1
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Li C, Xie Y, Cheng X, Xu L, Yao G, Li Q, Shen J, Fan C, Li M. Single-Molecule Assessment of DNA Hybridization Kinetics on Dye-Loaded DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2402870. [PMID: 38844986 DOI: 10.1002/smll.202402870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/18/2024] [Indexed: 10/04/2024]
Abstract
DNA nanostructures offer a versatile platform for precise dye assembly, making them promising templates for creating photonic complexes with applications in photonics and bioimaging. However, despite these advancements, the effect of dye loading on the hybridization kinetics of single-stranded DNA protruding from DNA nanostructures remains unexplored. In this study, the DNA points accumulation for imaging in the nanoscale topography (DNA-PAINT) technique is employed to investigate the accessibility of functional binding sites on DNA-templated excitonic wires. The results indicate that positively charged dyes on DNA frameworks can accelerate the hybridization kinetics of protruded ssDNA through long-range electrostatic interactions. Furthermore, the impacts of various charged dyes and binding sites are explored on diverse DNA frameworks with varying cross-sizes. The research underscores the crucial role of electrostatic interactions in DNA hybridization kinetics within DNA-dye complexes, offering valuable insights for the functionalization and assembly of biomimetic photonic systems.
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Affiliation(s)
- Cong Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yao Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinyi Cheng
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lifeng Xu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guangbao Yao
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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2
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Wang X, Gao Z, Tian W. An enzymolysis-induced energy transfer co-assembled system for spontaneously recoverable supramolecular dynamic memory. Chem Sci 2024; 15:11084-11091. [PMID: 39027284 PMCID: PMC11253121 DOI: 10.1039/d4sc02756f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/30/2024] [Indexed: 07/20/2024] Open
Abstract
The continuing growth of the digital world requires new ways of constructing memory devices to process and store dynamic data, because the current ones suffer from inefficiency, limited reads, and difficulty to manufacture. Here we propose a supramolecular dynamic memory (SDM) strategy based on an enzymolysis-induced energy transfer co-assembly derived from a naphthalene-based cationic monomer and organic dye sulforhodamine 101, enabling the construction of spontaneously recoverable dynamic memory devices. Benefitting from the large exciton migration rate (4.48 × 1015 L mol-1 s-1) between the monomer and sulforhodamine 101, the energy transfer process between the two is effectively achieved. Since alkaline phosphatase can selectively hydrolyze adenosine triphosphate, leading to the disruption of the co-assemblies, an enzyme-mediated time-dependent fluorochromic system is realized. On this basis, a SDM system featuring spontaneous recovery and enabling the memory of dynamic information in optical and electrical modes is successfully constructed. The current study represents a promising step in the nascent development of supramolecular materials for computational systems.
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Affiliation(s)
- Xuanyu Wang
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University Xi'an 710072 P. R. China
| | - Zhao Gao
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University Xi'an 710072 P. R. China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, Xi'an Key Laboratory of Hybrid Luminescent Materials and Photonic Device, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University Xi'an 710072 P. R. China
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3
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Akter R, Kirkwood N, Zaman S, Lu B, Wang T, Takakusagi S, Mulvaney P, Biju V, Takano Y. Bio-catalytic nanoparticle shaping for preparing mesoscopic assemblies of semiconductor quantum dots and organic molecules. NANOSCALE HORIZONS 2024; 9:1128-1136. [PMID: 38780444 DOI: 10.1039/d4nh00134f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
We report a unique bio-catalytic nanoparticle shaping (BNS) method for preparing a variety of mesoscopic particles by a facile process. For example, the BNS method affords mesoscopic QD assembly dispersions. Large-size sedimentations (>1 μm) of QDs are first formed using oligo-L-lysine linkers. These then undergo controlled enzymatic cleavage of the linkers using trypsin, which surprisingly leads to mesoscopic particles about 84 nm in size with a narrow size distribution. A detailed mechanism of the BNS method is investigated using tetrakis(4-carboxyphenyl)porphyrin (TCPP), instead of QDs, as a probe molecule. Interestingly, the BNS method can also be applied to other combinations of enzymes and enzymatically degradable linkers, such as hyaluronidase with hyaluronan. As a potential application, the mesoscopic particles of QDs and oligo-lysine exhibit their ability to act as a drug delivery carrier originating from the features of both QDs and oligo-lysine. The BNS method demonstrates the universality and versatility of preparing mesoscopic particles and opens new doors for studying QD assemblies and molecular-based mesoscopic particles.
