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Hou X, Ga L, Zhang X, Ai J. Advances in the application of logic gates in nanozymes. Anal Bioanal Chem 2024:10.1007/s00216-024-05240-w. [PMID: 38488951 DOI: 10.1007/s00216-024-05240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
Nanozymes are a class of nanomaterials with biocatalytic function and enzyme-like activity, whose advantages include high stability, low cost, and mass production. They can catalyze the substrates of natural enzymes based on specific nanostructures and serve as substitutes for natural enzymes. Their applied research involves a wide range of fields such as biomedicine, environmental governance, agriculture, and food. Molecular logic gates are a new cross-disciplinary discipline, which can simulate the function of silicon circuits on a molecular scale, perform single or multiple input logic operations, and generate logic outputs. A molecular logic gate is a binary operation that converts an input signal into an output signal according to the rules of Boolean logic, generating two signals, a high level, and a low level. The high and low levels represent the "true" and "false" values of the logic gates, and their outputs correspond to "l" and "0" of the molecular logic gates, respectively. The combination of nanozymes and logic gates is a novel and attractive research direction, and the cross-application of the two brings new opportunities and ideas for various fields, such as the construction of efficient biocomputers, intelligent drug delivery systems, and the precise diagnosis of diseases. This review describes the application of logic gates based on nanozymes, which is expected to provide a certain theoretical foundation for researchers' subsequent studies.
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Affiliation(s)
- Xiangru Hou
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China
| | - Lu Ga
- College of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot, 010110, China
| | - Xin Zhang
- College of Chemical Engineering, Inner Mongolia University of Technology, 49 Aimin Road, Hohhot, 010051, China.
| | - Jun Ai
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China.
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2
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Jiang C, Zhang Y, Wang F, Liu H. Toward Smart Information Processing with Synthetic DNA Molecules. Macromol Rapid Commun 2021; 42:e2100084. [PMID: 33864315 DOI: 10.1002/marc.202100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Indexed: 11/07/2022]
Abstract
DNA, a biological macromolecule, is a naturally evolved information material. From the structural point of view, an individual DNA strand can be considered as a chain of data with its bases working as single units. For decades, due to the high biochemical stability, large information storage capacity, and high recognition specificity, DNA has been recognized as an attractive material for information processing. Especially, the chemical synthesis strategies and DNA sequencing techniques have been rapidly developed recently, further enabling encoding information with synthetic DNA molecules. Herein, recent progresses are summarized on information processing based on synthetic DNA molecules from three aspects including information storage, computation, and encryption, and proposed the challenges and future development directions.
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Affiliation(s)
- Chu Jiang
- School of Chemical Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Shanghai Research Institute for Intelligent Autonomous Systems, Tongji University, Shanghai, 200092, China
| | - Yinan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Center for Molecular Design and Biomimetics, School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - 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, 200240, China
| | - Huajie Liu
- School of Chemical Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Shanghai Research Institute for Intelligent Autonomous Systems, Tongji University, Shanghai, 200092, China
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3
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Magri DC. Logical sensing with fluorescent molecular logic gates based on photoinduced electron transfer. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213598] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Zhang Y, Li CW, Zhou L, Chen Z, Yi C. "Plug and Play" logic gate construction based on chemically triggered fluorescence switching of gold nanoparticles conjugated with Cy3-tagged aptamer. Mikrochim Acta 2020; 187:437. [PMID: 32647943 DOI: 10.1007/s00604-020-04421-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/30/2020] [Indexed: 11/29/2022]
Abstract
Gold nanoparticles (AuNPs) conjugated with Cy3-tagged aptamer which can specifically recognize chloramphenicol (CAP) (referred to as AuNPs-AptCAP) are described. CAP can trigger the configuration change of CAP binding aptamer, and thus switching the fluorescence of AuNPs-AptCAP through changing the efficiency of the fluorescence resonance energy transfer (FRET) system with Cy3 as donors and AuNPs as recipients. AuNPs-AptCAP exhibits a linear range of CAP concentrations from 26.0 to 277 μg L-1 with a limit of detection of 8.1 μg L-1 when Cy3 was excited at 530 nm and emission was measured at 570 nm. More importantly, AuNPs-AptCAP can be utilized as signal transducers for the build-up of a series of logic gates including YES, PASS 0, INH, NOT, PASS 1, and NAND. Utilizing the principle of a metal ion-mediated fluorescence switch together with a strong metal ion chelator, the fluorescence of AuNPs-AptCAP could be modulated by adding metal ions and EDTA sequentially. Therefore, a "Plug and Play" logic system based on AuNPs-AptCAP has been realized by simply adding other components to create new logic functions. This work highlights the advantages of simple synthesis and facile fluorescence switching properties, which will provide useful knowledge for the establishment of molecular logic systems. Graphical abstract.
