1
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Fu R, Hou J, Wang Z, Xianyu Y. DNA Molecular Computation Using the CRISPR-Mediated Reaction and Surface Growth of Gold Nanoparticles. ACS NANO 2024; 18:14754-14763. [PMID: 38781600 DOI: 10.1021/acsnano.4c04265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
DNA has emerged as a promising tool to build logic gates for biocomputing. However, prevailing methodologies predominantly rely on hybridization reactions or structural alterations to construct DNA logic gates, which are limited in simplicity and diversity. Herein, we developed simple and smart DNA-based logic gates for biocomputing through the DNA-mediated growth of gold nanomaterials without precise structure design and probe modification. Capitalizing on their excellent plasmonic properties, the surface growth of gold nanomaterials enables distinct wavelength shifts and unique shapes, which are modulated by the composition, length, and concentration of the DNA sequences. Combined with a CRISPR-mediated reaction, we constructed DNA circuits to achieve complicated biocomputing to modulate the surface growth of gold nanomaterials. By implementing logic functions controlled by input-mediated growth of gold nanomaterials, we established YES/NOT, AND/NAND, OR/NOR, XOR, and INHIBIT gates and further constructed cascade logic circuits, parity checker for natural numbers, and gray code encoder, which are promising for DNA biocomputing.
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Affiliation(s)
- Ruijie Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Jinjie Hou
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Zexiang Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
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2
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Wang HP, Eichhöfer A, Gu ZG, Gruber N, Stadler AM. Anion-encapsulating, discrete prism and extended frusta, from trimetallated triangular macrocycles and linkers. Chem Commun (Camb) 2023; 59:13966-13969. [PMID: 37933533 DOI: 10.1039/d3cc00137g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Reaction of a trinuclear triangular macrocyclic complex Pb3L(CF3SO3)6 with bidentate linkers in a ratio of 3 equiv. of linker per 2 equiv. of complex, produces a prismatic structure with 4,4'-dipyridyl, and two unprecedented, extended 3D frustum-like structures with 1,2-di(4-pyridyl)ethylene and 1,4-di(4-pyridyl)benzene. The cavities of these structures encapsulate triflate anions.
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Affiliation(s)
- Hai-Ping Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, P. R. China
| | - Andreas Eichhöfer
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technolgoy (KIT), Eggenstein-Leopoldshafen 76344, Germany
- Lehn Institute of Functional Materials, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
- Karlsruhe Nano Micro Facility (KNMFi), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Zhi-Gang Gu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, P.R. China
| | - Nathalie Gruber
- Service de Radiocristallographie, Faculté de Chimie, 1, rue Blaise Pascal, Strasbourg, France
| | - Adrian-Mihail Stadler
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technolgoy (KIT), Eggenstein-Leopoldshafen 76344, Germany
- University of Strasbourg Institute for Advanced Study (USIAS), 5 Allée du Général Rouvillois, Strasbourg 67083, France
- Institut de Science et Ingénierie Supramoléculaires (ISIS), UMR 7006, CNRS and Université de Strasbourg, 8 Allée G. Monge, Strasbourg 67000, France.
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3
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Liu Y, Zhang X, Zhang X, Liu X, Wang B, Zhang Q, Wei X. Temporal logic circuits implementation using a dual cross-inhibition mechanism based on DNA strand displacement. RSC Adv 2023; 13:27125-27134. [PMID: 37701285 PMCID: PMC10493850 DOI: 10.1039/d3ra03995a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Molecular circuits crafted from DNA molecules harness the inherent programmability and biocompatibility of DNA to intelligently steer molecular machines in the execution of microscopic tasks. In comparison to combinational circuits, DNA-based temporal circuits boast supplementary capabilities, allowing them to proficiently handle the omnipresent temporal information within biochemical systems and life sciences. However, the lack of temporal mechanisms and components proficient in comprehending and processing temporal information presents challenges in advancing DNA circuits that excel in complex tasks requiring temporal control and time perception. In this study, we engineered temporal logic circuits through the design and implementation of a dual cross-inhibition mechanism, which enables the acceptance and processing of temporal information, serving as a fundamental building block for constructing temporal circuits. By incorporating the dual cross-inhibition mechanism, the temporal logic gates are endowed with cascading capabilities, significantly enhancing the inhibitory effect compared to a cross-inhibitor. Furthermore, we have introduced the annihilation mechanism into the circuit to further augment the inhibition effect. As a result, the circuit demonstrates sensitive time response characteristics, leading to a fundamental improvement in circuit performance. This architecture provides a means to efficiently process temporal signals in DNA strand displacement circuits. We anticipate that our findings will contribute to the design of complex temporal logic circuits and the advancement of molecular programming.
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Affiliation(s)
- Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
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4
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Jia Y, Yan B. Visual ratiometric fluorescence sensing of L-lactate in sweat by Eu-MOF and the design of logic devices. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122764. [PMID: 37119612 DOI: 10.1016/j.saa.2023.122764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/31/2023] [Accepted: 04/17/2023] [Indexed: 05/14/2023]
Abstract
Using 1, 4-H2NDC as ligand and Eu as the center metal, the lanthanide MOF Eu-NDC was synthesized by hydrothermal method. The material showed a fast ratiometric response to L-lactate, and the fluorescence of the material varied from red to blue with the growth of lactate concentration, which can be used as a fluorescent sensor for L-lactate in sweat. The sensor exhibited good fluorescence stability to interfering components in human sweat and good detection limits for lactate in artificial sweat. Based on this, a visualized molecular logic gate that can monitor sweat lactate levels was constructed, and the material's characteristic of showing different colors with lactate concentration changes was used to indicate possible hypoxia during exercise, opening a new path for combining sweat lactate monitoring with smart molecular devices.
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Affiliation(s)
- Yinghua Jia
- School of Chem. Science and Engineering, Tongji University, Siping Road 1239, Shanghai 200092, China
| | - Bing Yan
- School of Chem. Science and Engineering, Tongji University, Siping Road 1239, Shanghai 200092, China; School of Materials Science and Engineering, Liaocheng University, Liaocheng 252000, China.