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Affiliation(s)
- Rumana Akter
- Graduate School of Environmental Science, Hokkaido University, Sapporo 0600810, Japan.
| | - Nicholas Kirkwood
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Samantha Zaman
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Bang Lu
- Graduate School of Environmental Science, Hokkaido University, Sapporo 0600810, Japan.
- Institute for Catalysis, Hokkaido University, Sapporo 0010021, Japan
| | - Tinci Wang
- Graduate School of Environmental Science, Hokkaido University, Sapporo 0600810, Japan.
| | - Satoru Takakusagi
- Graduate School of Environmental Science, Hokkaido University, Sapporo 0600810, Japan.
- Institute for Catalysis, Hokkaido University, Sapporo 0010021, Japan
| | - Paul Mulvaney
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Vasudevanpillai Biju
- Graduate School of Environmental Science, Hokkaido University, Sapporo 0600810, Japan.
- Research Institute of Electronic Science, Hokkaido University, Sapporo 0010020, Japan
| | - Yuta Takano
- Graduate School of Environmental Science, Hokkaido University, Sapporo 0600810, Japan.
- Research Institute of Electronic Science, Hokkaido University, Sapporo 0010020, Japan
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4
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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5
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Yang S, Wang Y, Wang Q, Li F, Ling D. DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:340-355. [PMID: 37501793 PMCID: PMC10369495 DOI: 10.1021/cbmi.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/07/2023] [Indexed: 07/29/2023]
Abstract
DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.
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Affiliation(s)
- Shengfei Yang
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuqi Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Qiyue Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Fangyuan Li
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
| | - Daishun Ling
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
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6
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Shen P, Liu Y, Qu X, Zhu M, Huang T, Sun Q. An optical keypad lock with high resettability based on a quantum dot-porphyrin FRET nanodevice. NANOSCALE ADVANCES 2023; 5:2986-2993. [PMID: 37260500 PMCID: PMC10228340 DOI: 10.1039/d3na00030c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023]
Abstract
Due to their appealing properties, nanomaterials have become ideal candidates for the implementation of computing systems. Herein, an optical keypad lock based on a Förster resonance energy transfer (FRET) nanodevice is developed. The nanodevice is composed of a green-emission quantum dot with a thick silica shell (gQD@SiO2) and peripheric blue-emission quantum dots with ultrathin silica spacer (bQD@SiO2), on which 5,10,15,20-tetrakis(4-sulfophenyl)porphyrin (TSPP) is covalently linked. The nanodevice outputs dual emission-based ratiometric fluorescence, depending on the FRET efficiency of bQD-porphyrin pairs, which is highly sensitive to the metalation of TSPP: values are 59.7%, 44.8%, and 10.1% for bQD-Zn(ii)TSPP, bQD-TSPP, and bQD-Fe(iii)TSPP pairs, respectively. As such, by using the competitive chelation-induced transmetalation of TSPP, the nanodevice is capable of implementing a 3-input keypad lock that is unlocked only by the correct input order of Zn(ii) chelator, iron ions, and UV light. Interestingly, the reversible transmetalation of TSPP permits the reset (lock) operation of the keypad lock with the correct input order of ascorbic acid, Zn(ii), and UV light. Application of the nanodevice is exemplified by the construction of paper and cellular keypad locks, respectively, both of which feature signal readability and/or high resettability, showing high potential for personal information identification and bio-encryption applications.
