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.     

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.     

Chemiluminescent Logic Gates Based on Functionalized Gold Nanoparticles/Graphene Oxide Nanocomposites

Label‐free logic gates (AND, OR, and INHIBIT) based on chemiluminescence (CL) as new optical readout signal have been developed by taking advantage of the unique CL activity of luminol‐ and lucigenin‐functionalized gold nanoparticles/graphene oxide (luminol‐lucigenin/AuNPs/GO) nanocomposites. It was found that Fe²⁺ ions could induce the CL emission of luminol‐lucigenin/AuNPs/GO nanocomposites in alkaline solution. On this basis, by using Fe²⁺ ions and NaOH as the inputs and the CL signal as the output, an AND logic gate was fabricated. When the initial reaction system contained luminol‐lucigenin/AuNPs/GO nanocomposites and NaOH, either Fe²⁺ ions or Ag⁺ ions could react with the luminol‐lucigenin/AuNPs/GO nanocomposites to produce a strong CL emission. This result was used to design an OR logic gate using Fe²⁺ ions and Ag⁺ ions as the inputs and CL signal as the output. Moreover, two INHIBIT logic gates for Fe²⁺ and Ag⁺ were also developed using by NaClO and L ‐cysteine as their CL inhibitors, respectively. Furthermore, the proposed logic gates were successfully used to detect Fe²⁺, Ag⁺, and L ‐cysteine, respectively. The developed logic gates may find future applications in sensing, clinical diagnostics, and environmental monitoring.     

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.     

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.     

Rhodamine-Appended Bipyridine: XOR and OR Logic Operations Integrated in an Example of Controlled Metal Migration

A new bipyridyl derivative 1 bearing rhodamine B as visible fluorophore was designed, synthesized and characterized as a fluorescent and colorimetric sensor for metal ions. Interaction with Cu²⁺, Zn²⁺, Cd²⁺, Hg⁺, and Hg²⁺ ions was followed by UV/Vis and emission spectroscopy. Upon addition of these metal ions, different colorimetric and fluorescent responses were observed. “Off-on-off” (Cu²⁺, Zn²⁺, and Hg²⁺) and “off-on” (Hg⁺ and Cd²⁺) systems were obtained. Probe 1 was explored to mimic XOR and OR logic operations for the simultaneous detection of Hg⁺–Cu²⁺ and Hg⁺–Zn²⁺ pairs, respectively. DFT calculations were also performed to gain insight into the lowest-energy gas-phase conformation of free receptor 1 as well as the atomistic details of the coordination modes of the various metal ions.     

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.     

基于色胺酮衍生物的阴离子探针和分子逻辑门

通过色胺酮与苯肼反应生成一种新型的腙类化合物.在该化合物的DMF溶液中,用含有不同阴离子的四丁基铵盐测试了其对阴离子的识别能力.实验结果表明,加入F-,AcO-和H2PO-4后,溶液由黄色立即变为橙色,而加入Cl-,Br-,I-,ClO-4,NO-3和HSO-4离子则无变化.通过核磁共振波谱证实了探针的识别机制,并设计了一个四输入的分子逻辑门.     

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.     

Highly Selective and Sensitive Aggregation-Induced Emission of Fluorescein-Coated Metal Oxide Nanoparticles

We report the synthesis, characterization, and photophysical properties of novel metal oxide nanoparticles (NPs) coated with specially designed fluorescein substituents which are capped with electron-withdrawing groups. The fluorescein-coated nanoparticles were synthesized in excellent yields, and their structures were confirmed using various advanced spectroscopic, instrumental, and surface analysis techniques, revealing the formation of the target functionalized nanoparticles (FNPs) which show superior chemical and thermal stabilities. In addition, the photophysical properties of the FNPs were examined using UV-visible absorption and fluorescence spectroscopy. These latter techniques disclosed aggregation-induced emission (AIE) properties for most of the target FNPs, namely those which are soluble in common organic solvents at selective concentration ranges of water fractions in the solvent mixture.     