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Affiliation(s)
- Yali Zhang
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Cheuk-Wing Li
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Lefei Zhou
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhanpeng Chen
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Changqing Yi
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China. .,Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
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5
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Huang Y, Pu F, Ren J, Qu X. Artificial Enzyme-based Logic Operations to Mimic an Intracellular Enzyme-participated Redox Balance System. Chemistry 2017; 23:9156-9161. [DOI: 10.1002/chem.201701353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Yanyan Huang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences, Changchun; Jilin 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | - Fang Pu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences, Changchun; Jilin 130022 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences, Changchun; Jilin 130022 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences, Changchun; Jilin 130022 P. R. China
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New cofactors and inhibitors for a DNA-cleaving DNAzyme: superoxide anion and hydrogen peroxide mediated an oxidative cleavage process. Sci Rep 2017; 7:378. [PMID: 28336968 PMCID: PMC5428237 DOI: 10.1038/s41598-017-00329-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/21/2017] [Indexed: 01/08/2023] Open
Abstract
Herein, we investigated the effects of new cofactors and inhibitors on an oxidative cleavage of DNA catalysis, known as a pistol-like DNAzyme (PLDz), to discuss its catalytic mechanism. PLDz performed its catalytic activity in the presence of ascorbic acid (AA), in which Cu2+ promoted, whereas Fe2+ significantly inhibited the catalytic function. Since Fe2+/AA-generated hydroxyl radicals are efficient on DNA damage, implying that oxidative cleavage of PLDz had no relation with hydroxyl radical. Subsequently, we used Fe2+/H2O2 and Cu2+/H2O2 to identify the role of hydroxyl radicals in PLDz catalysis. Data showed that PLDz lost its activity with Fe2+/H2O2, but exhibited significant cleavage with Cu2+/H2O2. Because Fe2+/H2O2 and Cu2+/H2O2 are popular reagents to generate hydroxyl radicals and the latter also produces superoxide anions, we excluded the possibility that hydroxyl radical participated in oxidative cleavage and confirmed that superoxide anion was involved in PLDz catalysis. Moreover, pyrogallol, riboflavin and hypoxanthine/xanthine oxidase with superoxide anion and hydrogen peroxide generation also induced self-cleavage of PLDz, where catalase inhibited but superoxide dismutase promoted the catalysis, suggesting that hydrogen peroxide played an essential role in PLDz catalysis. Therefore, we proposed a catalytic mechanism of PLDz in which superoxide anion and hydrogen peroxide mediated an oxidative cleavage process.
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Chen H, Sun H, Zhang X, Sun X, Shi Y, Xu S, Tang Y. A colorimetric and fluorometric dual-modal DNA logic gate based on the response of a cyanine dye supramolecule to G-quadruplexes. NEW J CHEM 2016. [DOI: 10.1039/c5nj02652k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The INHIBIT DNA logic gate with dual-modal outputs based on the response of MTC aggregates to G-quadruplexes.
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Affiliation(s)
- Hongbo Chen
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Hongxia Sun
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Xiufeng Zhang
- College of Chemistry Engineering
- North China University of Science and Technology
- Tangshan
- China
| | - Xiaoran Sun
- College of Chemistry Engineering
- North China University of Science and Technology
- Tangshan
- China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Shujuan Xu
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Yalin Tang
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
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8
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Lee IJ, Patil SP, Fhayli K, Alsaiari S, Khashab NM. Probing structural changes of self assembled i-motif DNA. Chem Commun (Camb) 2015; 51:3747-9. [PMID: 25350559 DOI: 10.1039/c4cc06824f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change.
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Affiliation(s)
- Il Joon Lee
- Controlled Release and Delivery Lab (CRD), Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Kingdom of Saudi Arabia.
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Gao W, Zhang L, Liang RP, Qiu JD. Metal-Ion-Triggered Exonuclease III Activity for the Construction of DNA Colorimetric Logic Gates. Chemistry 2015; 21:15272-9. [DOI: 10.1002/chem.201502122] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Indexed: 01/05/2023]
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10
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Liu C, Sheng Y, Sun Y, Feng J, Wang S, Zhang J, Xu J, Jiang D. A glucose oxidase-coupled DNAzyme sensor for glucose detection in tears and saliva. Biosens Bioelectron 2015; 70:455-61. [PMID: 25863343 DOI: 10.1016/j.bios.2015.03.070] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/15/2015] [Accepted: 03/27/2015] [Indexed: 02/05/2023]
Abstract
Biosensors have been widely investigated and utilized in a variety of fields ranging from environmental monitoring to clinical diagnostics. Glucose biosensors have triggered great interest and have been widely exploited since glucose determination is essential for diabetes diagnosis. In here, we designed a novel dual-enzyme biosensor composed of glucose oxidase (GOx) and pistol-like DNAzyme (PLDz) to detect glucose levels in tears and saliva. First, GOx, as a molecular recognition element, catalyzes the oxidation of glucose forming H2O2; then PLDz recognizes the produced H2O2 as a secondary signal and performs a self-cleavage reaction promoted by Mn(2+), Co(2+) and Cu(2+). Thus, detection of glucose could be realized by monitoring the cleavage rate of PLDz. The slope of the cleavage rate of PLDz versus glucose concentration curve was fitted with a Double Boltzmann equation, with a range of glucose from 100 nM to 10mM and a detection limit of 5 μM. We further applied the GOx-PLDz 1.0 biosensor for glucose detection in tears and saliva, glucose levels in which are 720±81 μM and 405±56 μM respectively. Therefore, the GOx-PLDz 1.0 biosensor is able to determine glucose levels in tears and saliva as a noninvasive glucose biosensor, which is important for diabetic patients with frequent/continuous glucose monitoring requirements. In addition, induction of DNAzyme provides a new approach in the development of glucose biosensors.
