1
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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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2
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Li Y, Liu Z, Lu W, Zhao M, Xiao H, Hu T, Ma J, Zheng Z, Jia J, Wu H. A label-free electrochemical aptasensor based on the core-shell Cu-MOF@TpBD hybrid nanoarchitecture for the sensitive detection of PDGF-BB. Analyst 2020; 146:979-988. [PMID: 33554228 DOI: 10.1039/d0an01885f] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
As one of the significant serum cytokines, platelet-derived growth factor-BB (PDGF-BB) is a crucial protein biomarker overexpressed in human life-threatening tumors, the sensitive identification and quantification of which are urgently desired but challenging. Herein we report a novel core-shell nanoarchitecture consisting of Cu-based metal-organic frameworks (Cu-MOFs) and covalent organic frameworks (denoted as TpBD-COFs), which was used to prepare an aptasensor for the detection of platelet-derived growth factor-BB (PDGF-BB). The central Cu-MOFs function as signal labels with no need for extra redox media, whereas the porous TpBD serves as the shell to immobilize the PDGF-BB-targeted aptamer strands in abundance via strong interactions involving π-π stacking, electrostatic, and hydrogen bonding interactions. The proposed aptasensor based on Cu-MOF@TpBD can achieve a detection limit as low as 0.034 pg mL-1 within the dynamic detection range from 0.0001 to 60 ng mL-1. The hybridization of MOFs and COFs, together with the immobilization with the specific analyte targeted aptamer, provides a promising and propagable approach to prepare an aptasensor for the simple, sensitive, and selective detection of a specific biomarker in clinical diagnosis.
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Affiliation(s)
- Ya Li
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials Ministry of Education, School of Chemical and Material Science, Shanxi Normal University, Linfen 041004, China.
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3
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A molecular device: A DNA molecular lock driven by the nicking enzymes. Comput Struct Biotechnol J 2020; 18:2107-2116. [PMID: 32913580 PMCID: PMC7451616 DOI: 10.1016/j.csbj.2020.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022] Open
Abstract
As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.
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Tandon A, Song Y, Mitta SB, Yoo S, Park S, Lee S, Raza MT, Ha TH, Park SH. Demonstration of Arithmetic Calculations by DNA Tile-Based Algorithmic Self-Assembly. ACS NANO 2020; 14:5260-5267. [PMID: 32159938 DOI: 10.1021/acsnano.0c01387] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Owing to its high information density, energy efficiency, and massive parallelism, DNA computing has undergone several advances and made significant contributions to nanotechnology. Notably, arithmetic calculations implemented by multiple logic gates such as adders and subtractors have received much attention because of their well-established logic algorithms and feasibility of experimental implementation. Although small molecules have been used to implement these computations, a DNA tile-based calculator has been rarely addressed owing to complexity of rule design and experimental challenges for direct verification. Here, we construct a DNA-based calculator with three types of building blocks (propagator, connector, and solution tiles) to perform addition and subtraction operations through algorithmic self-assembly. An atomic force microscope is used to verify the solutions. Our method provides a potential platform for the construction of various types of DNA algorithmic crystals (such as flip-flops, encoders, and multiplexers) by embedding multiple logic gate operations in the DNA base sequences.
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Affiliation(s)
- Anshula Tandon
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Yongwoo Song
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sekhar Babu Mitta
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sanghyun Yoo
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Suyoun Park
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sungjin Lee
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Muhammad Tayyab Raza
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Tai Hwan Ha
- Future Biotechnology Research Division, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Sung Ha Park
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
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5
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Suo Z, Chen J, Hou X, Hu Z, Xing F, Feng L. Growing prospects of DNA nanomaterials in novel biomedical applications. RSC Adv 2019; 9:16479-16491. [PMID: 35516377 PMCID: PMC9064466 DOI: 10.1039/c9ra01261c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.
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Affiliation(s)
- Zhiguang Suo
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Jingqi Chen
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Xialing Hou
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Ziheng Hu
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Feifei Xing
- Department of Chemistry, College of Science, Shanghai University Shanghai 200444 China
| | - Lingyan Feng
- Materials Genome Institute, Shanghai University Shanghai 200444 China
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Zhong W, Tang W, Fan J, Zhang J, Zhou X, Liu Y. A domain-based DNA circuit for smart single-nucleotide variant identification. Chem Commun (Camb) 2018; 54:1311-1314. [PMID: 29177325 DOI: 10.1039/c7cc07733e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
According to the differential information of four homologous oligonucleotides, two domain-based encoders have been constructed with the molecular information as the input. Based on the one-to-one correspondence between the input and output, SNVs can be identified and their sites can be located at the domain level.
