An All-Photonic Molecular Amplifier and Binary Flip-flop

A chemical system is proposed that is capable of amplifying small optical inputs into large changes in internal composition, based on a feedback interaction between switchable fluorescence and visible-light photoswitching. This system would demonstrate bifurcating reaction kinetics under irradiation and reach one of two stable photostationary states depending on the initial composition of the system. This behavior would allow the system to act as a chemical realization of the flip-flop circuit, the fundamental element in sequential logic and binary memory storage. We use detailed numerical modeling to demonstrate the feasibility of the proposed behavior based on known molecular phenomena and comment on some of the conditions required to realize this system.

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.

A Janus-inspired amphichromatic system that kills two birds with one stone for operating a "DNA Janus Logic Pair" (DJLP) library

Although DNA computing has exhibited a magical power across diverse areas, current DNA logic gates with different functions are always separately operated and can only produce hard-to-visualize output. The fussy/obligatory gates' redesign/reconstruction and the non-intuitive output cause the wastage of time and costs, low efficiency and practicality. Herein, inspired by the ancient Roman mythical God Janus, for the first time, we propose the concept of "DNA Janus Logic Pair" (DJLP) to classify the DNA logic gates with contrary functions into "Positive + Negative" gates (DJLP = Pos + Neg). Based on the biocatalytic property of G-quadruplex DNAzyme (G4zyme) and the luminescence quenching ability of oxidized 3,3',5,5'-tetramethylbenzidine (OxTMB) towards the upconversion (UC) particles, we fabricated a universal amphichromatic platform that kills two birds with one stone for operating a versatile DJLP library. Different from the previous DNA logic systems, the "Pos + Neg" gates of each DJLP in this study were concomitantly achieved via the same one-time DNA reaction, which avoided the gates' redesign/reoperation and reduced the operating costs/time of the DNA gates by at least half. Besides, both the amphichromatic outputs (Visual-blue and UC luminescent-green) can be visualized under harmless-NIR, thus bringing greatly enhanced practicality to the method. Moreover, we constructed various concatenated logic circuits via logically modulating the G4zyme's biocatalytic property with glutathione, thus enabling the largely improved computing complexity. Furthermore, taking the circuit "YES-INH-1-2 decoder" as the "computing core", we designed an "antioxidant indicator" with ratiometric logical responses that could recognize the presence of antioxidants smartly (output changed from "10" to "01"), which provided a typical prototype for potential intelligent bio-applications.

A chemical/molecular 4-input/2-output keypad lock with easy resettability based on red-emission carbon dots-Prussian blue composite film electrodes

In this work, a resettable 4-input/2-output keypad lock system based on red-emission carbon dots (rCDs) and Prussian blue (PB) modified electrodes was developed. Electrochromic PB layers were first electrochemically deposited on the indium tin oxide (ITO) electrode surface. An admixture of rCDs and chitosan (Chi) was then cast on the surface of PB layers, forming rCDs-Chi/PB film electrodes. UV-vis absorption of the films was sensitive to the applied potential since the blue PB constituent of the films would be transformed to nearly colorless Prussian white (PW) at the reduction potential of -0.2 V and then from PW back to PB at the oxidation potential of 0.4 V, and the transformation between PB and PW would also influence the fluorescence emission of the rCD constituent in the films. The addition of cysteine (Cys) in the testing solution could reduce the PB in the films into PW and generate an amperometric electrocatalytic current at 0.4 V. Meanwhile, the addition of Fe3+ in solution could greatly quench the fluorescence from the rCD component in the films. Thus, the responses of UV-vis absorbance, fluorescence emission and amperometric current of the rCDs-Chi/PB film electrode system exhibited potential-, Cys- and Fe3+-responsive switching properties. Based on the aforementioned work, a combinational logic gate circuit with 3 inputs and 3 outputs was established. In particular, on the same platform, a novel chemical/molecular 4-input/2-output keypad lock with easy resettability was elaborately designed with amperometric current and fluorescence peak intensity as two different types of outputs, so that a higher security level could be achieved.