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Affiliation(s)
- Chengcheng Liu
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yongjie Sheng
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yanhong Sun
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Junkui Feng
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Shijin Wang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Jin Zhang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China.
| | - Jiacui Xu
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
| | - Dazhi Jiang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China.
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11
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Cao C, Zhang J, Li S, Xiong Q. Intelligent and ultrasensitive analysis of mercury trace contaminants via plasmonic metamaterial-based surface-enhanced Raman spectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3252-6. [PMID: 24729476 DOI: 10.1002/smll.201400165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Indexed: 05/18/2023]
Abstract
Label-free molecular logic gates (AND, INHIBIT, and OR) are constructed based on specific conformation modulation of a guanine- and thymine-rich DNA, while the optical readout is enabled by the tunable metamaterials which serve as a substrate for surface enhanced Raman spectroscopy. The DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions down to 2 × 10(-4) ppb.
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Affiliation(s)
- Cuong Cao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371
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12
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Pu F, Ren J, Qu X. "Plug and play" logic gates based on fluorescence switching regulated by self-assembly of nucleotide and lanthanide ions. ACS APPLIED MATERIALS & INTERFACES 2014; 6:9557-9562. [PMID: 24830828 DOI: 10.1021/am501949t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Molecular logic gates in response to chemical, biological, or optical input signals at a molecular level have received much interest over the past decade. Herein, we construct "plug and play" logic systems based on the fluorescence switching of guest molecules confined in coordination polymer nanoparticles generated from nucleotide and lanthanide ions. In the system, the addition of new modules directly enables new logic functions. PASS 0, YES, PASS 1, NOT, IMP, OR, and AND gates are successfully constructed in sequence. Moreover, different logic gates (AND, INH, and IMP) can be constructed using different guest molecules and the same input combinations. The work will be beneficial to the future logic design and expand the applications of coordination polymers.
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Affiliation(s)
- Fang Pu
- Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, People's Republic of China
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Huang Y, Wen W, Du D, Zhang X, Wang S, Lin Y. A universal lateral flow biosensor for proteins and DNAs based on the conformational change of hairpin oligonucleotide and its use for logic gate operations. Biosens Bioelectron 2014; 61:598-604. [PMID: 24967748 DOI: 10.1016/j.bios.2014.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/22/2014] [Accepted: 06/03/2014] [Indexed: 02/02/2023]
Abstract
A universal lateral flow biosensor for proteins and DNAs was designed on the base of target-induced conformational changes of hairpin oligonucleotide (HO). CEA (carcinoembryonic antigen) protein and c-DNA were detected both with the naked eye and a strip reader. The scheme of detecting proteins and DNAs were based on the unique molecular recognition properties of HO to the targets to form different quantities of "active" biotin groups on the surface of gold nanoparticles (AuNPs). The output of the strip is the color of the test line, which inspired us to combine strip biosensor with logic gate. Two strip logic gates ("OR" and "INH") were designed in our paper and the combinatorial logic gates in our paper could be used to make high-throughput judgment about what targets were present in the input samples according to the output results. The biosensor facilitates a portable analysis at ambient temperature as it is simple to be conducted and no requirement of training is needed. The strip logic system is proved an excellent selection and can operate effectively as well as in human serum samples. Therefore, we indicate that such logic strips a foreseeable promise in application of intelligent point-of-care and in-field diagnostics.
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Affiliation(s)
- Yan Huang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China
| | - Wei Wen
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China
| | - Dan Du
- School of Mechanical and Materials Engineering, Washington State University, Pullman 99164, USA; Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Yuehe Lin
- School of Mechanical and Materials Engineering, Washington State University, Pullman 99164, USA.
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14
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Brown CW, Lakin MR, Stefanovic D, Graves SW. Catalytic molecular logic devices by DNAzyme displacement. Chembiochem 2014; 15:950-4. [PMID: 24692254 DOI: 10.1002/cbic.201400047] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Indexed: 01/09/2023]
Abstract
Chemical reactions catalyzed by DNAzymes offer a route to programmable modification of biomolecules for therapeutic purposes. To this end, we have developed a new type of catalytic DNA-based logic gates in which DNAzyme catalysis is controlled via toehold-mediated strand displacement reactions. We refer to these as DNAzyme displacement gates. The use of toeholds to guide input binding provides a favorable pathway for input recognition, and the innate catalytic activity of DNAzymes allows amplification of nanomolar input concentrations. We demonstrate detection of arbitrary input sequences by rational introduction of mismatched bases into inhibitor strands. Furthermore, we illustrate the applicability of DNAzyme displacement to compute logic functions involving multiple logic gates. This work will enable sophisticated logical control of a range of biochemical modifications, with applications in pathogen detection and autonomous theranostics.
