is still a challenge. In this work, a series of DNA logic gates was designed by taking full advantage of the diversity and programmability of the G-quadruplex (G4) structure. More importantly, by further using the high affinity and specific endocytosis of cells to aptamer G4, an INHIBIT logic gate has been realized whose operational site is precisely restricted to specific live cells. The design strategy might have great potential in the field of molecular computation and smart bio-applications.     

A Reversible DNA Logic Gate Platform Operated by One‐ and Two‐Photon Excitations

We demonstrate the use of two different wavelength ranges of excitation light as inputs to remotely trigger the responses of the self‐assembled DNA devices (D‐OR). As an important feature of this device, the dependence of the readout fluorescent signals on the two external inputs, UV excitation for 1 min and/or near infrared irradiation (NIR) at 800 nm fs laser pulses, can mimic function of signal communication in OR logic gates. Their operations could be reset easily to its initial state. Furthermore, these DNA devices exhibit efficient cellular uptake, low cytotoxicity, and high bio‐stability in different cell lines. They are considered as the first example of a photo‐responsive DNA logic gate system, as well as a biocompatible, multi‐wavelength excited system in response to UV and NIR. This is an important step to explore the concept of photo‐responsive DNA‐based systems as versatile tools in DNA computing, display devices, optical communication, and biology.     

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.     

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.     

Versatile Logic Devices Based on Programmable DNA‐Regulated Silver‐Nanocluster Signal Transducers

A DNA‐encoding strategy is reported for the programmable regulation of the fluorescence properties of silver nanoclusters (AgNCs). By taking advantage of the DNA‐encoding strategy, aqueous AgNCs were used as signal transducers to convert DNA inputs into fluorescence outputs for the construction of various DNA‐based logic gates (AND, OR, INHIBIT, XOR, NOR, XNOR, NAND, and a sequential logic gate). Moreover, a biomolecular keypad that was capable of constructing crossword puzzles was also fabricated. These AgNC‐based logic systems showed several advantages, including a simple transducer‐introduction strategy, universal design, and biocompatible operation. In addition, this proof of concept opens the door to a new generation of signal transducer materials and provides a general route to versatile biomolecular logic devices for practical applications.     

Highly Sensitive INHIBIT and XOR Logic Gates Based on ICT and ACQ Emission Switching of a Porphyrin Derivative

Fluorescence‐switch‐based logic devices are very sensitive compared with most of the reported devices based on UV/Vis absorption systems. Herein, we demonstrate that a simple molecule, 5,10,15,20‐tetra‐(4‐aminophenyl)porphyrin (TAPP), shows protonation‐induced multiple emission switches through intramolecular charge transfer and/or aggregation‐caused quenching. Highly sensitive INHIBIT and XOR logic gates can be achieved by combining the intermolecular assembly with the intramolecular photoswitching of diprotonated TAPP (TAPPH₂²⁺). In addition, molecular simulations have been performed by DFT for a better understanding of the emission‐switching processes.     

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.     

Systems Chemistry: Logic Gates,Arithmetic Units,and Network Motifs in Small Networks

How much “systems chemistry” really exists within small networks? To answer this question, the authors study tertiary networks that facilitate molecular replication through all Boolean logic operations and show how such gates can be wired together to perform computational and feed‐forward based network motifs (see graphic).

     

Hetero‐oligophenylene‐Based AIEE Material as a Multiple Probe for Biomolecules and Metal Ions to Construct Logic Circuits: Application in Bioelectronics and Chemionics

New hetero‐oligophenylene derivative ( 2 ) was synthesized which exhibits aggregation‐induced emission enhancement (AIEE) in H₂O/THF (80:20). The aggregates serve as a biological probe for three different proteins, that is bovine serum albumin (BSA), cytochrome c, and lysozyme, and DNA in contrasting modes. Further, among 29 metal ions tested, the contrasting fluorescence behavior of aggregates of 2 is observed with only Pb²⁺ and Pd²⁺ ions. Multiple output logic circuits based upon the fluorescence behavior between BSA and cytochrome c and between Pb²⁺ and Pd²⁺ ions are constructed.     