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Affiliation(s)
- Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, P. R. China.
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7
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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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8
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Du Y, Han X, Wang C, Li Y, Li B, Duan H. Smart Sensing Based on DNA-Metal Interaction Enables a Label-Free and Resettable Security Model of Electrochemical Molecular Keypad Lock. ACS Sens 2018; 3:54-58. [PMID: 29250951 DOI: 10.1021/acssensors.7b00735] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recently, molecular keypad locks have received increasing attention. As a new subgroup of smart biosensors, they show great potential for protecting information as a molecular security data processor, rather than merely molecular recognition and quantitation. Herein, label-free electrochemically transduced Ag+ and cysteine (Cys) sensors were developed. A molecular keypad lock model with reset function was successfully realized based on the balanced interaction of metal ion with its nucleic acid and chemical ligands. The correct input of "1-2-3" (i.e., "Ag+-Cys-cDNA") is the only password of such molecular keypad lock. Moreover, the resetting process of either correct or wrong input order could be easily made by Cys, buffer, and DI water treatment. Therefore, our system provides an even smarter system of molecular keypad lock, which could inhibit illegal access of unauthorized users, holding great promise in information protection at the molecular level.
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Affiliation(s)
- Yan Du
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Xu Han
- School
of
Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, Jilin 130022, P.R. China
| | - Chenxu Wang
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457
| | - Yunhui Li
- School
of
Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, Jilin 130022, P.R. China
| | - Bingling Li
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Hongwei Duan
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457
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9
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A resettable and reprogrammable keypad lock based on electrochromic Prussian blue films and biocatalysis of immobilized glucose oxidase in a bipolar electrode system. Biosens Bioelectron 2018; 99:163-169. [DOI: 10.1016/j.bios.2017.07.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/08/2017] [Accepted: 07/21/2017] [Indexed: 12/19/2022]
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10
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User Authorization at the Molecular Scale. Chemphyschem 2017; 18:1678-1687. [DOI: 10.1002/cphc.201700506] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/01/2017] [Indexed: 12/31/2022]
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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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12
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Zhou C, Liu D, Wu C, Liu Y, Wang E. Integration of DNA and graphene oxide for the construction of various advanced logic circuits. NANOSCALE 2016; 8:17524-17531. [PMID: 27714033 DOI: 10.1039/c6nr01213b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Multiple advanced logic circuits including the full-adder, full-subtract and majority logic gate have been successfully realized on a DNA/GO platform for the first time. All the logic gates were implemented in an enzyme-free condition. The investigation provides a wider field of vision towards prototypical DNA-based algebra logical operations and promotes the development of advanced logic circuits.
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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. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Dali Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of 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. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Yaqing Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. and Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology), Ministry of Education, Tianjin, 300457, P. R. China. and State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
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13
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Wang L, Lian W, Liu H. A Resettable Keypad Lock with Visible Readout Based on Closed Bipolar Electrochemistry and Electrochromic Poly(3-methylthiophene) Films. Chemistry 2016; 22:4825-32. [DOI: 10.1002/chem.201504812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Lei Wang
- College of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
| | - Wenjing Lian
- College of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
| | - Hongyun Liu
- College of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
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14
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Zhou C, Wang K, Fan D, Wu C, Liu D, Liu Y, Wang E. An enzyme-free and DNA-based Feynman gate for logically reversible operation. Chem Commun (Camb) 2016; 51:10284-6. [PMID: 26028329 DOI: 10.1039/c5cc02865e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A logically reversible Feynman gate was successfully realized under enzyme-free conditions by integrating graphene oxide and DNA for the first time. The gate has a one-to-one mapping function to identify inputs from the corresponding outputs. This type of reversible logic gate may have great potential applications in information processing and biosensing systems.
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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.
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15
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Zhang S, Wang K, Huang C, Sun T. Reconfigurable and resettable arithmetic logic units based on magnetic beads and DNA. NANOSCALE 2015; 7:20749-20756. [PMID: 26602962 DOI: 10.1039/c5nr06733b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Based on the characteristics of magnetic beads and DNA, a simple and universal platform was developed for the integration of multiple logic gates to achieve resettable half adder and half subtractor functions. The signal reporter was composed of a split G-quadruplex DNAzyme and AuNP-surface immobilized molecular beacon molecule. The novel feature of the designed system is that the inputs (split G-quadruplexes) can interact with hairpin-modified Au NPs linked to magnetic particles. Another novel feature is that the logic operations can be reset by heating the output system and by using the magnetic separation of the computing modules. Moreover, the developed half adder and half subtractor are realized on a simple DNA/magnetic bead platform in an enzyme-free system and share a constant threshold setpoint. Due to the diversity and design flexibility of DNA, these investigations may provide a new method for the development of resettable DNA-based arithmetic operations.