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5
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Gao R, Ji R, Dong W. Catalytic hairpin assembly-assisted dual-signal amplification platform for ultrasensitive detection of tumor markers and intelligent diagnosis of gastric cancer. Talanta 2023; 265:124812. [PMID: 37327666 DOI: 10.1016/j.talanta.2023.124812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/05/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
Quantification of extracellular tumor markers has shown great promise for non-invasive cancer diagnosis. Combined detection of multiple tumor markers instead of a single one is valuable for accurate diagnosis. Here, we integrate CRISPR-Cas12a with DNA catalytic hairpin assembly (CHA) to doubly amplify the output signal for detecting microRNA-182 (miR-182), which is overexpressed by gastric cancer patients. Additionally, we develop a CHA system with self-replicating capacity (SRCHA) to realize dual-signal amplification for the detection of carcinoembryonic antigen (CEA), a broad-spectrum tumor marker. The proposed cascade amplification strategies enable ultrasensitive detection of miR-182 and CEA with low LODs of 0.063 fM and 4.8 pg mL-1, respectively. Moreover, we design a ternary "AND" logic gate using different concentrations of miR-182 and CEA as inputs, which demonstrates intelligent diagnosis of gastric cancer staging with a high accuracy of 93.3% in a clinical cohort of 30 individuals. Overall, our study expands the application of CRISPR-Cas12a in biosensing and provides a new diagnostic strategy for non-invasive liquid biopsy of gastric cancer before resorting to a traumatic tissue biopsy.
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Affiliation(s)
- Ruru Gao
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Ruoyang Ji
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Wei Dong
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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Hu K, Qin L, Ren X, Guo Z, Wang S, Hu Y. Deoxyribonucleic acid-guided dual-mode electro-chemical/chemiluminescent platform for sensitive and selective examination of Pb2+. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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7
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Wang M, Li X, He F, Li J, Wang HH, Nie Z. The Advances in Designer DNA Nanorobots Enabling Programmable Functions. Chembiochem 2022; 23:e202200119. [DOI: 10.1002/cbic.202200119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Fang He
- Hunan University College of Chemistry and Chemical Engineering CHINA
| | - Juan Li
- Hunan University College of Biology CHINA
| | - Hong-Hui Wang
- Hunan University College of Biology 410082 Changsha CHINA
| | - Zhou Nie
- Hunan University College of Chemistry and Chemical Engineering Yuelushan, Changsha, Hunan, 410082, P.R.China 410082 Changsha CHINA
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8
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Zhu L, Yu L, Yang X. Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:42250-42257. [PMID: 34452580 DOI: 10.1021/acsami.1c12650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.
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Affiliation(s)
- Liping Zhu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Linying Yu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Xiurong Yang
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
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9
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Li J, Xiao C, Wei W, Xiao R, Yao H, Liu H. Constructing a Facile Biocomputing Platform Based on Smart Supramolecular Hydrogel Film Electrodes with Immobilized Enzymes and Gold Nanoclusters. ACS APPLIED MATERIALS & INTERFACES 2021; 13:36632-36643. [PMID: 34288670 DOI: 10.1021/acsami.1c11206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Herein, fluorescent gold nanoclusters (AuNCs) and horseradish peroxidase (HRP) were simultaneously embedded into self-assembled dipeptide supramolecular films of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-FF) on the surface of ITO electrodes (Fmoc-FF/AuNCs/HRP) by using a simple single-step process. In the films, both the fluorescence property of AuNCs and the bioelectrocatalytic property of HRP were well maintained and could be reversibly regulated by pH-sensitive structural changes in the Fmoc-FF hydrogel films. Cu(II)/EDTA in the solution could lead to the aggregation/disaggregation of AuNCs and further quenching/dequenching the fluorescence signal from the films. Meanwhile, the blue complexes formed by Cu(II) and EDTA could produce a UV-vis signal in the solution. In addition, the coordinated Cu(II) in the films enhanced the electrocatalytic capacity toward the reduction of H2O2 and could switch the current signal. A biomolecular logic circuit was built based on the smart film electrode system by using pH, the concentrations of EDTA, Cu(II) and H2O2 as inputs, while the fluorescence intensity (FL), current (I) and UV-vis extinction (E) of the solution as outputs. Various logic devices were fabricated using the uniform platform, consisting of an encoder/decoder, demultiplexer, dual-transfer gate, keypad lock, digital comparator, half adder, and controlled NOT (CNOT) gate. Specifically, an electronic three-value logic gate, gullibility (ANY) gate, was first mimicked in this biocomputing system. This work not only demonstrated the construction of a new type of multivalued logic gate by using a dipeptide micromolecular matrix but also provided a new approach for designing sophisticated biologic functions, establishing smart multianalyte biosensing or fabricating biology information processing through the use of a simple film system.
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Affiliation(s)
- Jiaxuan Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Cong Xiao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Wenting Wei
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Ruiqi Xiao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Huiqin Yao
- School of Basic Medicine, Ningxia Medical University, Yinchuan 750004, People's Republic of China
| | - Hongyun Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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10
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Lv H, Li Q, Shi J, Fan C, Wang F. Biocomputing Based on DNA Strand Displacement Reactions. Chemphyschem 2021; 22:1151-1166. [PMID: 33871136 DOI: 10.1002/cphc.202100140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/10/2021] [Indexed: 11/12/2022]
Abstract
The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.
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Affiliation(s)
- Hui Lv
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
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11
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Wang YX, Wang DX, Wang J, Du YC, Cui YX, Tang AN, Jiang HX, Kong DM. Reversible assembly/disassembly of DNA frames and applications in logic design, ratiometric sensing and bioimaging. SENSORS AND ACTUATORS B: CHEMICAL 2021; 330:129335. [DOI: 10.1016/j.snb.2020.129335] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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12
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Fan D, Wang J, Wang E, Dong S. Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001766. [PMID: 33344121 PMCID: PMC7740092 DOI: 10.1002/advs.202001766] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Indexed: 05/11/2023]
Abstract
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.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- Present address:
Institute of ChemistryThe Hebrew University of JerusalemJerusalem91904Israel
| | - Juan Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
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13
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Feng C, Chen T, Mao D, Zhang F, Tian B, Zhu X. Construction of a Ternary Complex Based DNA Logic Nanomachine for a Highly Accurate Imaging Analysis of Cancer Cells. ACS Sens 2020; 5:3116-3123. [PMID: 32799436 DOI: 10.1021/acssensors.0c01166] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Due to the complexity and variability of the cellular metabolic process and the physiological environment inside and outside the cell, higher requirements are needed on the application of DNA molecular logic gate in cell analysis. In addition, heterogeneity of tumor cells tends to lead to false positives in the clinical diagnosis of a single target, even those with the same cancer type. To address these issues above, we have developed a novel DNA molecular logic gate responsive nanomachine for bispecific recognition and computation of cell membranes. Only when two membrane proteins, MUC1 and EpCAM as model proteins, exist simultaneously, the DNA molecular logic gate can be activated to perform "AND" logic operation and generate amplified "ON" fluorescence signal from the cell membrane. Therefore, our proposed dual-specific "recognition-biocomputing" DNA molecular logic gate has achieved highly accurate imaging analysis of dual-target membrane proteins in situ. Furthermore, the logic gate responsive DNA nanomachine can also be used to analyze target cells in complex cell samples with excellent specificity, which will meet the needs of biomedicine and their application in clinical diagnosis and provide new tools for the biomedical application of DNA molecular logic gates in complex cell systems.
