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.     

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.     

DNA‐Templated Assembly of a Heterobivalent Quantum Dot Nanoprobe For Extra‐ and Intracellular Dual‐Targeting and Imaging of Live Cancer Cells

Quantum dots (QDs) hold great promise for the molecular imaging of cancer because of their superior optical properties. Although cell‐surface biomarkers can be readily imaged with QDs, non‐invasive live‐cell imaging of critical intracellular cancer markers with QDs is a great challenge because of the difficulties in the automatic delivery of QD probes to the cytosol and the ambiguity of intracellular targeting signals. Herein, we report a new type of DNA‐templated heterobivalent QD nanoprobes with the ability to target and image two spatially isolated cancer markers (nucleolin and mRNA) present on the cell surface and in the cell cytosol. Bypassing endolysosomal sequestration, this type of QD nanoprobes undergo macropinocytosis following the nucleolin targeting and then translocate to the cytosol for mRNA targeting. Fluorescence resonance energy transfer (FRET) based confocal microscopy enables unambiguous signal deconvolution of mRNA‐targeted QD nanoprobes inside cancer cells.     

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.     

Lineal DNA logic gate for microRNA diagnostics with strand displacement and fluorescence resonance energy transfer

Designing molecular logic gates to operate programmably for molecular diagnostics in molecular computing still remains challenging. Here, we designed a novel linear DNA logic gates for microRNA analysis based on strand displacement and fluorescence resonance energy transfer (FRET). Two labeled strands closed each other produce to FRET through hybridization with a complementary strand to form a basic work unit of logic gate. Two indicators of heart failure (microRNA-195 and microRNA-21) were selected as the logic inputs and the fluorescence mode was used as the logic output. We have demonstrated that the molecular logic gate mechanism worked well with the construction of YES and AND gates.     

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.     

DNA-based visual majority logic gate with one-vote veto function

A molecular logic gate is a basic element and plays a key role in molecular computing. Herein, we have developed a label-free and enzyme-free three-input visual majority logic gate which is realized for the first time according to DNA hybridization only, without DNA replacement and enzyme catalysis. Furthermore, a one-vote veto function was integrated into the DNA-based majority logic gate, in which one input has priority over other inputs. The developed system can also implement multiple basic and cascade logic gates.     

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.     

Effect of Surface Modification on Semiconductor Nanocrystal Fluorescence Lifetime

Semiconductor nanocrystals, namely, quantum dots (QDs), present a set of unique photoluminescence properties, which has led to increased interest in using them as advantageous alternatives to conventional organic dyes. Many applications of QDs involve surface modification to enhance the solubility or biocompatibility of the QDs. One of the least exploited properties of QDs is the very long photoluminescence lifetime that usually has complex kinetics owing to the effect of quantum confinement. Herein, we describe the effect of different surface modifications on the photoluminescence decay kinetics of QDs. The different surface modifications were carefully chosen to provide lipophilic or water‐soluble QDs with either positive or negative surface net charges. We also survey the effect on the QD lifetime of several ligands that interact with the QD surface, such as organic chromophores or fluorescent proteins. The results obtained demonstrate that time‐resolved fluorescence is a useful tool for QD‐based sensing to set the basis for the development of time‐resolved‐based nanosensors.     

Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA‐Programmed Nanoparticle Disassembly

Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low‐abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal‐to‐background ratio of conventional molecular imaging probes. Herein, we report a class of DNA‐templated gold nanoparticle (GNP)–quantum dot (QD) assembly‐based probes for catalytic imaging of cancer‐related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA‐programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non‐catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells.     

Molecular Logic Gate Arrays

Chemists are now able to emulate the ideas and instruments of mathematics and computer science with molecules. The integration of molecular logic gates into small arrays has been a growth area during the last few years. The design principles underlying a collection of these cases are examined. Some of these computing molecules are applicable in medical‐ and biotechnologies. Cases of blood diagnostics, ‘lab‐on‐a‐molecule’ systems, and molecular computational identification of small objects are included.     