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Affiliation(s)
- Peng Shen
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Yuqian Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Joint International Research Lab of Lignocellulosic Functional Materials, College of Light Industry and Food Engineering, Nanjing Forestry University Nanjing 210037 China
| | - Xiaojun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Mingsong Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Ting Huang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
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7
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DNA computational device-based smart biosensors. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2022.116911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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8
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Chen C, Wei X, Parsons MF, Guo J, Banal JL, Zhao Y, Scott MN, Schlau-Cohen GS, Hernandez R, Bathe M. Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami. Nat Commun 2022; 13:4935. [PMID: 35999227 PMCID: PMC9399249 DOI: 10.1038/s41467-022-32662-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework to selectively attach spatially addressable QDs on 3D wireframe DNA origami scaffolds using interfacial control of the QD surface. Using optical spectroscopy and molecular dynamics simulation, we investigated the fabrication of monovalent QDs of different sizes using chimeric single-stranded DNA to control QD surface chemistry. By understanding the relationship between chimeric single-stranded DNA length and QD size, we integrated single QDs into wireframe DNA origami objects and visualized the resulting QD-DNA assemblies using electron microscopy. Using these advances, we demonstrated the ability to program arbitrary 3D spatial relationships between QDs and dyes on DNA origami objects by fabricating energy-transfer circuits and colloidal molecules. Our design and fabrication approach enables the geometric control and spatial addressing of QDs together with the integration of other materials including dyes to fabricate hybrid materials for functional nanoscale photonic devices.
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Affiliation(s)
- Chi Chen
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Xingfei Wei
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Molly F. Parsons
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Jiajia Guo
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,grid.458489.c0000 0001 0483 7922Present Address: Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - James L. Banal
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,Present Address: Cache DNA, Inc., 200 Lincoln Centre Drive, Foster City, CA 94404 USA
| | - Yinong Zhao
- grid.21107.350000 0001 2171 9311Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Madelyn N. Scott
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Gabriela S. Schlau-Cohen
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Rigoberto Hernandez
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Mark Bathe
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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9
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Mirzayi S, Ravan H, Soltanian S. Borderline Boolean states improve the biosensing applications of DNA circuits. Int J Biol Macromol 2022; 207:1005-1010. [PMID: 35378164 DOI: 10.1016/j.ijbiomac.2022.03.197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 11/28/2022]
Abstract
Molecular circuits have been used in a wide range of diagnosis applications, from the detection of chemical molecules in solution to the complex processing of cell surface receptors. One of the most important challenges of these systems is the lack of distinguishability between different circuit states when each circuit state represents a specific disease. In this work, we designed a molecular amplification circuit with borderline Boolean states that each state can be distinguished with different color intensity. For this purpose, two DNA complexes and four DNA hairpin structures were designed to detect miR-218 and miR-215 biomarkers. One of the designed DNA complexes has two G-quadruplex structures and the other has only one G-quadruplex structure. In the absence of the inputs, all three G-quadruplex structures are active and produce a high-intensity signal, while in the other three states, including the presence of miR-218, the presence of miR-215, and the presence of both inputs, respectively, one, two, and zero G-quadruplex structures are active. Therefore, the designed system can identify two different biomarkers simultaneously with different signal ratios, which can easily distinguish the different states of the circuit. This strategy is very promising to identify diseases in which any combination of biomarkers leads to a particular disease.
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Affiliation(s)
- Sedighe Mirzayi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Sara Soltanian
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
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10
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He X, Lam JWY, Kwok RTK, Tang BZ. Real-Time Visualization and Monitoring of Physiological Dynamics by Aggregation-Induced Emission Luminogens (AIEgens). ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:413-435. [PMID: 34314222 DOI: 10.1146/annurev-anchem-090420-101149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Physiological dynamics in living cells and tissues are crucial for maintenance and regulation of their normal activities and functionalities. Tiny fluctuations in physiological microenvironments can leverage significant influences on cell growth, metabolism, differentiation, and apoptosis as well as disease evolution. Fluorescence imaging based on aggregation-induced emission luminogens (AIEgens) exhibits superior advantages in real-time sensing and monitoring of the physiological dynamics in living systems, including its unique properties such as high sensitivity and rapid response, flexible molecular design, and versatile nano- to mesostructural fabrication. The introduction of canonic AIEgens with long-wavelength, near-infrared, or microwave emission, persistent luminescence, and diversified excitation source (e.g., chemo- or bioluminescence) offers researchers a tool to evaluate the resulting molecules with excellent performance in response to subtle fluctuations in bioactivities with broader dimensionalities and deeper hierarchies.