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Affiliation(s)
- Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China
| | - Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Fan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Bo Tian
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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14
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Zhang Q, Hao T, Hu D, Guo Z, Wang S, Hu Y. RNA aptamer-driven ECL biosensing for tracing histone acetylation based on nano-prism substrate and cascade DNA amplification strategy. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Xie N, Wang H, Quan K, Feng F, Huang J, Wang K. Self-assembled DNA-Based geometric polyhedrons: Construction and applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Tang W, Zhong W, Tan Y, Wang GA, Li F, Liu Y. DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants. Top Curr Chem (Cham) 2020; 378:10. [PMID: 31894426 DOI: 10.1007/s41061-019-0274-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023]
Abstract
Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.
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Affiliation(s)
- Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Guan A Wang
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada
| | - Feng Li
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada. .,College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China. .,Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, China.
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17
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Zhao S, Liu Y, Wang B, Zhou C, Zhang Q. DNA logic circuits based on FokI enzyme regulation. NEW J CHEM 2020. [DOI: 10.1039/c9nj05510j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A series of DNA logic devices was constructed based on the allosteric strategy of the enzyme-assisted cleavage regulation system, which are simple in scale, modular, and work efficiently.
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Affiliation(s)
- Sue Zhao
- Key Laboratory of Advanced Design and Intelligent Computing
- Ministry of Education
- School of Software Engineering
- Dalian University
- Dalian 116622
| | - Yuan Liu
- School of Computer Science and Technology
- Dalian University of Technology
- Dalian 116024
- China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing
- Ministry of Education
- School of Software Engineering
- Dalian University
- Dalian 116622
| | - Changjun Zhou
- College of Computer Science and Engineering
- Dalian Minzu University
- Dalian
- China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing
- Ministry of Education
- School of Software Engineering
- Dalian University
- Dalian 116622
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18
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Geng H, Zhou C, Guo C. DNA-based digital comparator systems constructed by multifunctional nanoswitches. NANOSCALE 2019; 11:21856-21866. [PMID: 31696192 DOI: 10.1039/c9nr08216f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this paper, we propose a strategy involving coupling DNA structural nanoswitches with toehold mediated strand displacement for constructing novel DNA-based digital comparator (DC) logic systems, which are a basic part of traditional electronic computers and can compare whether two or more input numbers are equal. However, when the number of DC inputs is increased to a certain level, the speed and quality of the computing circuit can be affected because of the limitations of conventional electronic computers when it comes to handling large-scale quantities of data. To solve this problem, in this work, we introduce a multi-input to multi-output DNA switch-based platform that can enable complex DC logical comparison. These multifunctional DNA-based switches, each including two hairpin-shaped molecular beacons and a G4/NMM complex, were used as platforms for the step-by-step realization of 2-3 DC, 3-3 DC, and 4-3 DC logic operations. Also, experiments were designed to further verify the excellent selectivity, achieving single-base mismatch operations with the digital comparator. Based on our design, comparators (">", "<" and "=") can be realized. Our prototype can inspire new designs and have intelligent digital comparator and in-field applications.
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Affiliation(s)
- Hongmei Geng
- The Guo China-US Photonics Laboratory, State Key Laboratory for Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyang Zhou
- The Guo China-US Photonics Laboratory, State Key Laboratory for Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, P. R. China.
| | - Chunlei Guo
- The Guo China-US Photonics Laboratory, State Key Laboratory for Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, P. R. China. and The Institute of Optics, University of Rochester, Rochester, New York 14627, USA
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19
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Fan D, Wang J, Wang E, Dong S. A Janus-inspired amphichromatic system that kills two birds with one stone for operating a "DNA Janus Logic Pair" (DJLP) library. Chem Sci 2019; 10:7290-7298. [PMID: 31588299 PMCID: PMC6686727 DOI: 10.1039/c9sc01865d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/12/2019] [Indexed: 12/27/2022] Open
Abstract
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.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
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20
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Wang S, Zhao J, Lu S, Huang J, Yang X. Establishment of Logic Gates Based on Conformational Changes in a Multiple-Factor Biomolecule Interaction Process by Dual Polarization Interferometry. Anal Chem 2019; 91:6971-6975. [PMID: 31081324 DOI: 10.1021/acs.analchem.9b01319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DNA-based logic gates stimulate the development of molecular scale computers and show enormous potential in nanotechnology, biotechnology, and medicine. However, the reported detectors to date usually require one to label appropriate signal probes, resulting in not only a high cost but also potentially tedious manipulation. For the first time, we established a label-free logic gate by regarding the structure-related signal as output. Dual polarization interferometry (DPI) was employed to reveal the detailed conformational transitions occurring in the multiple-factor biomolecule interactions and then was utilized as a detection tool of logic gate. As a vital merit of this system, the dependence of the density output signal on the interaction with multiple-factor input can mimic the function of signal communication in OR, INHIBIT, and IDENTITY logic gates and the INHIBIT-OR cascade circuit. Additionally, the DPI signal with logic stringency can unambiguously distinguish conformational polymorphisms and compare structural stability. This study provides a new way for the construction of a label-free logic gate, supplements information deficiency of reaction details, and extends the application of DPI in logic operation.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China.,University of Chinese Academy of Sciences , Beijing 100039 , China
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21
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Gong X, Wei J, Liu J, Li R, Liu X, Wang F. Programmable intracellular DNA biocomputing circuits for reliable cell recognitions. Chem Sci 2019; 10:2989-2997. [PMID: 30996878 PMCID: PMC6427941 DOI: 10.1039/c8sc05217d] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/15/2019] [Indexed: 12/14/2022] Open
Abstract
Dynamic nucleic acid-based biocircuits have spurred substantial research efforts for diagnosis or biomedical applications at the molecular level; nevertheless, it still remains a challenge to design programmable molecular circuit devices for autonomous and accurate diagnosis of low abundance biomolecules in a complex intracellular environment. Herein, a reconfigurable hybridization-based chain reaction is introduced to assemble modular biocomputing circuits that include a general sensing module and a versatile processing module. By modular sensing module design, we realized multiple endogenous miRNA-initiated biocomputing operations, including binary logic gates (OR, AND, INHIBIT and XOR), and more advanced concatenated logic circuits (XOR-AND, XOR-INHIBIT, and XOR-OR) in different living cells. The sensing module transduces the primary miRNA sensing event into an intermediate trigger for activating the processing module that further transduces the specific analyte recognition pattern into an amplified fluorescence readout. Based on an appropriate selection of multiple miRNA analytes, various miRNA expression patterns could be utilized for sensitive and selective cell discriminations. The inherent synergistically accelerated recognition and hybridization features of our biocomputing systems contribute to the amplified detection of multiplex endogenous miRNAs in living cells, thus providing an efficient toolbox for more accurate diagnosis and programmable therapeutics.