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Affiliation(s)
- Carl W Brown
- Center for Biomedical Engineering, MSC01 1141, 1 University of New Mexico, Albuquerque, NM 87131 (USA)
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15
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Design of multiplex logic gates: Combining regulation of DNA structure with logical calculation. Sci China Chem 2014. [DOI: 10.1007/s11426-013-4939-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Ding W, Xu M, Zhu H, Liang H. Mechanism of the hairpin folding transformation of thymine-cytosine-rich oligonucleotides induced by Hg(II) and Ag(I) ions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:101. [PMID: 24045985 DOI: 10.1140/epje/i2013-13101-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/10/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
The metal-induced folding of thymine-cytosine-rich oligonucleotides into hairpin-like structures was characterised by isothermal titration calorimetry, secondary structure analysis, equilibrium titrations, and fluorescence study. We find that designed thymine-cytosine-rich oligonucleotides can specifically bind with Hg(II) or Ag(I) ions to generate metal-mediated base pairs in a hairpin-like structure from a random coil structure. Isothermal titration calorimetry experiments were performed to reveal the detail of the whole binding process. The thermodynamic result exhibits two possible pathways of significant change upon the addition of Hg(II) ions. Furthermore, this transformation can be enhanced by the presence of Ag(I) ions. The fluorescence decreases through fluorescence resonance energy transfer (FRET) between the fluorophore and quencher confirms the process of formation of the hairpin-like structure. The analysis of optical titration data demonstrates that the saturated binding stoichiometries are 12:1 and 4:1 for Hg(II) and Ag(I) ions, respectively. Our result provides a promising strategy for the investigation of the mechanism of structural transformation of oligonucleotides influenced by metal-mediated base pairs, which may eventually lead to progress in constructing a metal-triggered DNA origami system and metal-containing DNA nanotechnology.
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Affiliation(s)
- Wei Ding
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, 230026, Hefei, Anhui, P. R. China
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Busseron E, Ruff Y, Moulin E, Giuseppone N. Supramolecular self-assemblies as functional nanomaterials. NANOSCALE 2013; 5:7098-140. [PMID: 23832165 DOI: 10.1039/c3nr02176a] [Citation(s) in RCA: 496] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In this review, we survey the diversity of structures and functions which are encountered in advanced self-assembled nanomaterials. We highlight their flourishing implementations in three active domains of applications: biomedical sciences, information technologies, and environmental sciences. Our main objective is to provide the reader with a concise and straightforward entry to this broad field by selecting the most recent and important research articles, supported by some more comprehensive reviews to introduce each topic. Overall, this compilation illustrates how, based on the rules of supramolecular chemistry, the bottom-up approach to design functional objects at the nanoscale is currently producing highly sophisticated materials oriented towards a growing number of applications with high societal impact.
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Affiliation(s)
- Eric Busseron
- SAMS Research Group, University of Strasbourg, Institut Charles Sadron, CNRS, 23 rue du Loess, BP 84087, 67034 Strasbourg Cedex 2, France
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18
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Zhang L, Wang ZX, Liang RP, Qiu JD. Easy design of colorimetric logic gates based on nonnatural base pairing and controlled assembly of gold nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8929-8935. [PMID: 23772834 DOI: 10.1021/la401887b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Utilizing the principles of metal-ion-mediated base pairs (C-Ag-C and T-Hg-T), the pH-sensitive conformational transition of C-rich DNA strand, and the ligand-exchange process triggered by DL-dithiothreitol (DTT), a system of colorimetric logic gates (YES, AND, INHIBIT, and XOR) can be rationally constructed based on the aggregation of the DNA-modified Au NPs. The proposed logic operation system is simple, which consists of only T-/C-rich DNA-modified Au NPs, and it is unnecessary to exquisitely design and alter the DNA sequence for different multiple molecular logic operations. The nonnatural base pairing combined with unique optical properties of Au NPs promises great potential in multiplexed ion sensing, molecular-scale computers, and other computational logic devices.
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Affiliation(s)
- Li Zhang
- Department of Chemistry, Nanchang University, Nanchang 330031, China
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Jiang Q, Wang ZG, Ding B. Programmed colorimetric logic devices based on DNA-gold nanoparticle interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:1016-1020. [PMID: 23293092 DOI: 10.1002/smll.201201760] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Indexed: 06/01/2023]
Abstract
A system including nucleic acid strands and unmodified gold nanopartcles is activated to perform programmed logic functions, using pH and DNA as inputs and the plasmonic-related color change of gold nanoparticles as the output. The complexity of the logic devices can be simply enhanced by appropriate engineering.