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Affiliation(s)
- Siqi Zhang
- College of Sciences, Northeastern University, Shenyang, 110819, China.
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16
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A simple three-input DNA-based system works as a full-subtractor. Sci Rep 2015; 5:10686. [PMID: 26095534 PMCID: PMC4476036 DOI: 10.1038/srep10686] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/21/2015] [Indexed: 12/28/2022] Open
Abstract
Over the past decade, DNA has demonstrated remarkable potential in fabrication of molecular logic and arithmetic systems. In this work, a simple DNA-based system mimicking a full-subtractor that handles three inputs including one minuend and two subtrahends for eight input/output conditions is successfully designed. The whole system is established by one gate molecule and three input sequences, all made of single-stranded DNA sequences.
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17
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He Y, Chen Y, Li C, Cui H. Molecular encoder-decoder based on an assembly of graphene oxide with dye-labelled DNA. Chem Commun (Camb) 2015; 50:7994-7. [PMID: 24915303 DOI: 10.1039/c4cc01242a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A general strategy was developed to fabricate 2-to-1, 4-to-2 and 8-to-3 molecular encoders and a 1-to-2 decoder by assembling graphene oxide with various dye-labeled DNAs.
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Affiliation(s)
- Yi He
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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18
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Fan D, Wang K, Zhu J, Xia Y, Han Y, Liu Y, Wang E. DNA-based visual majority logic gate with one-vote veto function. Chem Sci 2015; 6:1973-1978. [PMID: 28706647 PMCID: PMC5495993 DOI: 10.1039/c4sc03495c] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/07/2015] [Indexed: 12/27/2022] Open
Abstract
A molecular logic gate is a basic element and plays a key role in molecular computing. Herein, we have developed a label-free and enzyme-free three-input visual majority logic gate which is realized for the first time according to DNA hybridization only, without DNA replacement and enzyme catalysis. Furthermore, a one-vote veto function was integrated into the DNA-based majority logic gate, in which one input has priority over other inputs. The developed system can also implement multiple basic and cascade logic gates.
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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 , P. R. China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Kun Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
- Department of Chemistry and Environmental Engineering , Changchun University of Science and Technology , Changchun , China
| | - Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Yong Xia
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Yanchao Han
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Yaqing Liu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
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19
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Liu S, Li M, Yu X, Li CZ, Liu H. Biomacromolecular logic gate, encoder/decoder and keypad lock based on DNA damage with electrochemiluminescence and electrochemical signals as outputs. Chem Commun (Camb) 2015. [DOI: 10.1039/c5cc04412j] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Biomacromolecular logic devices including a keypad lock were developed based on the damage of natural DNA in Ru(bpy)32+ solution.
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Affiliation(s)
- Shuang Liu
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- People's Republic of China
| | - Menglu Li
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- People's Republic of China
| | - Xue Yu
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- People's Republic of China
| | - Chen-Zhong Li
- Nanobioengineering/Bioelectronics Laboratory
- Department of Biomedical Engineering
- Florida International University
- Miami
- USA
| | - Hongyun Liu
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- People's Republic of China
- Key Laboratory of Theoretical and Computational Photochemistry
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20
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Chen J, Zhou S, Wen J. Concatenated Logic Circuits Based on a Three-Way DNA Junction: A Keypad-Lock Security System with Visible Readout and an Automatic Reset Function. Angew Chem Int Ed Engl 2014; 54:446-50. [DOI: 10.1002/anie.201408334] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/27/2014] [Indexed: 12/19/2022]
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21
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Chen J, Zhou S, Wen J. Concatenated Logic Circuits Based on a Three-Way DNA Junction: A Keypad-Lock Security System with Visible Readout and an Automatic Reset Function. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408334] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Jiang XJ, Ng DKP. Sequential logic operations with a molecular keypad lock with four inputs and dual fluorescence outputs. Angew Chem Int Ed Engl 2014; 53:10481-4. [PMID: 25078949 DOI: 10.1002/anie.201406002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Indexed: 12/19/2022]
Abstract
A novel coumarin-rhodamine conjugate was prepared, and its metal binding properties were studied by UV/Vis and fluorescence spectroscopy. The conjugate serves as a ratiometric and highly selective fluorescent sensor for Hg(2+) ions. Its metal-responsive spectral properties were utilized to construct a molecular keypad lock with four inputs and dual fluorescence outputs. The complexity of this molecular logic network can greatly enhance the security level of this device.