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Affiliation(s)
- Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Jing Liu
- Department of Gastroenterology , Wuhan University Zhongnan Hospital , China
| | - Ruomeng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
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22
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Li F, Xiao M, Pei H. DNA‐Based Chemical Reaction Networks. Chembiochem 2019; 20:1105-1114. [DOI: 10.1002/cbic.201800721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Fan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound ImagingLaboratory of Evolutionary TheranosticsSchool of Biomedical EngineeringHealth Science CenterShenzhen University Nanhai Avenue 3688 518060 Shenzhen Guangzhou P.R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
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23
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Liu S, Ding J, Qin W. Dual-Analyte Chronopotentiometric Aptasensing Platform Based on a G-Quadruplex/Hemin DNAzyme and Logic Gate Operations. Anal Chem 2019; 91:3170-3176. [PMID: 30648390 DOI: 10.1021/acs.analchem.8b05971] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Conventional potentiometric ion sensors that rely on a specific ion carrier in a polymeric membrane can hardly achieve multianalyte detection. Inspired by the remarkable ability of built-in logic gate sensors for multianalyte detection, herein we report a potentiometric aptasensing platform based on a G-quadruplex/hemin DNAzyme and logic gate operations for determination of two analytes using a single membrane electrode. A bifunctional probe with two aptamer units and a signal reporter oligonucleotide with a DNAzyme sequence are assembled on the magnetic beads to form a DNA hybrid structure. The "OR" and "INHIBIT" logic functions can be performed by using the two aptamers and their targets as inputs, and using the chronopotentiometric response based on the G-quadruplex/hemin DNAzyme-H2O2-mediated oxidation of 3,3',5,5'-tetramethylbenzidine as output. Kanamycin and oxytetracycline, as commonly used antibiotics, have been employed as the models and successfully measured.
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Affiliation(s)
- Shuwen Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation and Shandong Provincial Key Laboratory of Coastal Environmental Processes , Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS) , Yantai , Shandong 264003 , P. R. China.,University of the Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Jiawang Ding
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation and Shandong Provincial Key Laboratory of Coastal Environmental Processes , Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS) , Yantai , Shandong 264003 , P. R. China.,Laboratory for Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266200 , P. R. China
| | - Wei Qin
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation and Shandong Provincial Key Laboratory of Coastal Environmental Processes , Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS) , Yantai , Shandong 264003 , P. R. China.,Laboratory for Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266200 , P. R. China
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24
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Yu Y, Zhou Y, Zhu M, Su G, Deng H, Chen W, Peng H. Dynamic split G-quadruplex programmed reversible nanodevice. Chem Commun (Camb) 2019; 55:389-392. [PMID: 30540300 DOI: 10.1039/c8cc08744j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We propose a dynamic nanodevice based on a split G-quadruplex (G4). By splitting it apart, we can successfully decouple the G-tetrad formation from external stimuli, greatly expanding the stimulus for G4 based devices. Taking advantage of the rigid force from a DNA duplex, the nanodevice can be switched reversibly through the conformational transformation.
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Affiliation(s)
- Yanyan Yu
- School of pharmacy, Nantong University, Nantong 226001, Jiangsu Province, China.
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25
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Xue C, Xiao S, Ouyang CH, Li CC, Gao ZH, Shen ZF, Wu ZS. Inverted mirror image molecular beacon-based three concatenated logic gates to detect p53 tumor suppressor gene. Anal Chim Acta 2018; 1051:179-186. [PMID: 30661615 DOI: 10.1016/j.aca.2018.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
Mutation of p53 tumor suppressor gene represents one of the early molecular events in tumor initiation and progression. Although molecular computing holds tremendous potential with important applications in diagnosis, prognosis and treatment of human diseases at the molecular level, designing molecular logic gates to implement cascade amplification via operating autonomously for the detection of point mutations still remains challenging. In this contribution, we developed a three concatenated logic gates (TCLG) to perform multiple strand displacement amplification (m-SDA) for screening the cancer-related point mutations only via designing an innovative molecular beacon (MB). Specifically, using p53 gene as model target, extending the two ends of a MB via adding two fragments with the same sequence achieves two unique terminal single-stranded (ss) overhangs. After self-folding of MB into hairpin structure, the two overhangs exhibit a near inverted mirror image (IM) relationship if taking the base nature and direction into account. For this, the probe is called IM-MB. Because cascade SDAs can occur on IM-MB and promote each other, the target gene can be detected down to 10 pM. Along this line, the TCLG circuit was proposed, and two primers and target gene serve as the indispensable input signals. Utilizing this logic circuit, the point mutation or absence of target gene can be sensitively screened. Moreover, its potential application in the recognition of point mutations in complex biomatrix has been demonstrated via blind test. The proof-of-concept scheme is expected to provide new insight into the development of DNA-based molecular logic gates and their applications in basic research, medical diagnosis and precise treatment and treatment of genetic diseases.
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Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Shuai Xiao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Chang-He Ouyang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Cong-Cong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Zhi-Hua Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhi-Fa Shen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.