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Affiliation(s)
- Qiao Jiang
- National Center for Nanoscience and Technology, Beijing, PR China
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20
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Xiao SJ, Hu PP, Chen LQ, Zhen SJ, Peng L, Li YF, Huang CZ. A visual dual-aptamer logic gate for sensitive discrimination of prion diseases-associated isoform with reusable magnetic microparticles and fluorescence quantum dots. PLoS One 2013; 8:e53935. [PMID: 23393552 PMCID: PMC3564804 DOI: 10.1371/journal.pone.0053935] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/07/2012] [Indexed: 01/07/2023] Open
Abstract
Molecular logic gates, which have attracted increasing research interest and are crucial for the development of molecular-scale computers, simplify the results of measurements and detections, leaving the diagnosis of disease either "yes" or "no". Prion diseases are a group of fatal neurodegenerative disorders that happen in human and animals. The main problem with a diagnosis of prion diseases is how to sensitively and selectively discriminate and detection of the minute amount of PrP(Res) in biological samples. Our previous work had demonstrated that dual-aptamer strategy could achieve highly sensitive and selective discrimination and detection of prion protein (cellular prion protein, PrP(C), and the diseases associated isoform, PrP(Res)) in serum and brain. Inspired by the advantages of molecular logic gate, we further conceived a new concept for dual-aptamer logic gate that responds to two chemical input signals (PrP(C) or PrP(Res) and Gdn-HCl) and generates a change in fluorescence intensity as the output signal. It was found that PrP(Res) performs the "OR" logic operation while PrP(C) performs "XOR" logic operation when they get through the gate consisted of aptamer modified reusable magnetic microparticles (MMPs-Apt1) and quantum dots (QDs-Apt2). The dual-aptamer logic gate simplifies the discrimination results of PrP(Res), leaving the detection of PrP(Res) either "yes" or "no". The development of OR logic gate based on dual-aptamer strategy and two chemical input signals (PrP(Res) and Gdn-HCl) is an important step toward the design of prion diseases diagnosis and therapy systems.
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Affiliation(s)
- Sai Jin Xiao
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, China
- Jiangxi Key Laboratory of Mass Spectrometry and Instrumentation, Department of Applied Chemistry, East China Institute of Technology, Nanchang, Jiangxi Province, China
| | - Ping Ping Hu
- College of Life Science, Southwest University, Chongqing, China
| | - Li Qiang Chen
- College of Life Science, Southwest University, Chongqing, China
| | - Shu Jun Zhen
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, China
| | - Li Peng
- College of Life Science, Southwest University, Chongqing, China
| | - Yuan Fang Li
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, China
| | - Cheng Zhi Huang
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, China
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
- * E-mail:
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Bhowmik S, Das RN, Parasar B, Dash J. pH dependent multifunctional and multiply-configurable logic gate systems based on small molecule G-quadruplex DNA recognition. Chem Commun (Camb) 2013; 49:1817-9. [DOI: 10.1039/c3cc38888c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Erbas-Cakmak S, Bozdemir OA, Cakmak Y, Akkaya EU. Proof of principle for a molecular 1 : 2 demultiplexer to function as an autonomously switching theranostic device. Chem Sci 2013. [DOI: 10.1039/c2sc21499g] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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23
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Using Thermally Regenerable Cerium Oxide Nanoparticles in Biocomputing to Perform Label-free, Resettable, and Colorimetric Logic Operations. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207587] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Lin Y, Xu C, Ren J, Qu X. Using Thermally Regenerable Cerium Oxide Nanoparticles in Biocomputing to Perform Label-free, Resettable, and Colorimetric Logic Operations. Angew Chem Int Ed Engl 2012; 51:12579-83. [DOI: 10.1002/anie.201207587] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Indexed: 01/23/2023]
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25
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Li B, Chen X, Ellington AD. Adapting enzyme-free DNA circuits to the detection of loop-mediated isothermal amplification reactions. Anal Chem 2012; 84:8371-7. [PMID: 22947054 PMCID: PMC3478682 DOI: 10.1021/ac301944v] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Loop-mediated isothermal amplification of DNA (LAMP) is a powerful isothermal nucleic acid amplification technique that can accumulate ~10(9) copies from less than 10 copies of input template within an hour or two. Unfortunately, while the amplification reactions are extremely powerful, the quantitative detection of LAMP products is still analytically difficult. In this article, to both improve the specificity of LAMP detection and to make direct readout of LAMP amplification simpler and much more reliable, we have developed a nonenzymatic nucleic acid circuit (catalyzed hairpin assembly, CHA) that can both amplify and integrate the specific sequence signals present in LAMP amplicons. Through a hairpin acceptor, one of the four loop products amplified from the LAMP is transduced to an active catalyst ssDNA which can in turn trigger a CHA reaction. After CHA detection, even less than 10 molecules/μL model templates (M13mp18) can produce significant signal, and both nonspecific template and parasitic amplicons cannot bring interference at all. More importantly, to further enhance the specificity, we have designed a dual-CHA circuit that only gave positive responses in presence of two LAMP loops. The AND-GATE detector will act as a simultaneous, specific readout of the LAMP product, rather than of competing and parasitic amplicons.