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Affiliation(s)
- Xuewen He
- Department of Chemistry, The Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; ,
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Jacky W Y Lam
- Department of Chemistry, The Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; ,
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Ryan T K Kwok
- Department of Chemistry, The Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; ,
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Ben Zhong Tang
- Department of Chemistry, The Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; ,
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
- AIE Institute, Guangzhou Development Distinct, Huangpu, Guangzhou 516530, China
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11
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He L, Mu J, Gang O, Chen X. Rationally Programming Nanomaterials with DNA for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003775. [PMID: 33898180 PMCID: PMC8061415 DOI: 10.1002/advs.202003775] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/23/2020] [Indexed: 05/05/2023]
Abstract
DNA is not only a carrier of genetic information, but also a versatile structural tool for the engineering and self-assembling of nanostructures. In this regard, the DNA template has dramatically enhanced the scalability, programmability, and functionality of the self-assembled DNA nanostructures. These capabilities provide opportunities for a wide range of biomedical applications in biosensing, bioimaging, drug delivery, and disease therapy. In this review, the importance and advantages of DNA for programming and fabricating of DNA nanostructures are first highlighted. The recent progress in design and construction of DNA nanostructures are then summarized, including DNA conjugated nanoparticle systems, DNA-based clusters and extended organizations, and DNA origami-templated assemblies. An overview on biomedical applications of the self-assembled DNA nanostructures is provided. Finally, the conclusion and perspectives on the self-assembled DNA nanostructures are presented.
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Affiliation(s)
- Liangcan He
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
| | - Jing Mu
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Oleg Gang
- Department of Chemical Engineering and Department of Applied Physics and Applied MathematicsColumbia UniversityNew YorkNY10027USA
- Center for Functional NanomaterialsBrookhaven National LaboratoryUptonNY11973USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
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12
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Zhao S, Yu L, Yang S, Tang X, Chang K, Chen M. Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies. NANOSCALE HORIZONS 2021; 6:298-310. [PMID: 33877218 DOI: 10.1039/d0nh00587h] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.
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Affiliation(s)
- Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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13
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Fan D, Wang J, Wang E, Dong S. Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001766. [PMID: 33344121 PMCID: PMC7740092 DOI: 10.1002/advs.202001766] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Indexed: 05/11/2023]
Abstract
DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- Present address:
Institute of ChemistryThe Hebrew University of JerusalemJerusalem91904Israel
| | - Juan Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
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14
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Abstract
In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.
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Affiliation(s)
- Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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15
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Interfacing DNA with nanoparticles: Surface science and its applications in biosensing. Int J Biol Macromol 2020; 151:757-780. [DOI: 10.1016/j.ijbiomac.2020.02.217] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
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16
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Biswas PK, Saha S, Gaikwad S, Schmittel M. Reversible Multicomponent AND Gate Triggered by Stoichiometric Chemical Pulses Commands the Self-Assembly and Actuation of Catalytic Machinery. J Am Chem Soc 2020; 142:7889-7897. [DOI: 10.1021/jacs.0c01315] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Pronay Kumar Biswas
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Suchismita Saha
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Sudhakar Gaikwad
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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17
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He X, Peng C, Qiang S, Xiong LH, Zhao Z, Wang Z, Kwok RT, Lam JW, Ma N, Tang BZ. Less is more: Silver-AIE core@shell nanoparticles for multimodality cancer imaging and synergistic therapy. Biomaterials 2020; 238:119834. [DOI: 10.1016/j.biomaterials.2020.119834] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/07/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
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18
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Xiong LH, Tu JW, Zhang YN, Yang LL, Cui R, Zhang ZL, Pang DW. Designer cell-self-implemented labeling of microvesicles in situ with the intracellular-synthesized quantum dots. Sci China Chem 2020. [DOI: 10.1007/s11426-019-9697-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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20
