Fluorescent Molecular Logic Gates Driven by Temperature and by Protons in Solution and on Solid

Temperature-driven fluorescent NOT logic is demonstrated by exploiting predissociation in a 1,3,5-trisubstituted Δ²-pyrazoline on its own and when grafted onto silica microparticles. Related Δ²-pyrazolines become proton-driven YES and NOT logic gates on the basis of fluorescent photoinduced electron transfer (PET) switches. Additional PASS 1 and YES+PASS 1 logic gates on silica are also demonstrated within the same family. Beside these small-molecule systems, a polymeric molecular thermometer based on a benzofurazan-derivatized N-isopropylacrylamide copolymer is attached to silica to produce temperature-driven fluorescent YES logic.     

Molecular Logic Gates for DNA Analysis: Detection of Rifampin Resistance in M. tuberculosis DNA

Elementary, Dr. Watson! A combination of YES and OR logic gates was applied to differentiate between DNA sequences of wild-type and rifampin-resistant (Rif(r) ) Mycobacterium tuberculosis (Mtb) in a multiplex real-time fluorescent assay.     

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.     

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.     

A smart gelator as a chemosensor: application to integrated logic gates in solution, gel, and film

A gelator that consisted of one benzimidazole moiety and four amide units was used as a chemosensor. We found that its absorption and emission spectra in solution were sensitive to two complementary chemical stimuli: protons and anions. Thus, YES and INH logic gates were obtained when absorbance was defined as an output. A combination gate of XNOR and AND with an emission output was also obtained. Moreover, wet gels in two solvents were used to construct two more-complicated three-input-three-output gates, owing to the existence of the gel phase as an additional output. Finally, in xerogel films that were formed from two kinds of wet gels, reversible changes in their emission spectra were observed when they were sequentially exposed to volatile acid and NH(3). Another combination two-output logic gate was obtained for xerogel films. Finally, three states of the gelator were used to construct not only basic logic gate, but also some combination gates because of their response to multiple chemical stimuli and their multiple output signals, in which one chemical input could erase the effect of another chemical input.     

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.     

Multiple molecular logic functions and molecular calculations facilitated by surfactant's versatility

Two isomeric compounds and , combining intramolecular charge transfer (ICT) and photoinduced electron transfer (PET) mechanisms together, were designed and used as logic gates with configurable multiple outputs; ten different logic functions (AND, NAND, OR, NOR, XNOR, INHIBIT, YES, NO, PASS 1 and PASS 0) were achieved by varying the inputs threshold or by altering the inputs; furthermore, half addition and half subtraction were performed within (or ); the concept demonstrated here may provide a strategy for constructing more integrated molecular level devices with multiple functions.     

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.     

Biocomputing for Portable,Resettable, and Quantitative Point‐of‐Care Diagnostics: Making the Glucose Meter a Logic‐Gate Responsive Device for Measuring Many Clinically Relevant Targets

It is recognized that biocomputing can provide intelligent solutions to complex biosensing projects. However, it remains challenging to transform biomolecular logic gates into convenient, portable, resettable and quantitative sensing systems for point‐of‐care (POC) diagnostics in a low‐resource setting. To overcome these limitations, the first design of biocomputing on personal glucose meters (PGMs) is reported, which utilizes glucose and the reduced form of nicotinamide adenine dinucleotide as signal outputs, DNAzymes and protein enzymes as building blocks, and demonstrates a general platform for installing logic‐gate responses (YES, NOT, INHIBIT, NOR, NAND, and OR) to a variety of biological species, such as cations (Na⁺), anions (citrate), organic metabolites (adenosine diphosphate and adenosine triphosphate) and enzymes (pyruvate kinase, alkaline phosphatase, and alcohol dehydrogenases). A concatenated logical gate platform that is resettable is also demonstrated. The system is highly modular and can be generally applied to POC diagnostics of many diseases, such as hyponatremia, hypernatremia, and hemolytic anemia. In addition to broadening the clinical applications of the PGM, the method reported opens a new avenue in biomolecular logic gates for the development of intelligent POC devices for on‐site applications.     