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Affiliation(s)
- Bingling Li
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Xi Chen
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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26
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Orbach R, Mostinski L, Wang F, Willner I. Nucleic Acid Driven DNA Machineries Synthesizing Mg2+-Dependent DNAzymes: An Interplay between DNA Sensing and Logic-Gate Operations. Chemistry 2012; 18:14689-94. [DOI: 10.1002/chem.201201995] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Indexed: 12/22/2022]
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27
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Chen J, Fang Z, Lie P, Zeng L. Computational lateral flow biosensor for proteins and small molecules: a new class of strip logic gates. Anal Chem 2012; 84:6321-5. [PMID: 22780691 DOI: 10.1021/ac301508b] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The first example of strip logic gates ("OR" and "AND" functions) for proteins and small molecules has been constructed on the basis of target-induced self-assembly of split aptamer fragments. Using thrombin and ATP as inputs, the corresponding split/integrated aptamers as molecular recognition elements, and gold nanoparticles as a tracer, the output signals can be directly visualized by observing the red bands on the test zones of the strips. The assay is simple, easy to perform, and cost-effective, allowing portable analysis at ambient temperature. The strip logic system is resistant to nonspecific interfering agents and can operate effectively even in human serum samples. Such logic strips hold great promise for application in intelligent point-of-care and in-field diagnostics.
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28
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Li L, Cai P, Deng Y, Yang L, He X, Pu L, Wu D, Liu J, Xiang H, Zhou X. Water-soluble porphyrin-based logic gates. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424611004397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of simple logic gates based on a water-soluble porphyrin molecule, 5,10,15,20-tetrakis-(4-sulfonatophenyl)porphyrin (TPPS4) is designed. Logic operations, including OR, NOR, INHIBIT and AND, have been built by two inputs of acid/base or metal ions (Al3+ and/or Sn4+) and two outputs of UV-vis absorption and fluorescent spectra. An OFF–ON switch triggered by Al3+ ion in vitro is developed based on TPPS4.
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Affiliation(s)
- Lili Li
- Institute of Homogeneous Catalysis, College of Chemistry, Sichuan University, 610064 Chengdu, China
| | - Peiying Cai
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610064 Chengdu, China
| | - Yuefei Deng
- Department of Neurosurgery, The Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, 510120 Guangzhou, China
| | - Liutao Yang
- Institute of Homogeneous Catalysis, College of Chemistry, Sichuan University, 610064 Chengdu, China
| | - Xuan He
- Institute of Homogeneous Catalysis, College of Chemistry, Sichuan University, 610064 Chengdu, China
| | - Lingsong Pu
- Institute of Homogeneous Catalysis, College of Chemistry, Sichuan University, 610064 Chengdu, China
| | - Di Wu
- Institute of Homogeneous Catalysis, College of Chemistry, Sichuan University, 610064 Chengdu, China
- State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Nanjing University, 210093 Nanjing, China
| | - Jin Liu
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610064 Chengdu, China
| | - Haifeng Xiang
- Institute of Homogeneous Catalysis, College of Chemistry, Sichuan University, 610064 Chengdu, China
| | - Xiangge Zhou
- Institute of Homogeneous Catalysis, College of Chemistry, Sichuan University, 610064 Chengdu, China
- State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Nanjing University, 210093 Nanjing, China
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29
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Wang Z, Ning L, Duan A, Zhu X, Wang H, Li G. A set of logic gates fabricated with G-quadruplex assembled at an electrode surface. Chem Commun (Camb) 2012; 48:7507-9. [DOI: 10.1039/c2cc33088a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Gerasimova YV, Kolpashchikov DM. Connectable DNA Logic Gates: OR and XOR Logics. Chem Asian J 2011; 7:534-40. [DOI: 10.1002/asia.201100664] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Indexed: 01/11/2023]
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31
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Ultrasensitive DNA detection by cycle isothermal amplification based on nicking endonuclease and its application to logic gates. Biosens Bioelectron 2011; 30:241-8. [DOI: 10.1016/j.bios.2011.09.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/15/2011] [Accepted: 09/16/2011] [Indexed: 01/24/2023]
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32
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Zhang C, Yang J, Xu J. Molecular logic computing model based on self-assembly of DNA nanoparticles. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4725-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Pu F, Ren J, Yang X, Qu X. Multivalued Logic Gates Based on DNA. Chemistry 2011; 17:9590-4. [DOI: 10.1002/chem.201101140] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/27/2011] [Indexed: 11/09/2022]
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34
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Xu X, Zhang J, Yang F, Yang X. Colorimetric logic gates for small molecules using split/integrated aptamers and unmodified gold nanoparticles. Chem Commun (Camb) 2011; 47:9435-7. [PMID: 21779550 DOI: 10.1039/c1cc13459k] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Herein we report the "OR" and "AND" colorimetric logic gates for small molecules using split/integrated aptamers and unmodified gold nanoparticles, which generate visually observed outputs according to Boolean operations.
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Affiliation(s)
- Xiaowen Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, PR China
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35
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Li B, Ellington AD, Chen X. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res 2011; 39:e110. [PMID: 21693555 PMCID: PMC3167626 DOI: 10.1093/nar/gkr504] [Citation(s) in RCA: 381] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Signal amplification is a key component of molecular detection. Enzyme-free signal amplification is especially appealing for the development of low-cost, point-of-care diagnostics. It has been previously shown that enzyme-free DNA circuits with signal-amplification capacity can be designed using a mechanism called ‘catalyzed hairpin assembly’. However, it is unclear whether the efficiency and modularity of such circuits is suitable for multiple analytical applications. We have therefore designed and characterized a simplified DNA circuit based on catalyzed hairpin assembly, and applied it to multiple different analytical formats, including fluorescent, colorimetric, and electrochemical and signaling. By optimizing the design of previous hairpin-based catalytic assemblies we found that our circuit has almost zero background and a high catalytic efficiency, with a kcat value above 1 min−1. The inherent modularity of the circuit allowed us to readily adapt our circuit to detect both RNA and small molecule analytes. Overall, these data demonstrate that catalyzed hairpin assembly is suitable for analyte detection and signal amplification in a ‘plug-and-play’ fashion.