Insights into the Aggregation Behaviour of a Benzoselenadiazole-Based Compound and Generation of White Light Emission

We have designed and synthesized the benzoselenadiazole (BDS) based donor-acceptor-donor (D-A-D) π-conjugated compound 4,7-di((E)styryl)benzo[2,1,3]selenadiazole ( 1 ). A single-crystal study of 1 shows J-type molecular aggregation in the solid state. The crystal packing of 1 shows head-to-head dimeric intermolecular assembly via Se⋅⋅⋅N interactions while staircase-type interlock molecular packing has occurred via Se⋅⋅⋅π interaction. The staircase-type interlock packing of dimeric molecular arrangement induces sheet-type, herringbone type architecture along crystallographic a axis and ab plane via CH⋅⋅⋅π interactions. Interestingly, the J-type aggregation of 1 in solid state changes to H-type aggregation upon UV-irradiation. Moreover, our spectroscopic findings in solution state reveal H-type of aggregation of 1 in 90 % aqueous THF. We have further demonstrated white light emission in the binary mixture of 1 and 1-pyrenemethanol ( 2 ) in 90 % aqueous THF. Our study reveals solvent specific co-assembly of H-aggregated 1 and 2 in 90 % aqueous THF solution, which shows white light emissive properties with the Commission Internationale de l'Eclairage (CIE) chromaticity coordinates (0.32, 0.31). The observed white light emission arises mainly due to the combination of red light from H-aggregated 1 , blue light from monomeric 2 and green light from excimers of 2 .     

Aqueous Phase Sensing of Fe3+ and Ascorbic Acid by a Metal–Organic Framework and Its Implication in the Construction of Multiple Logic Gates

A new Hf^IV‐based metal‐organic framework with UiO‐66 topology was synthesized via a one‐step solvothermal method by using 3‐methyl‐4‐phenylthieno[2,3‐b]thiophene‐2,5‐dicarboxylic acid (H₂MPTDC) as a ligand. The MOF material showed a high stability in a broad pH range (from pH 2 to pH 12) in an aqueous medium. The presence of hydrophobic methyl and phenyl substituents in the carboxylic acid ligand and strong Hf?O bond play crucial roles in its stability. The new MOF material was systematically characterized by various techniques such as XRPD, N₂ sorption, thermogravimetric analyses and FT‐IR spectroscopy. The photophysical properties of the MOF material were also examined by steady‐state and time‐resolved fluorescence studies. It was observed that the blue fluorescence of the MOF material was selectively quenched in the presence of Fe³⁺ ion in pure aqueous medium. A mechanistic study disclosed that quenching occurs via a strong inner filter effect (IFE) arising from Fe³⁺ ion in aqueous medium. Interestingly, the fluorescence of the MOF material can be recovered by elimination of the IFE of Fe³⁺ ion via reduction of Fe³⁺ ion by ascorbic acid (AA). Based on the fluorescence recovery by AA, a MOF based on‐off‐on probe was developed for the sensing of Fe³⁺ ion and AA in aqueous medium. Inspired by this reversible sensing event, we demonstrate basic (NOT, OR, YES, INHIBIT and IMP) and higher integrated logic operations utilizing this fluorescent MOF. This MOF‐based logic systems could be potentially used for next‐generation logic‐gate based analytical applications as well as for the detection and discrimination of targeted molecules in various complex domains.     

Molecular Switches and Multiple Logic Gates Based on 4-(2-Pyridylazo)resorcinol

A simple‐structured 4‐(2‐pyridylazo)resorcinol (PAR) system presents interesting properties with dual fluorescent outputs. Modulated by solution pH two kinds of reversible switch behaviors, "ON‐OFF" and "OFF‐ON", were realized with the PAR system. Stimulated by different combination of external stimulus, such as metal ions, UV irradiation and solution pH, the PAR system could perform multiple logic functions including three inputs AND, two inputs INHIBIT and combinatorial "NOR/AND" in parallel. The operation of the designed system is very simple and detected with a high sensitive fluorescent signal.     

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.     

基于氰基化9-苯基芴衍生物的激基复合物发光与性质研究

激基复合物发光器件因给、受体材料掺杂比例易调且易实现小的单线态-三线态能隙差等优势, 在发展工艺简单、性能高效的有机发光二极管方面显示出很大的应用潜力. 针对目前激基复合物受体材料的种类仍较为匮乏, 器件性能仍需改善等问题, 本工作设计合成出新型基于9-苯基芴的电子受体材料(TCNDPFCz)用于构筑激基复合物发光器件. 实验表明, 受体分子TCNDPFCz与给体分子1,1-bis[(di-4-tolylamino)phenyl]cyclohexane (TAPC)掺杂后(TAPC: TCNDPFCz)呈现明显的激基复合物发光, 其光致发光效率为54%, 电流效率为27.2 cd•A^‒1, 功率效率为32.9 lm•W^‒1, 外量子效率为12.5%. 经分析, 我们推测激基复合物TAPC:TCNDPFCz形成的过程得益于TCNDPFCz具有很强的吸电子能力. 本工作表明9-苯基芴可以作为骨架单元来构筑受体分子, 为开发新型电子受体材料提供了新策略.     

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.