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26
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Zhou C, Geng H, Guo C. Design of DNA-based innovative computing system of digital comparison. Acta Biomater 2018; 80:58-65. [PMID: 30223093 DOI: 10.1016/j.actbio.2018.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/20/2018] [Accepted: 09/12/2018] [Indexed: 01/04/2023]
Abstract
Despite great potential and extensive interest in developing biomolecule-based computing, the development of even basic molecular logic gates is still in its infancy. Digital comparator (DC) is the basic unit in traditional electronic computers, but it is difficult to construct a system for achieving large-scale integration. Here, we construct, for the first time, a novel logic computing system of DCs that can compare whether two or more numbers are equal. Our approach is by taking advantage of facile preparation and unique properties of graphene oxide and DNA. The DC system reported in this work is developed by the DNA hybridization and effective combination of GO and single-stranded DNA, which is regarded as the reacting platform. On the basis of this platform and reaction principle, we have developed 2-inputs, 3-inputs, and 4-inputs DCs to realize the comparison of two or more binary numbers. We predict that such a state-of-the-art logic system enables its functionality with large-scale input signals, providing a new direction toward prototypical DNA-based logic operations and promoting the development of advanced logic computing. STATEMENT OF SIGNIFICANCE: The overarching objective of this paper is to explore the construction of a novel DNA computing system of digital comparator driven by the interaction of DNA and graphene oxide (GO). GO can efficient bind the dye-labeled, single-stranded DNA probe and then quench its fluorescence. In the case of the target appearing, specific binding between the single-stranded probe and its target occurs, changing the conformation and relationship with GO, then restoring the fluorescence of the dye. We have developed the 2-inputs, 3-inputs, and 4-inputs digital comparator circuits, which are expected to realize the comparison of large-scale input signals and can avoid the problems of design complexity and manufacturing cost of integrated circuits in traditional computing.
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Affiliation(s)
- Chunyang Zhou
- The Guo China-US Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, PR China
| | - Hongmei Geng
- The Guo China-US Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, PR China
| | - Chunlei Guo
- The Guo China-US Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, PR China; The Institute of Optics, University of Rochester, Rochester, NY 14627, USA.
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27
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Yang C, Yang S, Li J, Du Y, Song L, Huang D, Chen J, Zhou Q, Yang Q, Tang Y. Intelligent Sensors of Lead Based on a Reconfigurable DNA-Supramolecule Logic Platform. Anal Chem 2018; 90:10585-10590. [PMID: 30085646 DOI: 10.1021/acs.analchem.8b02782] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Chunrong Yang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shu Yang
- Key Laboratory of Drug Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610064, P. R. China
| | - Jicheng Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yuanyuan Du
- West China School of Public Health, No.4 West Teaching Hospital, Sichuan University, Chengdu 610041, China
| | - Lingbo Song
- Key Laboratory of Drug Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610064, P. R. China
| | - Dan Huang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jianchi Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Qiuju Zhou
- Analysis & Testing Center, Xinyang Normal University, Xinyang 464000, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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28
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Zhang J, Lu Y. 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. Angew Chem Int Ed Engl 2018; 57:9702-9706. [PMID: 29893502 PMCID: PMC6261302 DOI: 10.1002/anie.201804292] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/30/2018] [Indexed: 12/19/2022]
Abstract
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.
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Affiliation(s)
- Jingjing Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801 (USA),
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801 (USA),
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29
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Peng R, Zheng X, Lyu Y, Xu L, Zhang X, Ke G, Liu Q, You C, Huan S, Tan W. Engineering a 3D DNA-Logic Gate Nanomachine for Bispecific Recognition and Computing on Target Cell Surfaces. J Am Chem Soc 2018; 140:9793-9796. [PMID: 30021431 DOI: 10.1021/jacs.8b04319] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Among the vast number of recognition molecules, DNA aptamers generated from cell-SELEX exhibit unique properties for identifying cell membrane biomarkers, in particular protein receptors on cancer cells. To integrate all recognition and computing modules within a single structure, a three-dimensional (3D) DNA-based logic gate nanomachine was constructed to target overexpressed cancer cell biomarkers with bispecific recognition. Thus, when the Boolean operator "AND" returns a true value, it is followed by an "ON" signal when the specific cell type is presented. Compared with freely dispersed double-stranded DNA (dsDNA)-based molecular circuits, this 3D DNA nanostructure, termed DNA-logic gate triangular prism (TP), showed better identification performance, enabling, in turn, better molecular targeting and fabrication of recognition nanorobotics.
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Affiliation(s)
- Ruizi Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Xiaofang Zheng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China.,Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , United States
| | - Liujun Xu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Changjun You
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Shuangyan Huan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , People's Republic of China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China.,Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , United States
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30
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Peveler WJ, Algar WR. More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing. ACS Chem Biol 2018; 13:1752-1766. [PMID: 29461796 DOI: 10.1021/acschembio.7b01022] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.
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Affiliation(s)
- William J. Peveler
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - W. Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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31
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Fan D, Fan Y, Wang E, Dong S. A simple, label-free, electrochemical DNA parity generator/checker for error detection during data transmission based on "aptamer-nanoclaw"-modulated protein steric hindrance. Chem Sci 2018; 9:6981-6987. [PMID: 30210773 PMCID: PMC6124900 DOI: 10.1039/c8sc02482k] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/15/2018] [Indexed: 01/01/2023] Open
Abstract
The first electrochemical DNA parity generator/checker system for error detection during data transmission was constructed based on “aptamer-nanoclaw”-modulated protein steric hindrance.
Versatile DNA logic devices have exhibited magical power in molecular-level computing and data processing. During any type of data transmission, the appearance of erroneous bits (which have severe impacts on normal computing) is unavoidable. Luckily, the erroneous bits can be detected via placing a parity generator (pG) at the sending module and a parity checker (pC) at the receiving module. However, all current DNA pG/pC systems use optical signals as outputs. In comparison, sensitive, facilely operated, electric-powered electrochemical outputs possess inherent advantages in terms of potential practicability and future integration with semiconductor transistors. Herein, taking an even pG/pC as a model device, we construct the first electrochemical DNA pG/pC system so far. Innovatively, a thrombin aptamer is integrated into the input-strand and it functions as a “nanoclaw” to selectively capture thrombin; the electrochemical impedance changes induced by the “nanoclaw/thrombin” complex are used as label-free outputs. Notably, this system is simple and can be operated within 2 h, which is comparable with previous fluorescent ones, but avoids the high-cost labeled-fluorophore and tedious nanoquencher. Moreover, taking non-interfering poly-T strands as additional inputs, a cascade logic circuit (OR-2 to 1 encoder) and a parity checker that could distinguish even/odd numbers from natural numbers (0 to 9) is also achieved based on the same system. This work not only opens up inspiring horizons for the design of novel electrochemical functional devices and complicated logic circuits, but also lays a solid foundation for potential logic-programmed target detection.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Yongchao Fan
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Erkang Wang
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Shaojun Dong
- State Key Laboratory of Electro Analytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . .,University of Chinese Academy of Sciences , Beijing , 100039 , China
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32
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Zhang J, Lu Y. 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. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jingjing Zhang
- Department of Chemistry, Beckman Institute for Advanced Science and Technology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Yi Lu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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33
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Bader A, Cockroft SL. Simultaneous G-Quadruplex DNA Logic. Chemistry 2018; 24:4820-4824. [DOI: 10.1002/chem.201800756] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Antoine Bader
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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34
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Lian W, Liang J, Shen L, Jin Y, Liu H. Enzymatic logic calculation systems based on solid-state electrochemiluminescence and molecularly imprinted polymer film electrodes. Biosens Bioelectron 2018; 100:326-332. [DOI: 10.1016/j.bios.2017.09.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022]
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35
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Liu YL, Wu HP, Zhou Q, Song QX, Rui JZ, Guan XX, Zhou GH, Zou BJ. Controllable extension of hairpin-structured flaps to allow low-background cascade invasive reaction for a sensitive DNA logic sensor for mutation detection. Chem Sci 2017; 9:1666-1673. [PMID: 29675214 PMCID: PMC5887964 DOI: 10.1039/c7sc04210h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/14/2017] [Indexed: 01/05/2023] Open
Abstract
A sensitive DNA logic sensor was constructed based on a controllable-extension bridged cascade invasive reaction.