A Brief Overview of Some Physical Studies on the Relaxation Dynamics and Förster Resonance Energy Transfer of Semiconductor Quantum Dots

This article highlights some physical studies on the relaxation dynamics and Förster resonance energy transfer (FRET) of semiconductor quantum dots (QDs) and the way these phenomena change with size, shape, and composition of the QDs. The understanding of the excited‐state dynamics of photoexcited QDs is essential for technological applications such as efficient solar energy conversion, light‐emitting diodes, and photovoltaic cells. Here, our emphasis is directed at describing the influence of size, shape, and composition of the QDs on their different relaxation processes, that is, radiative relaxation rate, nonradiative relaxation rate, and number of trap states. A stochastic model of carrier relaxation dynamics in semiconductor QDs was proposed to correlate with the experimental results. Many recent studies reveal that the energy transfer between the QDs and a dye is a FRET process, as established from 1/d⁶ distance dependence. QD‐based energy‐transfer processes have been used in applications such as luminescence tagging, imaging, sensors, and light harvesting. Thus, the understanding of the interaction between the excited state of the QD and the dye molecule and quantitative estimation of the number of dye molecules attached to the surface of the QD by using a kinetic model is important. Here, we highlight the influence of size, shape, and composition of QDs on the kinetics of energy transfer. Interesting findings reveal that QD‐based energy‐transfer processes offer exciting opportunities for future applications. Finally, a tentative outlook on future developments in this research field is given.     

Enzyme-free and DNA-based universal platform for the construction of various logic devices based on graphene oxide and G-quadruplex

In the fields of biocomputing and biomolecular, DNA molecules are applicable to be regarded as data of logical computing platform that uses elaborate logic gates to perform a variety of tasks. Graphene oxide (GO) is a type of novel nanomaterial, which brings new research focus to materials science and biosensors due to its special selectivity and excellent quenching ability. G-quadruplex as a unique DNA structure stimulates the intelligent application of DNA assembly on the strength of its exceptional binding activity. In this paper, we report a universal logic device assisted with GO and G-quadruplex under an enzyme-free condition. Integrated with the quenching ability of GO to the TAMRA (fluorophore, Carboxytetramethylrhodamine) and the enhancement of fluorescence intensity produced by the peculiar binding of G-quadruplex to the NMM (N-methylmesoporphyrin IX), a series of basic binary logic gates (AND. OR. INHIBIT. XOR) have been designed and verified through biological experiments. Given the modularity and programmability of this strategy, two advanced logic gates (half adder and half subtractor) were realized on the basis of the same work platform. The fluorescence signals generated from different input combinations possessed satisfactory results, which provided proof of feasibility. We believe that the proposed universal logical platform that operates at the nanoscale is expected to be utilized for future applications in molecular computing as well as disease diagnosis.     

Hot‐Hole Extraction from Quantum Dot to Molecular Adsorbate

Ultrafast thermalized and hot‐hole‐transfer processes have been investigated in CdSe quantum dot (QD)/catechol composite systems in which hole transfer from photoexcited QDs to the catechols is thermodynamically favorable. A series of catechol derivatives were selected with different electron‐donating and ‐withdrawing groups, and the effect of these groups on hole transfer and charge recombination (CR) dynamics has been investigated. The hole‐transfer time was determined using the fluorescence upconversion technique and found to be 2–10 ps depending on the molecular structure of the catechol derivatives. The hot‐hole‐transfer process was followed after monitoring 2S luminescence of CdSe QDs. Interestingly, hot‐hole extraction was observed only in the CdSe/3‐methoxycatechol (3‐OCH₃) composite system owing to the higher electron‐donating property of the 3‐methoxy group. To confirm the extraction of the hot hole and to monitor the CR reaction in CdSe QD/catechol composite systems, ultrafast transient absorption studies have been carried out. Ultrafast transient‐absorption studies show that the bleach recovery kinetics of CdSe QD at the 2S excitonic position is much faster in the presence of 3‐OCH₃. This faster bleach recovery at the 2S position in CdSe/3‐OCH₃ suggests hot‐hole transfer from CdSe QD to 3‐OCH₃. CR dynamics in CdSe QD/catechol composite systems was followed by monitoring the excitonic bleach at the 1S position and was found to decrease with free energy of the CR reaction.     