An intelligent 1:2 demultiplexer as an intracellular theranostic device based on DNA/Ag cluster-gated nanovehicles

The logic device demultiplexer can convey a single input signal into one of multiple output channels. The choice of the output channel is controlled by a selector. Several molecules and biomolecules have been used to mimic the function of a demultiplexer. However, the practical application of logic devices still remains a big challenge. Herein, we design and construct an intelligent 1:2 demultiplexer as a theranostic device based on azobenzene (azo)-modified and DNA/Ag cluster-gated nanovehicles. The configuration of azo and the conformation of the DNA ensemble can be regulated by light irradiation and pH, respectively. The demultiplexer which uses light as the input and acid as the selector can emit red fluorescence or a release drug under different conditions. Depending on different cells, the intelligent logic device can select the mode of cellular imaging in healthy cells or tumor therapy in tumor cells. The study incorporates the logic gate with the theranostic device, paving the way for tangible applications of logic gates in the future.

A colorimetric and fluorescent chemosensor for Hg2+ based on a photochromic diarylethene with a quinoline unit

A new colorimetric and fluorescent ‘on–off’ chemosensor, 1O, based on a photochromic diarylethene with a quinoline unit was designed and synthesized. The chemosensor 1O demonstrated selective and sensitive detection of Hg²⁺ ions in the presence of other competitive metal ions in acetonitrile. The stoichiometric ratio of the sensor 1O for Hg²⁺ was determined to be 1 : 1, and the limit of detection of the probe 1O was calculated to be 56.3 nM for Hg²⁺. In addition, a molecular logic circuit with four inputs and one output was successfully constructed with UV/vis light and metal-responsive behavior. ESI-MS spectroscopy, Job's plot analysis, and ¹H NMR titration experiments confirm the binding behavior between 1O and Hg²⁺.

A new colorimetric and fluorescent ‘on–off’ chemosensor, 1O, based on a photochromic diarylethene with a quinoline unit was designed and synthesized.

Performing Logical Operations with Stimuli-Responsive Building Blocks

Chemical logic gates can be fabricated by synthesizing molecules that have the ability to detect external stimuli (e.g., temperature or pH) and provide logical outputs. It is, however, challenging to fabricate a system that consists of many logic gates using this method: complex molecules can be difficult to synthesize and these logic gates typically cannot be integrated together. Here, we fabricated different types of logic gates by assembling a combination of different types of stimuli-responsive hydrogels that change their size under the influence of one type of stimulus. Importantly, the preparation of these stimuli-responsive hydrogels is widely reported and technically simple. Through designing the geometry of the systems, we fabricated the YES, NOT, OR, AND, NOR, and NAND gates. Although the hydrogels respond to different types of stimuli, their outputs are the same: a change in size of the hydrogel. Hence, we show that the logic gates can be integrated easily (e.g., by connecting an AND gate to an OR gate). In addition, we fabricated a standalone system with the size of a normal drug tablet (i.e., a "smart tablet") that can analyze (or diagnose) different stimuli and control the release of a chemical (or drug) via the logic gates.

Multifunctional Photonic Molecular Logic Gate Based On A Biphotochromic Dyad With Reduced Energy Transfer

Using molecular logic gates (MLGs) for information processing attracts attention due to perspectives of creating molecular computers. Biphotochromic dyads are suitable models of photonic MLGs. However, they suffer from one weakness: the activity of one of the photochromes is often quenched because of Förster resonance energy transfer (FRET). Herein, we designed a dyad with reduced FRET, in which both photochromes keep their photoactivity thanks to spectral and spatial separation, allowing MLG switching between different states. This novel dyad reproduces the functionality of the full set of 16 two-input gates, as well a reversible gate-dual inverter, all gates are photonic.

Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform

A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis.

A multi-addressable diarylethene for the selective detection of Al3+ and the construction of a logic circuit

A multi-addressable diarylethene was designed and synthesized, which not only acted as a fluorescent sensor for Al³⁺ with high selectivity, but was also used to construct a combinational logic circuit.

Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications

This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications of these systems. The assembly of computational modules composed of DNAzymes has led to the operation of a universal set of logic gates, to field programmable logic gates and computing circuits, to the development of multiplexers/demultiplexers, and to full-adder systems. Also, DNAzyme cascades operating as logic gates and computing circuits were demonstrated. DNAzyme logic systems find important practical applications. These include the use of DNAzyme-based systems for sensing and multiplexed analyses, for the development of controlled release and drug delivery systems, for regulating intracellular biosynthetic pathways, and for the programmed synthesis and operation of cascades.

Room-temperature phosphorescence logic gates developed from nucleic acid functionalized carbon dots and graphene oxide

Room-temperature phosphorescence (RTP) logic gates were developed using capture ssDNA (cDNA) modified carbon dots and graphene oxide (GO). The experimental results suggested the feasibility of these developed RTP-based "OR", "INHIBIT" and "OR-INHIBIT" logic gate operations, using Hg(2+), target ssDNA (tDNA) and doxorubicin (DOX) as inputs.

Tris(8-methoxy-2-quinolylmethyl)amine (8-MeOTQA) as a highly fluorescent Zn2+probe prepared by convenient C3-symmetric tripodal amine synthesis

The convenient synthesis ofC₃-symmetric tribenzylamines utilizing acetaldehyde ammonia trimer (1) revealed tris(8-methoxy-2-quinolylmethyl)amine (8-MeOTQA) as a fluorescent zinc sensor with high sensitivity.

pH and light-controlled self-assembly of bistable [c2] daisy chain rotaxanes

Triarylamine – [c2] daisy chain rotaxane conjugates behave as logic-gates controlled by pH and light modulations to self-assemble in supramolecular fibers.

Multiconfigurable logic gates based on fluorescence switching in adaptive coordination polymer nanoparticles

Fluorescence switching of guest molecules confined in coordination polymer nanoparticles (CPNs) generated from nucleotides and lanthanide ions are used to construct multiconfigurable logic gates. Moreover, the potential of the material as fluorescent probe with large Stokes shift is demonstrated for cellular imaging. In this work the logic gate is integrated into the therapeutic agent and this will be highly beneficial in future molecular computing.

Fluorescent 1:2 demultiplexer and half-subtractor based on the hydrolysis of N-salicylidene-3-aminopyridine

In moist chloroform solution, the ultraviolet light irradiation would cause N-salicylidene-3-aminopyridine (L) to hydrolyze into salicylaldehyde and 3-aminopyridine. To consider an optical signal (UV light) and a chemical signal (Zn(2+)) as inputs, the luminescence signals as outputs, the logic behavior of compound L was investigated. Interestingly, excited by two different wavelengths lights, two sharp distinct fluorescent spectra were collected. Consequently, a fluorescent 1:2 demultiplexer and a fluorescent half-subtractor were respectively expressed.

Retracted Article: Upconversion luminescent logic gates and turn-on sensing of glutathione based on two-photon excited quantum dots conjugated with dopamine

This article reported the two-photon excited quantum dots-based novel upconversion luminescent logic gates for turn-on sensing of glutathione.

An all-photonic molecule-based parity generator/checker for error detection in data transmission

The function of a parity generator/checker, which is an essential operation for detecting errors in data transmission, has been realized with multiphotochromic switches by taking advantage of a neuron-like fluorescence response and reversible light-induced transformations between the implicated isomers.

Development of a DNA sensor using a molecular logic gate

This communication reports the increase in fluorescence resonance energy transfer (FRET) efficiency between two laser dyes in the presence of deoxyribonucleic acid (DNA). Two types of molecular logic gates have been designed where DNA acts as input signal and fluorescence intensity of different bands are taken as output signal. Use of these logic gates as a DNA sensor has been demonstrated.

Analog applications of photochemical switches

Molecules that change their structure in response to a stimulus such as light or an added chemical can act as molecular switches. Such switches can be chemically linked to other active moieties to create molecular "devices" for various purposes. There has been much activity of late in the use of molecular switches such as photochromes in the construction of molecular logic gates that carry out binary or digital functions. However, ensembles of such molecules can also act as analog devices. Here, examples of a molecular photonic signal transducer and two mimics of photosynthetic photoregulatory processes are discussed.