A DNA logic sensor was constructed for gene mutation analysis based on a novel signal amplification cascade by controllably extending a hairpin-structured flap to bridge two invasive reactions. The detection limit was as low as 0.07 fM, and the analytical specificity is high enough to unambiguously pick up 0.02% mutants from a large amount of wild-type DNA. Gene mutations related to the personalized medicine of gefitinib, a typical tyrosine kinase inhibitor, were analyzed by the DNA logic sensor with only a 15 minute response time. Successful assay of tissue samples and cell-free plasma DNA indicates that the new concept we proposed here could benefit clinicians for straightforward prescription of a mutation-targeted drug.
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Affiliation(s)
- Yun-Long Liu
- Department of Pharmacology , Jinling Hospital , Medical School of Nanjing University , Nanjing 210002 , China . ; .,State Key Laboratory of Natural Medicines , Department of Biomedical Engineering , School of Engineering , China Pharmaceutical University , Nanjing 210009 , China
| | - Hai-Ping Wu
- Huadong Research Institute for Medicine and Biotechnics , Nanjing 210002 , China
| | - Qiang Zhou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education , China Pharmaceutical University , Nanjing 210009 , China
| | - Qin-Xin Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education , China Pharmaceutical University , Nanjing 210009 , China
| | - Jian-Zhong Rui
- Department of Pharmacology , Jinling Hospital , Medical School of Nanjing University , Nanjing 210002 , China . ;
| | - Xiao-Xiang Guan
- Department of Pharmacology , Jinling Hospital , Medical School of Nanjing University , Nanjing 210002 , China . ;
| | - Guo-Hua Zhou
- Department of Pharmacology , Jinling Hospital , Medical School of Nanjing University , Nanjing 210002 , China . ;
| | - Bing-Jie Zou
- Department of Pharmacology , Jinling Hospital , Medical School of Nanjing University , Nanjing 210002 , China . ;
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36
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Xu XY, Lian X, Hao JN, Zhang C, Yan B. A Double-Stimuli-Responsive Fluorescent Center for Monitoring of Food Spoilage based on Dye Covalently Modified EuMOFs: From Sensory Hydrogels to Logic Devices. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29. [PMID: 28745439 DOI: 10.1002/adma.201702298] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/01/2017] [Indexed: 05/06/2023]
Abstract
Unsafe food is a huge threat to human health and the economy, and detecting food spoilage early is an ongoing and imperative need. Herein, a simple and effective strategy combining a fluorescence sensor and one-to-two logic operation is designed for monitoring biogenic amines, indicators of food spoilage. Sensors (methyl red@lanthanide metal-organic frameworks (MR@EuMOFs)) are created by covalently modifying MR into NH2 -rich EuMOFs, which have a high quantum yield (48%). A double-stimuli-responsive fluorescence center is produced via energy transfer from the ligands to Eu3+ and MR. Portable sensory hydrogels are obtained by dispersing and solidifying MR@EuMOFs in water-phase sodium salt of carboxy methyl cellulose (CMC-Na). The hydrogels exhibit a color transition upon "smelling" histamine (HI) vapor. This transition and shift in the MR-based emission peak are closely related to the HI concentration. Using the HI concentration as the input signal and the two fluorescence emissions as output signals, an advanced analytical device based on a one-to-two logic gate is constructed. The four output combinations, NOT (0, 1), YES (1, 0), PASS 1 (1, 1), and PASS 0 (0, 0), allow the direct analysis of HI levels, which can be used for real-time food-freshness evaluation. The novel strategy suggested here may be a new application for a molecular logic system in the sensing field.
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Affiliation(s)
- Xiao-Yu Xu
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Xiao Lian
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Ji-Na Hao
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Chi Zhang
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
| | - Bing Yan
- China-Australia Joint Lab of Functional Molecules and Ordered Matters, School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, China
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37
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Wu D, Wang L, Li W, Xu X, Jiang W. DNA nanostructure-based drug delivery nanosystems in cancer therapy. Int J Pharm 2017; 533:169-178. [PMID: 28923770 DOI: 10.1016/j.ijpharm.2017.09.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 01/04/2023]
Abstract
DNA as a novel biomaterial can be used to fabricate different kinds of DNA nanostructures based on its principle of GC/AT complementary base pairing. Studies have shown that DNA nanostructure is a nice drug carrier to overcome big obstacles existing in cancer therapy such as systemic toxicity and unsatisfied drug efficacy. Thus, different types of DNA nanostructure-based drug delivery nanosystems have been designed in cancer therapy. To improve treating efficacy, they are also developed into more functional drug delivery nanosystems. In recent years, some important progresses have been made. The objective of this review is to make a retrospect and summary about these different kinds of DNA nanostructure-based drug delivery nanosystems and their latest progresses: (1) active targeting; (2) mutidrug co-delivery; (3) construction of stimuli-responsive/intelligent nanosystems.
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Affiliation(s)
- Dandan Wu
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Wei Li
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Xiaowen Xu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China
| | - Wei Jiang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China; School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China.