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Affiliation(s)
- Xiong-Jie Jiang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China)
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23
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Jiang XJ, Ng DKP. Sequential Logic Operations with a Molecular Keypad Lock with Four Inputs and Dual Fluorescence Outputs. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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24
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Li H, Hong W, Dong S, Liu Y, Wang E. A resettable and reprogrammable DNA-based security system to identify multiple users with hierarchy. ACS NANO 2014; 8:2796-2803. [PMID: 24564320 DOI: 10.1021/nn406523y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Molecular-level security devices have raised ever-increasing interest in recent years to protect data and information from illegal invasion. Prior molecular keypad locks have an output signal dependent upon not only the appropriate combination but also the exact sequence of inputs, but it cannot be reset or reprogrammed. Here, a DNA-based security system with reset and never-reported reprogram function is successfully developed in proof-of-principle, with which one can change the password in case that the system is cracked. The previous password becomes invalid in the reprogrammed security system. Interestingly, more than one password is designed to permit multiple users to access. By harnessing the intrinsic merit of the different passwords, the system can distinguish different user who is endowed with prior authority. The intelligent device is addressed on solid support and facilitates electronic processes, avoiding chemical accumulation in the system by simple removal of the electrode from the input solution and indicating a main avenue for its further development.
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Affiliation(s)
- Hailong Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun 130022, China
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25
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Orbach R, Remacle F, Levine RD, Willner I. DNAzyme-based 2:1 and 4:1 multiplexers and 1:2 demultiplexer. Chem Sci 2014. [DOI: 10.1039/c3sc52752b] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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26
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Wang K, Ren J, Fan D, Liu Y, Wang E. Integration of graphene oxide and DNA as a universal platform for multiple arithmetic logic units. Chem Commun (Camb) 2014; 50:14390-3. [DOI: 10.1039/c4cc06033d] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple logic gates were integrated on a universal GO–DNA platform to implement both half adder and half subtractor functions.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022, China
- University of Chinese Academy of Sciences
| | - Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022, China
- University of Chinese Academy of Sciences
| | - Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022, China
- University of Chinese Academy of Sciences
| | - Yaqing Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022, China
- University of Chinese Academy of Sciences
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022, China
- University of Chinese Academy of Sciences
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27
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Rout B, Milko P, Iron MA, Motiei L, Margulies D. Authorizing Multiple Chemical Passwords by a Combinatorial Molecular Keypad Lock. J Am Chem Soc 2013; 135:15330-3. [PMID: 24088016 DOI: 10.1021/ja4081748] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Bhimsen Rout
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Petr Milko
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mark A. Iron
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leila Motiei
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Margulies
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
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28
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Chen S, Guo Z, Zhu S, Shi WE, Zhu W. A multiaddressable photochromic bisthienylethene with sequence-dependent responses: construction of an INHIBIT logic gate and a keypad lock. ACS APPLIED MATERIALS & INTERFACES 2013; 5:5623-5629. [PMID: 23734835 DOI: 10.1021/am4009506] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A photochromic bisthienylethene derivative (BIT) containing two imidazole units has been synthesized and fully characterized. When triggered by chemical ions (Ag(+)), protons, and light, BIT can behave as an absorbance switch, leading to a multiaddressable system. BIT exhibits sequence-dependent responses via efficient interaction of the specific imidazole unit with protons and Ag(+). Furthermore, an INHIBIT logic gate and a keypad lock with three inputs are constructed with the unimolecular platform by employing an absorption mode at different wavelengths as outputs on the basis of an appropriate combination of chemical and photonic stimuli.
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Affiliation(s)
- Shangjun Chen
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, PR China
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29
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Zhu J, Yang X, Zhang L, Zhang L, Lou B, Dong S, Wang E. A visible multi-digit DNA keypad lock based on split G-quadruplex DNAzyme and silver microspheres. Chem Commun (Camb) 2013; 49:5459-61. [PMID: 23665889 DOI: 10.1039/c3cc42028k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel visible multi-digit DNA keypad lock system was fabricated based on split G-quadruplex DNAzyme and silver microspheres. The final result of the keypad lock can be easily recognized by the naked eye and the number of inputs for the keypad lock can be flexibly adjusted. This molecular platform showed excellent scalability and flexibility.
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Affiliation(s)
- Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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30
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Zhou Z, Liu Y, Dong S. DNA-templated Ag nanoclusters as signal transducers for a label-free and resettable keypad lock. Chem Commun (Camb) 2013; 49:3107-9. [PMID: 23471116 DOI: 10.1039/c3cc39272d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a unique, label-free and resettable molecular keypad lock that utilizes DNA-modulated Ag nanoclusters (Ag NCs) as signal responsers. The present work demonstrates the first example that exonuclease-catalyzed DNA hydrolysis reaction could be used to achieve the RESET function of a molecular keypad without complicated procedures.
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Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
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