Ascorbic Acid Induced Enhancement of Room Temperature Phosphorescence of Sodium Tripolyphosphate‐Capped Mn‐Doped ZnS Quantum Dots: Mechanism and Bioprobe Applications

Although quantum dot (QD)‐based room temperature phosphorescence (RTP) probes are promising for practical applications in complex matrixes such as environmental, food and biological samples, current QD‐based‐RTP probes are not only quite limited but also exclusively based on the RTP quenching mechanism. Here we report an ascorbic acid (AA) induced phosphorescence enhancement of sodium tripolyphosphate‐capped Mn‐doped ZnS QDs, and its application for turn‐on RTP detection. The chelating ability allows AA to extract the Mn and Zn from the surface of the QDs and to generate more holes which are subsequently trapped by Mn²⁺, while the reducing property permits AA to reduce Mn³⁺ to Mn²⁺ in the excited state, thereby enhancing the excitation and orange emission of the QDs. The enhanced RTP intensity of the QDs increases linearly with the concentration of AA in the range of 0.05–0.8 μM . Thus, a QD‐based RTP probe for AA is developed. The proposed QD‐based turn‐on RTP probe avoids tedious sample pretreatment, and offers good sensitivity and selectivity for AA in the presence of the main relevant metal ions and other molecules in biological fluids. The limit of detection (3s) of the developed method is 9 nM AA, and the relative standard deviation is 4.8 % for 11 replicate detections of 0.1 μM AA. The developed method is successfully applied to the analysis of real samples of human urine and plasma for AA with quantitative recoveries from 96 to 105 %.     

Chemical approaches to molecular logic elements for addition and subtraction

Molecular and supramolecular logic gates are candidates for computation at the nanoscale level. Nowadays all common logic operations can be mimicked with molecular devices based on chemical approaches. One step further towards molecular systems with increased logic capabilities is the addition or subtraction of binary digits. This Minireview describes recent developments to attain this goal, including bioinspired systems based on DNA and enzymes. Furthermore, chemical molecular logic gates are discussed and compared critically with regard to alternative concepts.     

Logic Information Communication in a Fluorescent Molecular Switch

Based on the chemical‐sensitive fluorescence emission behaviors of the molecular switch 4‐bromo‐5‐methoxy‐2‐(2‐pyridyl)thiazole ( 2‐BMPT ), the communication of logic information between two functional units has been realized. With the rational control of the protonation and coordination reaction of 2‐BMPT , an upstream switching unit (a 1:2 demultiplexer) and two downstream data‐processing units are involved and interconnected in the communication. The two output states of the 1:2 demultiplexer serve as the initial input states of the two parallel downstream data‐processing units, which execute the information communication between the two circuit layers. Furthermore, in the parallel data‐processing layer, the logic gates of INHIBIT and YES accomplish their specific logic functions. Therefore, a molecular cascade circuit composed of an upstream switch and two downstream processing units has been constructed based on the chemical‐modulated fluorescence properties of 2‐BMPT .     

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.     

Current Advances in Quantum‐Dots‐Based Photoelectrochemical Immunoassays

As a newly developed technique, photoelectrochemical (PEC) immunoassays have attracted great attention in recent years because of their low cost and desirable sensitivity. Because the detection signal originates from the photoelectric conversion of photoelectric materials, the appearance and application of quantum dots (QDs), which possess unique photophysical properties and regulated optoelectronic characteristics, has taken the development of PEC immunoassays to new heights. This review concisely introduces the general mechanism of QDs‐based photoelectric conversion for immunoassays and summarizes the current advances in QD applications in immunoassays. Given that signal strategies and photoactive materials are the key elements in PEC biosensor systems, we comprehensively highlight the state‐of‐the‐art signaling strategies and various applications of QDs in PEC immunoassays to introduce advances in QDs‐based PEC immunoassays. Finally, challenges and future developmental trends are briefly discussed     

Boolean Logic Gates Realized with Enzyme-catalyzed Reactions – Unusual Look at Usual Chemical Reactions

Research in the area of molecular computing systems, in the general framework of unconventional computing, has received high attention and resulted in rapid progress in formulating signal-controlled switchable molecules capable to perform Boolean logic operations and basic arithmetic functions. Extension of this research to biomolecular systems allowed sophisticated computational functions much easier than using synthetic molecular and supramolecular species. The advantage of biomolecular systems comparing with synthetic molecular systems is in their complementarity and compatibility allowing easy assembling multi-component systems from various biomolecules, thus increasing their functional complexity. While DNA-based computing systems are promising faster computing than Si-based electronics, at least for solving some combinatorial problems, due to massive parallel operation, enzyme-based logic systems are less promising for computational applications in their narrow definition. However, they offer novel biosensing and bioactuation features operating in binary Yes/No format. The present review article overviews different kinds of enzyme logic gates exemplified with specific enzymatic reactions/cascades. Motivation for this research and its possible applications are discussed. The review will be helpful to researchers working in this specific area to see the comprehensive collection of logic operations performed by the enzyme reactions. The newcomers to the reviewed area will benefit from the example systems representing various logic functions systematically.