Nucleic Acid Driven DNA Machineries Synthesizing Mg2+‐Dependent DNAzymes: An Interplay between DNA Sensing and Logic‐Gate Operations

Polymerase/nicking enzymes and nucleic‐acid scaffolds are implemented as DNA machines for the development of amplified DNA‐detection schemes, and for the design of logic gates. The analyte nucleic acid target acts, also, as input for the logic gates. In the presence of two DNA targets, acting as inputs, and appropriate DNA scaffolds, the polymerase‐induced replication of the scaffolds, followed by the nicking of the replication products, are activated, leading to the autonomous synthesis of the Mg²⁺‐dependent DNAzyme or the Mg²⁺‐dependent DNAzyme subunits. These biocatalysts cleave a fluorophore/quencher‐functionalized nucleic‐acid substrate, thus providing fluorescence signals for the sensing events or outputs for the logic gates. The systems are used to develop OR, AND, and Controlled‐AND gates, and the DNA‐analyte targets represent two nucleic acid sequences of the smallpox viral genome.     

A New Compound for Sequential Sensing of Picric Acid and Aliphatic Amines: Physicochemical Details and Construction of Molecular Logic Gates

Picric acid (PA) at low concentration is a serious water pollutant. Alongside, aliphatic amines (AAs) add to the queue to pollute surface water. Plenty of reports are available to sense PA with an ultralow limit of detection (LOD). However, only a handful of works are testified to detect AAs. A new fluorescent donor-acceptor compound has been synthesized with inherent intramolecular charge transfer (ICT) character that enables selective and sensitive colorimetric quantitative detection of PA and AAs with low LODs in non-aqueous as well as aqueous solutions. The synthesized compound is based on a hemicyanine skeleton containing two pyridenylmethylamino groups at the donor and a benzothiazole moiety at the acceptor ends. The detailed mechanisms and reaction dynamics are explained spectroscopically along with computational support. The fluorescence property of the detecting compound changes due to protonation of its pyridinyl centers by PA leading to quenching of fluorescence and subsequently de-protonation by AAs to revive the signal. We have further designed logic circuits from the acquired optical responses by sequential interactions.     

Label‐Free Logic Modules and Two‐Layer Cascade Based on Stem‐Loop Probes Containing a G‐Quadruplex Domain

A simple, versatile, and label‐free DNA computing strategy was designed by using toehold‐mediated strand displacement and stem‐loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two‐layer logic cascade were constructed. The probes contain a G‐quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light‐up fluorescent signal of G‐quadruplex/NMM complex was used as the output readout. The inputs are the disease‐specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label‐free and modular strategy might be adapted in multi‐target diagnosis through DNA hybridization and aptamer‐target interaction.     

PNIPAM Copolymers Containing Light‐Responsive Chromophores: A Method Toward Molecular Logic Gates

A series of thermo‐responsive PNIPAM copolymers containing different amounts of fulgimide moieties has been synthesized via a polymer analogous reaction of poly(pentafluorophenyl acrylate). All copolymers were designed to exhibit a lower critical solution temperature (LCST) in water, which was only weakly dependent on the amount of incorporated chromophoric fulgimide groups. The copolymers showed a photocyclization of the fulgimide side groups upon irradiation with UV‐light accompanied with a color change. The closed form of the chromophore had a halftime of 136 min for the visible reisomerization and did not affect the LCST of the polymer. This led to the realization of a logic “NOT A” for the fulgimide containing PNIPAM, while a corresponding azobenzene containing PNIPAM resulted in a different logic “A implies B”.

     

Biofuel Cells for Self‐Powered Electrochemical Biosensing and Logic Biosensing: A Review

This article reviews recent advances and progress in developing electrochemical (EC) biosensing and logic biosensing systems based on self‐powered biofuel cells (BFCs). BFCs that exploit enzymes and microbes have attracted a considerable recent interest owing to their unique ability to provide sustainable energy from renewable fuel source under mild conditions. This review focuses on recently introduced novel concepts for using BFCs as the basic element for EC‐biosensing and especially EC‐logic biosensing applications. The fabrication and design of such self‐powered EC‐biosensing and EC‐logic biosensing are described along and different new approaches for BFCs‐based EC‐biosensing and EC‐logic biosensing involving substrate effects, inhibition effects, blocking effects and gene regulation effects. Latest advances in coupling a self‐powered diagnostic operation with logic‐activated drug release functionality are discussed. We conclude with the implications of the new self‐powered biosensing/logic‐biosensing platforms along with future prospects and challenges.