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Affiliation(s)
- Bingling Li
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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36
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Park KS, Jung C, Park HG. "Illusionary" polymerase activity triggered by metal ions: use for molecular logic-gate operations. Angew Chem Int Ed Engl 2011; 49:9757-60. [PMID: 20979061 DOI: 10.1002/anie.201004406] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
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37
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Liu D, Chen W, Sun K, Deng K, Zhang W, Wang Z, Jiang X. Resettable, Multi-Readout Logic Gates Based on Controllably Reversible Aggregation of Gold Nanoparticles. Angew Chem Int Ed Engl 2011; 50:4103-7. [DOI: 10.1002/anie.201008198] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 02/07/2011] [Indexed: 11/11/2022]
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38
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Liu D, Chen W, Sun K, Deng K, Zhang W, Wang Z, Jiang X. Resettable, Multi-Readout Logic Gates Based on Controllably Reversible Aggregation of Gold Nanoparticles. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008198] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Ma DL, Kwan MHT, Chan DSH, Lee P, Yang H, Ma VPY, Bai LP, Jiang ZH, Leung CH. Crystal violet as a fluorescent switch-on probe for i-motif: label-free DNA-based logic gate. Analyst 2011; 136:2692-6. [DOI: 10.1039/c1an15091j] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Sreejith S, Divya KP, Manojkumar TK, Ajayaghosh A. Multiple Analyte Response and Molecular Logic Operations by Excited-State Charge-Transfer Modulation in a Bipyridine Integrated Fluorophore. Chem Asian J 2010; 6:430-7. [DOI: 10.1002/asia.201000637] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Indexed: 11/06/2022]
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41
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Park KS, Jung C, Park HG. “Illusionary” Polymerase Activity Triggered by Metal Ions: Use for Molecular Logic-Gate Operations. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004406] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Jiang D, Xu J, Sheng Y, Sun Y, Zhang J. An allosteric DNAzyme with dual RNA-cleaving and DNA-cleaving activities. FEBS J 2010; 277:2543-9. [PMID: 20553490 DOI: 10.1111/j.1742-4658.2010.07669.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of RNA-cleaving or DNA-cleaving DNAzymes have been obtained by in vitro selection. However, engineering an allosteric DNAzyme with dual RNA-cleaving and DNA-cleaving activities is very challenging. We used an in vitro-selected pistol-like (PL) DNAzyme as a DNA scaffold for designing a DNAzyme with dual catalytic activities. We prepared the 46-nucleotide DNAzyme with DNA-cleaving activity (PL DNAzyme), and then grafted the deoxyribonucleotide residues from an 8-17 variant DNAzyme into the region of stem-loop I and the catalytic core of the PL DNAzyme scaffold. This deoxyribonucleotide residue grafting resulted in a DNAzyme with dual RNA-cleaving and DNA-cleaving activities (DRc DNAzyme). Drc DNAzyme has properties different from those of the original PL DNAzyme, including DNA cleavage sites and the required metal ion concentration. Interestingly, the RNA substrate and RNase A can act as effectors to mediate the DNA cleavage. Our results show that RNA-cleaving and DNA-cleaving activities simultaneously coexist in DRc DNAzyme, and the DNA cleavage activity can be reversibly regulated by a conformational transition.
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Affiliation(s)
- Dazhi Jiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, China
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43
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Pu F, Wang C, Hu D, Huang Z, Ren J, Wang S, Qu X. Logic gates and pH sensing devices based on a supramolecular telomere DNA/conjugated polymer system. MOLECULAR BIOSYSTEMS 2010; 6:1928-32. [PMID: 20603667 DOI: 10.1039/c004215c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A conceptually new class of telomere DNA/conjugated polymer system has been constructed to enable sensing of pH changes and create robust logic gates capable of multiplex logic operations. It combines the advantages of quadruplex-duplex conversion and efficient energy transfer from the polymer to the DNA binding molecule. The system is simple in design, fast in operation, and allows the detection of pH changes with high accuracy and sensitivity. In addition, the approach could be adopted for the investigation of other biomolecular conformational changes upon binding to their targets. More importantly, the present logic operations showed advantages over other nucleic acid-based logic gates: (1) The system does not require any CP modification or oligonucleotide labeling, which offers the advantages of simplicity and cost efficiency. (2) The reversibility of the switch makes the logic gates feasible to realize system reset. (3) The system could be implemented to perform multiple logic functions by using distinct input signals.