Coupling of Biomolecular Logic Gates with Electronic Transducers: From Single Enzyme Logic Gates to Sense/Act/Treat Chips

The integration of biomolecular logic principles with electronic transducers allows designing novel digital biosensors with direct electrical output, logically triggered drug‐release, and closed‐loop sense/act/treat systems. This opens new opportunities for advanced personalized medicine in the context of theranostics. In the present work, we will discuss selected examples of recent developments in the field of interfacing enzyme logic gates with electrodes and semiconductor field‐effect devices. Special attention is given to an enzyme OR/Reset logic gate based on a capacitive field‐effect electrolyte‐insulator‐semiconductor sensor modified with a multi‐enzyme membrane. Further examples are a digital adrenaline biosensor based on an AND logic gate with binary YES/NO output and an integrated closed‐loop sense/act/treat system comprising an amperometric glucose sensor, a hydrogel actuator, and an insulin (drug) sensor.     

Biocomputing for Portable,Resettable, and Quantitative Point‐of‐Care Diagnostics: Making the Glucose Meter a Logic‐Gate Responsive Device for Measuring Many Clinically Relevant Targets

It is recognized that biocomputing can provide intelligent solutions to complex biosensing projects. However, it remains challenging to transform biomolecular logic gates into convenient, portable, resettable and quantitative sensing systems for point‐of‐care (POC) diagnostics in a low‐resource setting. To overcome these limitations, the first design of biocomputing on personal glucose meters (PGMs) is reported, which utilizes glucose and the reduced form of nicotinamide adenine dinucleotide as signal outputs, DNAzymes and protein enzymes as building blocks, and demonstrates a general platform for installing logic‐gate responses (YES, NOT, INHIBIT, NOR, NAND, and OR) to a variety of biological species, such as cations (Na⁺), anions (citrate), organic metabolites (adenosine diphosphate and adenosine triphosphate) and enzymes (pyruvate kinase, alkaline phosphatase, and alcohol dehydrogenases). A concatenated logical gate platform that is resettable is also demonstrated. The system is highly modular and can be generally applied to POC diagnostics of many diseases, such as hyponatremia, hypernatremia, and hemolytic anemia. In addition to broadening the clinical applications of the PGM, the method reported opens a new avenue in biomolecular logic gates for the development of intelligent POC devices for on‐site applications.     

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 .     

A Taco Complex Derived from a Bis-Crown Ether Capable of Executing Molecular Logic Operation through Reversible Complexation

As learned from natural systems, self-assembly and self-sorting help in interconnecting different molecular logic gates and thus achieve high-level logic functions. In this context, demonstration of important logic operations using changes in optical responses due to the formation of molecular assemblies is even more desirable for the construction of a molecular computer. Synthesis of an appropriate divalent as well as a luminescent crown ether based host 1 and paraquat derivatives, 2(PF(6))(2) and 3(PF(6))(2), as guests helped in demonstrating a reversible [3](taco complex) (1·{2(PF(6))(2)}(2) or 1·{3(PF(6))(2)}(2)) formation in nonpolar solvent. Detailed (1)H NMR studies revealed that two paraquat units were bound cooperatively by the two crown units in 1. Because of preorganization, the flexible host molecule 1 adopts a folded conformation, where each of two paraquat units remain sandwiched between the two aromatic units of each folded crown ether moiety in 1. Disassembly of the "taco" complex in the presence of KPF(6) and reassembly on subsequent addition of DB18C6 was initially demonstrated by (1)H NMR spectral studies, which were subsequently corroborated through luminescence spectral studies. Further, luminescence spectral responses as output signals with appropriate and two independent molecular inputs could be correlated to demonstrate basic logic operation like OR and YES gates, while the results of the three molecular inputs could be utilized to demonstrate important logic operation like an INHIBIT gate.     