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38
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Peng R, Wang H, Lyu Y, Xu L, Liu H, Kuai H, Liu Q, Tan W. Facile Assembly/Disassembly of DNA Nanostructures Anchored on Cell-Mimicking Giant Vesicles. J Am Chem Soc 2017; 139:12410-12413. [PMID: 28841373 PMCID: PMC5877790 DOI: 10.1021/jacs.7b07485] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanostructures assembled on living cell membranes have become powerful research tools. Synthetic lipid membranes have been used as a membrane model to study the dynamic behavior of DNA nanostructures on fluid soft lipid bilayers, but without the inherent complexity of natural membranes. Herein, we report the assembly and disassembly of DNA nanoprisms on cell-mimicking micrometer-scale giant membrane vesicles derived from living mammalian cells. Three-dimensional DNA nanoprisms with a DNA arm and a cholesterol anchor were efficiently localized on the membrane surface. The assembly and disassembly of DNA nanoprisms were dynamically manipulated by DNA strand hybridization and toehold-mediated strand displacement. Furthermore, the heterogeneity of reversible assembly/disassembly of DNA nanoprisms was monitored by Förster resonance energy transfer. This study suggests the feasibility of DNA-mediated functional biomolecular assembly on cell membranes for biomimetics studies and delivery systems.
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Affiliation(s)
- Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Huijing Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liujun Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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39
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Massey M, Medintz IL, Ancona MG, Algar WR. Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR. ACS Sens 2017; 2:1205-1214. [PMID: 28787151 DOI: 10.1021/acssensors.7b00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.
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Affiliation(s)
- Melissa Massey
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | | | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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40
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Gao RR, Yao TM, Lv XY, Zhu YY, Zhang YW, Shi S. Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing. Chem Sci 2017; 8:4211-4222. [PMID: 28626564 PMCID: PMC5469004 DOI: 10.1039/c7sc00361g] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/05/2017] [Indexed: 11/30/2022] Open
Abstract
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.
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Affiliation(s)
- Ru-Ru Gao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Tian-Ming Yao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Xiao-Yan Lv
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yan-Yan Zhu
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Yi-Wei Zhang
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
| | - Shuo Shi
- Shanghai Key Laboratory of Chemical Assessment and Sustainability , School of Chemical Science and Engineering , Tongji University , Shanghai , 200092 , P. R. China . ;
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41
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Liu Y, Chen Q, Liu J, Yang X, Guo Q, Li L, Liu W, Wang K. Design of a Modular DNA Triangular-Prism Sensor Enabling Ratiometric and Multiplexed Biomolecule Detection on a Single Microbead. Anal Chem 2017; 89:3590-3596. [DOI: 10.1021/acs.analchem.6b04918] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yu Liu
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Qiaoshu Chen
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Qiuping Guo
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Li Li
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Wei Liu
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
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Lilienthal S, Klein M, Orbach R, Willner I, Remacle F, Levine RD. Continuous variables logic via coupled automata using a DNAzyme cascade with feedback. Chem Sci 2017; 8:2161-2168. [PMID: 28507669 PMCID: PMC5407271 DOI: 10.1039/c6sc03892a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/24/2016] [Indexed: 01/19/2023] Open
Abstract
The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To enable reactive chemical systems to compute we show how, using the Cox interpretation of probability theory, one can transcribe the equations of chemical kinetics as a sequence of coupled logic gates operating on continuous variables. It is discussed how the distinct chemical identity of a molecule allows us to create a common language for chemical kinetics and Boolean logic. Specifically, the logic AND operation is shown to be equivalent to a bimolecular process. The logic XOR operation represents chemical processes that take place concurrently. The values of the rate constants enter the logic scheme as inputs. By designing a reaction scheme with a feedback we endow the logic gates with a built in memory because their output then depends on the input and also on the present state of the system. Technically such a logic machine is an automaton. We report an experimental realization of three such coupled automata using a DNAzyme multilayer signaling cascade. A simple model verifies analytically that our experimental scheme provides an integrator generating a power series that is third order in time. The model identifies two parameters that govern the kinetics and shows how the initial concentrations of the substrates are the coefficients in the power series.
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Affiliation(s)
- S Lilienthal
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - M Klein
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - R Orbach
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - I Willner
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - F Remacle
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
- Department of Chemistry , University of Liege , B6c , 4000 Liege , Belgium
| | - R D Levine
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
- Department of Molecular and Medical Pharmacology , David Geffen School of Medicine , Department of Chemistry and Biochemistry , University of California , Los Angeles , CA 90095 , USA
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Zhao K, Tang Y, Wang Z, Zhang J, Lei C, Wang H, Li H, Huang Y, Nie Z, Yao S. Surface charge tuneable fluorescent protein-based logic gates for smart delivery of nucleic acids. Chem Commun (Camb) 2017; 53:11326-11329. [DOI: 10.1039/c7cc06833f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A versatile bio-logic system based on H39GFP is operated in living cells with transfection of functional nucleic acids as the readout.
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Li M, Yu X, Liu H. A New Biocomputing Platform Based on Potential- and pH-Sensitive Bioelectrocatalysis and Layer-by-Layer Films Assembled with Graphene Derivatives and Weak Polyelectrolyte. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.10.128] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Zhou C, Liu D, Wu C, Dong S, Wang E. Multifunctional Graphene/DNA-Based Platform for the Construction of Enzyme-Free Ternary Logic Gates. ACS APPLIED MATERIALS & INTERFACES 2016; 8:30287-30293. [PMID: 27750411 DOI: 10.1021/acsami.6b09021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this work, we have successfully realized multivalued logic circuits including ternary INHIBIT and ternary OR logic gates in an enzyme-free condition by integration of graphene oxide and DNA for the first time. Compared to the binary logic gate with two states of "0" and "1", the multivalued logic gate contains three different states of "0", "1", and "2", which can increase the information content in a system and further improve the ability of information processing. Such types of multivalued logic operations provide a wider field of vision toward DNA-based algebra logical operations to make applications more accurate with complexity reduction and accelerate the development of advanced logic gates.
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Affiliation(s)
- Chunyang Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, P. R. China
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University , Changchun, China
| | - Dali Liu
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University , Changchun, China
| | - Changtong Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, P. R. China
- Department of Chemistry and Environmental Engineering, Changchun University of Science and Technology , Changchun, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, P. R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, P. R. China
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Zhou C, Liu D, Dong S. Innovative Bimolecular-Based Advanced Logic Operations: A Prime Discriminator and An Odd Parity Checker. ACS APPLIED MATERIALS & INTERFACES 2016; 8:20849-20855. [PMID: 27459592 DOI: 10.1021/acsami.6b05505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Herein, a novel logic operation of prime discriminator is first performed for the function of identifying the prime numbers from natural numbers less than 10. The prime discriminator logic operation is developed by DNA hybridizations and the conjugation of graphene oxide and single-stranded DNA as a reacting platform. On the basis of the similar reaction principle, an odd parity checker is also developed. The odd parity checker logic operation can identify the even numbers and odd numbers from natural numbers less than 10. Such advanced logic operations with digital recognition ability can provide a new field of vision toward prototypical DNA-based logic operations and promote the development of advanced logic circuits.