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He MQ, Chen S, Yao K, Meng J, Wang K, Yu YL, Wang JH. Precisely Tuning LSPR Property via “Peptide-Encoded” Morphological Evolution of Gold Nanorods for Quantitative Visualization of Enzyme Activity. Anal Chem 2019; 92:1395-1401. [DOI: 10.1021/acs.analchem.9b04573] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Meng-Qi He
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Shuai Chen
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China
| | - Kan Yao
- Texas Materials Institute, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jie Meng
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Kun Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
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21
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Filipov Y, Bollella P, Katz E. Not-XOR (NXOR) Logic Gate Realized with Enzyme-Catalyzed Reactions: Optical and Electrochemical Signal Transduction. Chemphyschem 2019; 20:2082-2092. [PMID: 31233266 DOI: 10.1002/cphc.201900528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/19/2019] [Indexed: 11/06/2022]
Abstract
The studied enzyme-based biocatalytic system mimics NXOR Boolean logic gate, which is a logical operator that corresponds to equality in Boolean algebra. It gives the functional value true (1) if both functional arguments (input signals) have the same logical value (0,0 or 1,1), and false (0) if they are different (0,1 or 1,0). The output signal producing reaction is catalyzed by pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH), which is inhibited at acidic and basic pH values. Two other reactions catalyzed by esterase and urease produce acetic acid and ammonium hydroxide, respectively, shifting solution pH from the optimum pH for PQQ-GDH to acidic and basic values (1,0 and 0,1 input combinations, respectively), thus switching the enzyme activity off (output 0). When the input signals are not applied (0,0 combination) or both applied compensating each other (1,1 combination) the optimum pH is preserved, thus keeping PQQ-GDH running at the high rate (output 1). The biocatalytic cascade mimicking the NXOR gate was characterized optically and electrochemically. In the electrochemical experiments the PQQ-GDH enzyme communicated electronically with a conducting electrode support, thus resulting in the electrocatalytic current when signal combinations 0,0 and 1,1 were applied. The logic gate operation, when it was realized electrochemically, was also extended to the biomolecular release controlled by the gate. The release system included two electrodes, one performing the NXOR gate and another one activated for the release upon electrochemically stimulated alginate hydrogel dissolution. The studied system represents a general approach to the biocatalytic realization of the NXOR logic gate, which can be included in different catalytic cascades mimicking operation of concatenated gates in sophisticated logic circuitries.
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Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699 (USA)
| | - Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699 (USA)
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699 (USA)
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22
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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23
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He X, Xiong LH, Zhao Z, Wang Z, Luo L, Lam JWY, Kwok RTK, Tang BZ. AIE-based theranostic systems for detection and killing of pathogens. Theranostics 2019; 9:3223-3248. [PMID: 31244951 PMCID: PMC6567968 DOI: 10.7150/thno.31844] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
Pathogenic bacteria, fungi and viruses pose serious threats to the human health under appropriate conditions. There are many rapid and sensitive approaches have been developed for identification and quantification of specific pathogens, but many challenges still exist. Culture/colony counting and polymerase chain reaction are the classical methods used for pathogen detection, but their operations are time-consuming and laborious. On the other hand, the emergence and rapid spread of multidrug-resistant pathogens is another global threat. It is thus of utmost urgency to develop new therapeutic agents or strategies. Luminogens with aggregation-induced emission (AIEgens) and their derived supramolecular systems with unique optical properties have been developed as fluorescent probes for turn-on sensing of pathogens with high sensitivity and specificity. In addition, AIE-based supramolecular nanostructures exhibit excellent photodynamic inactivation (PDI) activity in aggregate, offering great potential for not only light-up diagnosis of pathogen, but also image-guided PDI therapy for pathogenic infection.
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Affiliation(s)
- Xuewen He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Ling-Hong Xiong
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Zheng Zhao
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Zaiyu Wang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Liang Luo
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jacky Wing Yip Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Ryan Tsz Kin Kwok
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong
- HKUST-Shenzhen Research Institute, Shenzhen 518057, China
- NSFC Center for Luminescence from Molecular Aggregates, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
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24
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Tang W, Zhong W, Fan J, Tan Y, Huang Q, Liu Y. Addressable activated cascade DNA sequential logic circuit model for processing identical input molecules. Chem Commun (Camb) 2019; 55:6381-6384. [DOI: 10.1039/c9cc02632k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 3-bit register sequential logic circuit, constructed based on a state and activation mechanism, has a sequential storage function.