Facile and diverse logic circuits based on dumbbell DNA-templated fluorescent copper nanoclusters and S1 nuclease detection

DNA-based logic gates promote the development of molecular computing and show enormous potential in the fields of nanotechnology and biotechnology. Dumbbell oligonucleotides（DNA） with poly-thymine（poly-T） loops and a nicked random double strand have been demonstrated to be an efficient template for the formation of fluorescent copper nanoclusters（Cu NCs） in our previous work. Herein, a new platform technology is presented with which to construct molecular logic gates by employing Cu NCs probe as...     

An optical DNA logic gate based on strand displacement and magnetic separation,with response to multiple microRNAs in cancer cell lysates

A battery of logic gates, “YES”, “AND” and “OR”, are constructed using magnetic beads (MBs) modified by DNA which consists of a substrate strand (S) and a signal strand on which the logic operates. Inputs stemming from micro-RNA (which represent three cancer biomarkers) take the place of signal DNA. The released signal strand self-assembles into the hemin-G-quadruplex complex (DNAzyme) that catalyzes a blue-green dye (ABTS⁺) from the precursor ABTS. This dye (quantified at a wavelength of 414 nm) represents the output signal for the various logic gates. The method allows quantitative detection of microRNA of three kinds of logic gates in the range of 5 nM–500 nM with detection limits of 3.8 nM, 4.9 nM, 5.4 nM. Boolean logic circuitry is also achieved following the principles of multilevel strand displacement. Based on strand displacement and magnetic separation, this work demonstrates the possibility of designing a logic system using micro-RNA in live cell lysate as inputs, and its potential application in DNA computation and cancer diagnosis.

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Graphical abstract Schematic representation of a battery of logic gates and the Boolean logic circuitry based on strand displacement and magnetic separation responding to multiple microRNA in cancer cell lysate.

     

Experimental parameters affecting sensitivity and specificity of a yeast assay for estrogenic compounds: results of an interlaboratory validation exercise

In vitro assays are considered as the first step in a tiered approach to compound screening for hormonal activity. Although many new assays have been developed in recent years, little attention has been paid towards assay validation. Our objective was to identify critical experimental parameters in a yeast estrogen screen (YES) that affect its sensitivity and specificity. We investigated the role of incubation time, solvent type, yeast inoculum growth stage and concentration on the outcome of the YES. Compounds tested included new and established agonists, antagonists and negative controls, and results were evaluated according to prefixed statistical criteria. In addition, we assessed the assay’s performance in a blind interlaboratory validation exercise (IVE). An incubation time of five days was necessary to positively identify the estrogenic properties of all agonists tested, when dissolved in DMSO. Longer incubation times were required when using an ethanol protocol. Similar estrogenic activity was reported for benzyl butyl phthalate, bisphenol-A, methoxychlor, permethrin and genistein in the IVE. One out of the three laboratories did not classify α,β-endosulfan, dissolved in DMSO, as an estrogen. The same was true for 4,4′-DDE and lindane, dissolved in ethanol, a result that might be attributable to an inappropriate yeast start concentration and/or growth stage. These validation experiments show that under appropriate experimental conditions the YES yields sensitive, specific and reliable results. Therefore it fulfills the requirements as a first step screening assay to evaluate the capacity of chemicals to interact with the estrogen receptor.     

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 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.     

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.     

Resettable fluorescence logic gate based on calcein/layered double hydroxide ultrathin films

A fluorescent logic gate was fabricated based on calcein/layered double hydroxide ultrathin films (UTFs) via alternate assembly technique, which exhibits high stability, reversibility, and resettability. The logic gate was manipulated by utilizing pH value, Hg(2+) and Cl(-) ion as inputs, and the fluorescence emission of the (calcein/LDH)(16) UTF as output, serving as a three-input logic gate that combines the YES and INHIBIT operation.