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Affiliation(s)
- Fang Pu
- Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China
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44
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Bai YC, Zhang C, Fang CJ, Yan CH. Logic Information Communication in a Fluorescent Molecular Switch. Chem Asian J 2010; 5:1870-4. [DOI: 10.1002/asia.201000105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Gerasimova YV, Cornett E, Kolpashchikov DM. RNA-cleaving deoxyribozyme sensor for nucleic acid analysis: the limit of detection. Chembiochem 2010; 11:811-7, 729. [PMID: 20301161 PMCID: PMC2949061 DOI: 10.1002/cbic.201000006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Indexed: 12/31/2022]
Abstract
Along with biocompatibility, chemical stability, and simplicity of structural prediction and modification, deoxyribozyme-based molecular sensors have the potential of an improved detection limit due to their ability to catalytically amplify signal. This study contributes to the understanding of the factors responsible for the limit of detection (LOD) of RNA-cleaving deoxyribozyme sensors. A new sensor that detects specific DNA/RNA sequences was designed from deoxyribozyme OA-II [Chiuman, W.; Li, Y. (2006) J. Mol. Biol. 357, 748-754]. The sensor architecture allows for a unique combination of high selectivity, low LOD and the convenience of fluorescent signal monitoring in homogeneous solution. The LOD of the sensor was found to be approximately 1.6 x 10(-10) M after 3 h of incubation. An equation that allows estimation of the lowest theoretical LOD using characteristics of parent deoxyribozymes and their fluorogenic substrates was derived and experimentally verified. According to the equation, "catalytically perfect" enzymes can serve as scaffolds for the design of sensors with the LOD not lower than approximately 2 x 10(-15) M after 3 h of incubation. A new value termed the detection efficiency (DE) is suggested as a time-independent characteristic of a sensor's sensitivity. The expressions for the theoretical LOD and DE can be used to evaluate nucleic acid and protein enzymes for their application as biosensing platforms.
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Affiliation(s)
| | | | - Dmitry M. Kolpashchikov
- Dr. Y. V. Gerasimova, E. Cornett, Dr. D. M. Kolpashchikov Chemistry Department, University of Central Florida 4000 Central Florida Blvd, Orlando, FL 32816-2366 (USA)
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46
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Bozdemir OA, Guliyev R, Buyukcakir O, Selcuk S, Kolemen S, Gulseren G, Nalbantoglu T, Boyaci H, Akkaya EU. Selective Manipulation of ICT and PET Processes in Styryl-Bodipy Derivatives: Applications in Molecular Logic and Fluorescence Sensing of Metal Ions. J Am Chem Soc 2010; 132:8029-36. [DOI: 10.1021/ja1008163] [Citation(s) in RCA: 357] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- O. Altan Bozdemir
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Ruslan Guliyev
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Onur Buyukcakir
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Sencer Selcuk
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Safacan Kolemen
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Gulcihan Gulseren
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Tugrul Nalbantoglu
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Hande Boyaci
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Engin U. Akkaya
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
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47
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Li T, Wang E, Dong S. Potassium-lead-switched G-quadruplexes: a new class of DNA logic gates. J Am Chem Soc 2010; 131:15082-3. [PMID: 19919152 DOI: 10.1021/ja9051075] [Citation(s) in RCA: 313] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A cation-driven allosteric G-quadruplex DNAzyme (PW17) was utilized to devise a conceptually new class of DNA logic gate based on cation-tuned ligand binding and release. K(+) favors the binding of hemin to parallel-stranded PW17, thereby promoting the DNAzyme activity, whereas Pb(2+) induces PW17 to undergo a parallel-to-antiparallel conformation transition and thus drives hemin to release from the G-quadruplex, deactivating the DNAzyme. Such a K(+)-Pb(2+) switched G-quadruplex, in fact, functions as a two-input INHIBIT logic gate. With the introduction of another input EDTA, this G-quadruplex can be further utilized to construct a reversibly operated IMPLICATION gate.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
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Richards JL, Seward GK, Wang YH, Dmochowski IJ. Turning the 10-23 DNAzyme on and off with light. Chembiochem 2010; 11:320-4. [PMID: 20077457 PMCID: PMC2908382 DOI: 10.1002/cbic.200900702] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Indexed: 11/10/2022]
Affiliation(s)
- Julia L. Richards
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Garry K. Seward
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Yu-Hsiu Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
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Zhang C, Yang J, Xu J. Circular DNA logic gates with strand displacement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1416-1419. [PMID: 19957974 DOI: 10.1021/la903137f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Circular DNA logic gates were constructed on the basis of DNA three-way branch migration. In this logic system, circular DNA was used as a basic work unit and linear single-strand DNA was used as input and output signals. Making use of the circular structure, most of the DNA-specific recognition regions were designed in a single DNA ring. Depending on accurate DNA sequence recognition and highly effective strand displacement, the logic gates yielded correct results. In addition, the positions of gold nanoparticles (AuNPs) were detected as an alternative approach to determine logic results. Thus, the accurate and tunable control of DNA/AuNPs may be applied widely in DNA nanotechnology.
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Affiliation(s)
- Cheng Zhang
- Institute of Software, School of Electronics Engineering and Computer Science, Key Laboratory of High Confidence Software Technologies, Ministry of Education, Peking University, Beijing, China, 100871.
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