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.     

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.     

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.     

Coherent Activation of DNA Tweezers: A “SET–RESET” Logic System

Open sesame : Aptamer–substrate complexes activate the coherent operation of two tweezers that act as a “SET–RESET” logic system. Each tweezer cycles between a fluorescent open state and a closed quenched state (Q=quencher, F=fluorophore) when triggered by adenosine monophosphate (AMP) and adenosine deaminase (AD).

     

A Reversible Multi‐Stimuli‐Responsive Fluorescence Probe and the Design for Combinational Logic Gate Operations

Here, a novel multi‐stimuli‐responsive fluorescence probe is developed by incorporating spiropyran group into the coumarin‐substituted polydiacetylene (PDA) vesicles. The fluorescence of PDA can be turned on upon heating, and can be quenched upon exposure to UV light irradiation or pH stimuli owing to the fluorescene resonance energy transfer (FRET) between the red‐phase PDA and the open merocyanine (MC) form of spiropyran. Moreover, we have designed and experimentally realized a set of logic gate operations for the first time based on the fluorescence modulation of the designed system upon thermal, photo, and pH stimuli. This novel type of resettable logic gates augur well for practical applications in information storage, optical recording, and sensing in complicated microenvironments.

     

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.     

Separation/Concentration‐signal‐amplification in‐One Method Based on Electrochemical Conversion of Magnetic Nanoparticles for Electrochemical Biosensing

We propose a separation/concentration‐signal‐amplification in‐one method based on electrochemical conversion (ECC) of magnetic nanoparticles (MNPs) to develop a facile and sensitive electrochemical biosensor for chloramphenicol (CAP) detection. Briefly, aptamer‐modified magnetic nanoparticles (MNPs‐Apt) was designed to capture CAP in sample, then the MNPs‐Apt composite was conjugated to Au electrode through the DNA hybridization between the unoccupied aptamer and a strand of complementary DNA. The ECC method was applied to transfer MNPs labels to electrochemically active Prussian blue (PB). The anodic and cathodic currents of PB were taken for signal readout. Comparing with conventional methods that require electrochemically active labels and related sophisticated labelling procedures, this method explored and integrated the magnetic and electrochemical properties of MNPs into one system, in turn realized magnetic capturing of CAP and signal generation without any additional conventional labels. Taking advantages of the high abundance of iron content in MNPs and the refreshing effect deriving from ECC process, the method significantly promoted the signal amplification. Therefore, the proposed biosensors exhibited linear detection range from 1 to 1000 ng mL⁻¹ and a limit of detection down to 1 ng mL⁻¹, which was better than or comparable with those of most analogues, as well as satisfactory specificity, storage stability and feasibility for real samples. The developed method may lead to new concept for rapid and facile biosensing in food safety, clinic diagnose/therapy and environmental monitoring fields.     

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.     

3,4,9,10‐Perylenetetracarboxylic Acid/Hemin Nanocomposites Act as Redox Probes and Electrocatalysts for Constructing a Pseudobienzyme‐Channeling Amplified Electrochemical Aptasensor

A simple wet‐chemical strategy for the synthesis of 3,4,9,10‐perylenetetracarboxylic acid (PTCA)/hemin nanocomposites through π–π interactions is demonstrated. Significantly, the hemin successfully conciliates PTCA redox activity with a pair of well‐defined redox peaks and intrinsic peroxidase‐like activity, which provides potential application of the PTCA self‐derived redox activity as redox probes. Additionally, PTCA/hemin nanocomposites exhibit a good membrane‐forming property, which not only avoids the conventional fussy process for redox probe immobilization, but also reduces the participation of the membrane materials that act as a barrier of electron transfer. On the basis of these unique properties, a pseudobienzyme‐channeling amplified electrochemical aptasensor is developed that is coupled with glucose oxidase (GOx) for thrombin detection by using PTCA/hemin nanocomposites as redox probes and electrocatalysts. With the addition of glucose to the electrolytic cell, the GOx on the aptasensor surface bioelectrocatalyzed the reduction of glucose to produce H₂O₂, which in turn was electrocatalyzed by the PTCA/hemin nanocomposites. Cascade schemes, in which an enzyme is catalytically linked to another enzyme, can produce signal amplification and therefore increase the biosensor sensitivity. As a result, a linear relationship for thrombin from 0.005 to 20 nM and a detection limit of 0.001 nM were obtained.     

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.     

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.     

Molecular Logic Operations Based on Surfactant Nanoaggregates

Two molecular logic gates, FS1 and FS2, which display a UV and fluorescence behavior that is dependent on the pH value and the sodium dodecyl sulfate (SDS) surfactant concentration, are demonstrated based on the intramolecular charge‐transfer mechanism. They are constructed according to the inorganic salts that induce transformation from premicelle to micelle. The absorption band of FS1 at 480 nm is significantly enhanced only when both SDS and Na₂SO₄ are the input at high concentrations, in accordance with an AND logic gate. The OR logic function can be realized in a 3.5 mM SDS/FS2 aqueous solution with SDS and Na₂SO₄ as inputs along with the emission intensity as output. Furthermore, half addition and half subtraction can be incorporated in FS1. This is facilitated by the surfactant, due to its versatility.     

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.     

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.     

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.