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Affiliation(s)
- Weiyang Tang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Jin Fan
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Yun Tan
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Qichen Huang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
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25
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Wang H, Zheng J, Sun Y, Li T. Cellular environment-responsive intelligent DNA logic circuits for controllable molecular sensing. Biosens Bioelectron 2018; 117:729-735. [DOI: 10.1016/j.bios.2018.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/12/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022]
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26
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Xiong LH, He X, Zhao Z, Kwok RTK, Xiong Y, Gao PF, Yang F, Huang Y, Sung HHY, Williams ID, Lam JWY, Cheng J, Zhang R, Tang BZ. Ultrasensitive Virion Immunoassay Platform with Dual-Modality Based on a Multifunctional Aggregation-Induced Emission Luminogen. ACS NANO 2018; 12:9549-9557. [PMID: 30148962 DOI: 10.1021/acsnano.8b05270] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sensitive and accurate detection of highly contagious virus is urgently demanded for disease diagnosis and treatment. Herein, based on a multifunctional aggregation-induced emission luminogen (AIEgen), a dual-modality readout immunoassay platform for ultrasensitive detection of viruses has been successfully demonstrated. The platform is relied on virions immuno-bridged enzymatic hydrolysis of AIEgen, accompanying with the in situ formation of highly emissive AIE aggregates and shelling of silver on gold nanoparticles. As a result, robust turn-on fluorescence and naked-eye discernible plasmonic colorimetry composed dual-signal is achieved. By further taking advantage of effective immunomagnetic enrichment, EV71 virions, as an example, can be specifically detected with a limit of detection down to 1.4 copies/μL under fluorescence modality. Additionally, semiquantitative discerning of EV71 virions is realized in a broad range from 1.3 × 103 to 2.5 × 106 copies/μL with the naked eye. Most importantly, EV71 virions in 24 real clinical samples are successfully diagnosed with 100% accuracy. Comparing to the gold standard polymerase chain reaction (PCR) assay, our immunoassay platform do not need complicated sample pretreatment and expensive instruments. This dual-modality strategy builds a good capability for both colorimetry based convenient preliminary screening and fluorescence based accurate diagnosis of suspect infections in virus-stricken areas.
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Affiliation(s)
- Ling-Hong Xiong
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- Shenzhen Center for Disease Control and Prevention , Shenzhen 518055 , China
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
| | - Xuewen He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
| | - Zheng Zhao
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
| | - Ryan T K Kwok
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
| | - Yu Xiong
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
| | - Peng Fei Gao
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
| | - Fan Yang
- Shenzhen Center for Disease Control and Prevention , Shenzhen 518055 , China
| | - Yalan Huang
- Shenzhen Center for Disease Control and Prevention , Shenzhen 518055 , China
| | - Herman H-Y Sung
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
| | - Ian D Williams
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
| | - Jinquan Cheng
- Shenzhen Center for Disease Control and Prevention , Shenzhen 518055 , China
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention , Shenzhen 518055 , China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration and Reconstruction, Institute for Advanced Study and Division of Life Science , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon 00852, Hong Kong
- HKUST-Shenzhen Research Institute , Shenzhen 518057 , China
- NSFC Center for Luminescence from Molecular Aggregates, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Devices , South China University of Technology , Guangzhou 510640 , China
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27
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Tregubov AA, Nikitin PI, Nikitin MP. Advanced Smart Nanomaterials with Integrated Logic-Gating and Biocomputing: Dawn of Theranostic Nanorobots. Chem Rev 2018; 118:10294-10348. [DOI: 10.1021/acs.chemrev.8b00198] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Andrey A. Tregubov
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
| | - Petr I. Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, Moscow 119991, Russia
| | - Maxim P. Nikitin
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
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28