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Affiliation(s)
- Chunyang Zhou
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University , Changchun, Jilin Province 130022, P. R. China
| | - Dali Liu
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University , Changchun, Jilin Province 130022, P. R. China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, P. R. China
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Chen J, Wen J, Zhuang L, Zhou S. An enzyme-free catalytic DNA circuit for amplified detection of aflatoxin B1 using gold nanoparticles as colorimetric indicators. NANOSCALE 2016; 8:9791-9797. [PMID: 27119550 DOI: 10.1039/c6nr01381c] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An enzyme-free biosensor for the amplified detection of aflatoxin B1 has been constructed based on a catalytic DNA circuit. Three biotinylated hairpin DNA probes (H1, H2, and H3) were designed as the assembly components to construct the sensing system (triplex H1-H2-H3 product). Cascaded signal amplification capability was obtained through toehold-mediated strand displacement reactions to open the hairpins and recycle the trigger DNA. By the use of streptavidin-functionalized gold nanoparticles as the signal indicators, the colorimetric readout can be observed by the naked eye. In the presence of a target, the individual nanoparticles (red) aggregate into a cross-linked network of nanoparticles (blue) via biotin-streptavidin coupling. The colorimetric assay is ultrasensitive, enabling the visual detection of trace levels of aflatoxin B1 (AFB1) as low as 10 pM without instrumentation. The calculated limit of detection (LOD) is 2 pM in terms of 3 times standard deviation over the blank response. The sensor is robust and works even when challenged with complex sample matrices such as rice samples. Our sensing platform is simple and convenient in operation, requiring only the mixing of several solutions at room temperature to achieve visible and intuitive results, and holds great promise for the point-of-use monitoring of AFB1 in environmental and food samples.
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Affiliation(s)
- Junhua Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China.
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Zhang L, He Y, Zhang N, Liu D, Han J, Gong W. Construction of a novel INHIBIT logic gate through a fine-tuned assembly of anthryl fluorophores via selective anion recognition and host–guest interactions. RSC Adv 2016. [DOI: 10.1039/c5ra20120a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel ligand containing of anthryl fluorophore was achieved. The assembly and disassembly of anthryl fluorophore by Pi and β-CD as chemical inputs and emission around 500 nm as output resulted in the construction of novel INHIBIT gate.
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Affiliation(s)
- Lei Zhang
- College of Chemistry
- Chemical Engineering and Environmental Engineering
- Liaoning Shihua University
- Fushun 113001
- China
| | - Yilong He
- College of Chemistry
- Chemical Engineering and Environmental Engineering
- Liaoning Shihua University
- Fushun 113001
- China
| | - Na Zhang
- Department of Chemical Engineering
- Fushun Vocational Technology Institute
- Fushun 113122
- China
| | - Daosheng Liu
- College of Chemistry
- Chemical Engineering and Environmental Engineering
- Liaoning Shihua University
- Fushun 113001
- China
| | - Jiao Han
- College of Chemistry
- Chemical Engineering and Environmental Engineering
- Liaoning Shihua University
- Fushun 113001
- China
| | - Weitao Gong
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- School of Chemistry
- Dalian University of Technology
- Dalian 116024
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Bi S, Ye J, Dong Y, Li H, Cao W. Target-triggered cascade recycling amplification for label-free detection of microRNA and molecular logic operations. Chem Commun (Camb) 2016; 52:402-5. [DOI: 10.1039/c5cc07046e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A cascade recycling amplification (CRA) that implements cascade logic circuits with feedback amplification function is developed for label-free chemiluminescence detection of microRNA-122 with an ultrahigh sensitivity of 0.82 fM and excellent specificity, which is applied to construct a series of molecular-scale two-input logic gates by using microRNAs as inputs and CRA products as outputs.
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Affiliation(s)
- Sai Bi
- College of Chemical Science and Engineering
- Laboratory of Fiber Materials and Modern Textiles
- the Growing Base for State Key Laboratory
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
| | - Jiayan Ye
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Ying Dong
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Haoting Li
- College of Chemical Science and Engineering
- Laboratory of Fiber Materials and Modern Textiles
- the Growing Base for State Key Laboratory
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
| | - Wei Cao
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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Bi S, Xiu B, Ye J, Dong Y. Target-Catalyzed DNA Four-Way Junctions for CRET Imaging of MicroRNA, Concatenated Logic Operations, and Self-Assembly of DNA Nanohydrogels for Targeted Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2015; 7:23310-23319. [PMID: 26420675 DOI: 10.1021/acsami.5b07827] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Here we report a target-catalyzed DNA four-way junction (DNA-4WJ) on the basis of toehold-mediated DNA strand displacement reaction (TM-SDR), which is readily applied in enzyme-free amplified chemiluminescence resonance energy transfer (CRET) imaging of microRNA. In this system, the introduction of target microRNA-let-7a (miR-let-7a) activates a cascade of assembly steps with four DNA hairpins, followed by a disassembly step in which the target microRNA is displaced and released from DNA-4WJ to catalyze the self-assembly of additional branched junctions. As a result, G-quadruplex subunit sequences and fluorophore fluorescein amidite (FAM) are encoded in DNA-4WJ in a close proximity, stimulating a CRET process in the presence of hemin/K(+) to form horseradish peroxidase (HRP)-mimicking DNAzyme that catalyzes the generation of luminol/H2O2 chemiluminescence (CL), which further transfers to FAM. The background signal is easily reduced using magnetic graphene oxide (MGO) to remove unreacted species through magnetic separation, which makes a great contribution to improve the detection sensitivity and achieves a detection limit as low as 6.9 fM microRNA-let-7a (miR-let-7a). In addition, four-input concatenated logic circuits with an automatic reset function have been successfully constructed relying on the architecture of the proposed DNA-4WJ. More importantly, DNA nanohydrogels are self-assembled using DNA-4WJs as building units after centrifugation, which are driven by liquid crystallization and dense packaging of building units. Moreover, the DNA nanohydrogels are readily functionalized by incorporating with aptamers, bioimaging agents, and drug loading sites, which thus are served as efficient nanocarriers for targeted drug delivery and cancer therapy with high loading capacity and excellent biocompatibility.
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Affiliation(s)
- Sai Bi
- Shandong Province Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University , Linyi 276005, China
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemical Science and Engineering, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University , Qingdao 266071, China
| | - Bao Xiu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, China
| | - Jiayan Ye
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, China
| | - Ying Dong
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, China
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