Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes.
ABSTRACT: The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.
Project description: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.
Project description:Multiplex miRNA analysis is a fundamental issue for exploring a complex biological system and early diagnosis of miRNA-related diseases. Herein, we have developed a series of novel logic gates for miRNA analysis coupling DNA nanostructures and chameleon silver nanoclusters (AgNCs). DNA dumbbell structures are firstly designed with two independent nucleation sequences for AgNCs at the 5' and 3' ends, respectively. By introducing different miRNA inputs, separations of two AgNCs are controlled and the fluorescence property of AgNCs changes. By studying the ratiometric fluorescence responses, sensitive and selective analysis of multiple miRNAs can be achieved. The present work provides powerful tools for miRNA diagnostics and may also guide future DNA nanostructure-based logic gates.
Project description:Powerful information processing and ubiquitous computing are crucial for all machines and living organisms. The Watson-Crick base-pairing principle endows DNA with excellent recognition and assembly abilities, which facilitates the design of DNA computers for achieving intelligent systems. However, current DNA computational systems are always constrained by poor integration efficiency, complicated device structures or limited computational functions. Here, we show a DNA arithmetic logic unit (ALU) consisting of elemental DNA logic gates using polymerase-mediated strand displacement. The use of an enzyme resulted in highly efficient logic gates suitable for multiple and cascaded computation. Based on our basic single-rail DNA configuration, additional combined logic gates (e.g., a full adder and a 4:1 multiplexer) have been constructed. Finally, we integrate the gates and assemble the crucial ALU. Our strategy provides a facile strategy for assembling a large-scale complex DNA computer system, highlighting the great potential for programming the molecular behaviors of complicated biosystems.
Project description:To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2?:?1 multiplexer, and a 1?:?2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.
Project description:Using nanoparticles as substrates for computation enables algorithmic and autonomous controls of their unique and beneficial properties. However, scalable architecture for nanoparticle-based computing systems is lacking. Here, we report a platform for constructing nanoparticle logic gates and circuits at the single-particle level on a supported lipid bilayer. Our "lipid nanotablet" platform, inspired by cellular membranes that are exploited to compartmentalize and control signaling networks, uses a lipid bilayer as a chemical circuit board and nanoparticles as computational units. On a lipid nanotablet, a single-nanoparticle logic gate senses molecules in solution as inputs and triggers particle assembly or disassembly as an output. We demonstrate a set of Boolean logic operations, fan-in/fan-out of logic gates, and a combinational logic circuit such as a multiplexer. We envisage that our approach to modularly implement nanoparticle circuits on a lipid bilayer will create new paradigms and opportunities in molecular computing, nanoparticle circuits, and systems nanoscience.
Project description:Wiring a series of simple logic gates to process complex data is significantly important and a large challenge for untraditional molecular computing systems. The programmable property of DNA endows its powerful application in molecular computing. In our investigation, it was found that DNA exhibits excellent peroxidase-like activity in a colorimetric system of TMB/H2O2/Hemin (TMB, 3,3', 5,5'-Tetramethylbenzidine) in the presence of K+ and Cu2+, which is significantly inhibited by the addition of an antioxidant. According to the modulated catalytic activity of this DNA-based catalyst, three cascade logic gates including AND-OR-INH (INHIBIT), AND-INH and OR-INH were successfully constructed. Interestingly, by only modulating the concentration of Cu2+, a majority logic gate with a single-vote veto function was realized following the same threshold value as that of the cascade logic gates. The strategy is quite straightforward and versatile and provides an instructive method for constructing multiple logic gates on a simple platform to implement complex molecular computing.
Project description:A novel DNA-stabilized silver nanoclusters (AgNCs)-based label-free fluorescent platform for simultaneously detecting two human immunodeficiency virus oligonucleotides (HIV DNAs) was developed. The sensing platform was established based on fluorescence enhancement of guanine (G)-rich and the phenomenon in the process of two silver nanoclusters (AgNCs) forming a nanoclusters dimer. The probe (AgNCs/G) utilized for HIV-1 detection adopted an effective conformation based on enhancement effect of G-rich sequence (at 500 nm ex / 565 nm em) while the probe (AgNCs/AgNCs) for HIV-2 generated fluorescence signals (at 580 nm ex / 630 nm em) with bright fluorescence only in nanoclusters dimer. The nanoprobe shows high selectivity for multiplexed analysis of target DNA with a detection limit of 11 pM, respectively. Moreover, this is the first time to use the affectivity of fluorescent AgNCs and two HIV DNAs simultaneous detection integrated into a novel method, which shows a great promise in biomedical research and early clinical diagnosis.
Project description:Diverse advanced logic circuits are fabricated to implement arithmetic functions based on a simple and single molecular beacon platform, including half adder, half subtractor, full adder, full subtractor, and a digital comparator. Dual fluorescence outputs are generated in parallel and a constant threshold value is set to build all the logic circuits. The developed enzyme-free DNA system provides a novel prototype for the design of high-level molecular logic circuits on a biomolecular platform.
Project description:Photochromes are photoswitchable, bistable chromophores which, like transistors, can implement binary logic operations. When several photochromes are combined in one molecule, interactions between them such as energy and electron transfer allow design of simple Boolean logic gates and more complex logic devices with all-photonic inputs and outputs. Selective isomerization of individual photochromes can be achieved using light of different wavelengths, and logic outputs can employ absorption and emission properties at different wavelengths, thus allowing a single molecular species to perform several different functions, even simultaneously. Here, we report a molecule consisting of three linked photochromes that can be configured as AND, XOR, INH, half-adder, half-subtractor, multiplexer, demultiplexer, encoder, decoder, keypad lock, and logically reversible transfer gate logic devices, all with a common initial state. The system demonstrates the advantages of light-responsive molecules as multifunctional, reconfigurable nanoscale logic devices that represent an approach to true molecular information processing units.
Project description: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.