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Zhang J, Lu Y. Biocomputing for Portable, Resettable, and Quantitative Point-of-Care Diagnostics: Making the Glucose Meter a Logic-Gate Responsive Device for Measuring Many Clinically Relevant Targets. Angew Chem Int Ed Engl 2018; 57:9702-9706. [PMID: 29893502 PMCID: PMC6261302 DOI: 10.1002/anie.201804292] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/30/2018] [Indexed: 12/19/2022]
Abstract
It is recognized that biocomputing can provide intelligent solutions to complex biosensing projects. However, it remains challenging to transform biomolecular logic gates into convenient, portable, resettable and quantitative sensing systems for point-of-care (POC) diagnostics in a low-resource setting. To overcome these limitations, the first design of biocomputing on personal glucose meters (PGMs) is reported, which utilizes glucose and the reduced form of nicotinamide adenine dinucleotide as signal outputs, DNAzymes and protein enzymes as building blocks, and demonstrates a general platform for installing logic-gate responses (YES, NOT, INHIBIT, NOR, NAND, and OR) to a variety of biological species, such as cations (Na+ ), anions (citrate), organic metabolites (adenosine diphosphate and adenosine triphosphate) and enzymes (pyruvate kinase, alkaline phosphatase, and alcohol dehydrogenases). A concatenated logical gate platform that is resettable is also demonstrated. The system is highly modular and can be generally applied to POC diagnostics of many diseases, such as hyponatremia, hypernatremia, and hemolytic anemia. In addition to broadening the clinical applications of the PGM, the method reported opens a new avenue in biomolecular logic gates for the development of intelligent POC devices for on-site applications.
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Affiliation(s)
- Jingjing Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801 (USA),
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801 (USA),
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29
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Wang G, Li Z, Ma N. Next-Generation DNA-Functionalized Quantum Dots as Biological Sensors. ACS Chem Biol 2018; 13:1705-1713. [PMID: 29257662 DOI: 10.1021/acschembio.7b00887] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-functionalized quantum dots (DNA-QDs) have found considerable application in biosensing and bioimaging. Different from the first generation (I-G) DNA-QDs prepared via conventional bioconjugation chemistry, the second generation (II-G) DNA-QDs prepared via one-step DNA-templated QD synthesis features a defined number of DNA valencies (usually monovalency), which is preferable for controlled assembly and biological targeting. In this review, we summarize recent progress in designing QD probes based on II-G DNA-QDs for advanced sensing and imaging applications. It opens up new avenues for highly sensitive and intelligent sensing of a range of disease-relevant biomolecules in vitro and in living cells.
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Affiliation(s)
- Ganglin Wang
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People’s Republic of China
| | - Zhi Li
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People’s Republic of China
| | - Nan Ma
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People’s Republic of China
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30
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Peveler WJ, Algar WR. More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing. ACS Chem Biol 2018; 13:1752-1766. [PMID: 29461796 DOI: 10.1021/acschembio.7b01022] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.
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Affiliation(s)
- William J. Peveler
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - W. Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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31
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Zhang Q, Xie S, Yang Y, Wu Y, Wang X, Wu J, Zhang L, Chen J, Wang Y. A Facile Synthesis of Highly Nitrogen-Doped Carbon Dots for Imaging and Detection in Biological Samples. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:7890937. [PMID: 30116649 PMCID: PMC6079530 DOI: 10.1155/2018/7890937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/17/2018] [Indexed: 05/24/2023]
Abstract
A facile, green, and high-output hydrothermal synthesis was proposed for the fabrication of highly fluorescent nitrogen-doped carbon quantum dots (N-doped CDs). The nitrogen content in N-doped CDs reached 19.2% and demonstrated strong blue fluorescence emission was obtained with fluorescence quantum yield (QY) of up to 32.9%, which exhibit high fluorescence quantum yield, high photostability, and excellent biocompatibility. The N-doped CDs possess high photostability, low toxicity, and excellent biocompatibility, based on which the N-doped CDs were successfully applied as a fluorescence probe for cell imaging. Moreover, it was then successfully demonstrated for sensitive and selective detection of Fe3+ in serum.
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Affiliation(s)
- Qianchun Zhang
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Siqi Xie
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Yanqun Yang
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Yun Wu
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Xingyi Wang
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Jincheng Wu
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Li Zhang
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Junyu Chen
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Yuan Wang
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
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32
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Zhang J, Lu Y. Biocomputing for Portable, Resettable, and Quantitative Point-of-Care Diagnostics: Making the Glucose Meter a Logic-Gate Responsive Device for Measuring Many Clinically Relevant Targets. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jingjing Zhang
- Department of Chemistry, Beckman Institute for Advanced Science and Technology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Yi Lu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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33
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Shen J, Tang Q, Li L, Li J, Zuo X, Qu X, Pei H, Wang L, Fan C. Valence-Engineering of Quantum Dots Using Programmable DNA Scaffolds. Angew Chem Int Ed Engl 2017; 56:16077-16081. [DOI: 10.1002/anie.201710309] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/17/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Jianlei Shen
- Institute of Molecular Medicine; Renji Hospital; School of Medicine and School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; Shanghai 200127 China
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Qian Tang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Jiang Li
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine; Renji Hospital; School of Medicine and School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; Shanghai 200127 China
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
- School of Life Science and Technology; ShanghaiTech University; Shanghai 201210 China
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34
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Shen J, Tang Q, Li L, Li J, Zuo X, Qu X, Pei H, Wang L, Fan C. Valence-Engineering of Quantum Dots Using Programmable DNA Scaffolds. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jianlei Shen
- Institute of Molecular Medicine; Renji Hospital; School of Medicine and School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; Shanghai 200127 China
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Qian Tang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Jiang Li
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine; Renji Hospital; School of Medicine and School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; Shanghai 200127 China
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; Shanghai 200241 China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
- School of Life Science and Technology; ShanghaiTech University; Shanghai 201210 China
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35
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Gao J, Liu Y, Lin X, Deng J, Yin J, Wang S. Implementation of cascade logic gates and majority logic gate on a simple and universal molecular platform. Sci Rep 2017; 7:14014. [PMID: 29070871 PMCID: PMC5656625 DOI: 10.1038/s41598-017-14416-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 10/11/2017] [Indexed: 12/18/2022] Open
Abstract
Wiring a series of simple logic gates to process complex data is significantly important and a large challenge for untraditional molecular computing systems. The programmable property of DNA endows its powerful application in molecular computing. In our investigation, it was found that DNA exhibits excellent peroxidase-like activity in a colorimetric system of TMB/H2O2/Hemin (TMB, 3,3′, 5,5′-Tetramethylbenzidine) in the presence of K+ and Cu2+, which is significantly inhibited by the addition of an antioxidant. According to the modulated catalytic activity of this DNA-based catalyst, three cascade logic gates including AND-OR-INH (INHIBIT), AND-INH and OR-INH were successfully constructed. Interestingly, by only modulating the concentration of Cu2+, a majority logic gate with a single-vote veto function was realized following the same threshold value as that of the cascade logic gates. The strategy is quite straightforward and versatile and provides an instructive method for constructing multiple logic gates on a simple platform to implement complex molecular computing.
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Affiliation(s)
- Jinting Gao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Yaqing Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China.
| | - Xiaodong Lin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Jiankang Deng
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Jinjin Yin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China.
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36
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Zhang L, Jean SR, Ahmed S, Aldridge PM, Li X, Fan F, Sargent EH, Kelley SO. Multifunctional quantum dot DNA hydrogels. Nat Commun 2017; 8:381. [PMID: 28851869 PMCID: PMC5575008 DOI: 10.1038/s41467-017-00298-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/19/2017] [Indexed: 02/02/2023] Open
Abstract
Biotemplated nanomaterials offer versatile functionality for multimodal imaging, biosensing, and drug delivery. There remains an unmet need for traceable and biocompatible nanomaterials that can be synthesized in a precisely controllable manner. Here, we report self-assembled quantum dot DNA hydrogels that exhibit both size and spectral tunability. We successfully incorporate DNA-templated quantum dots with high quantum yield, long-term photostability, and low cytotoxicity into a hydrogel network in a single step. By leveraging DNA-guided interactions, we introduce multifunctionality for a variety of applications, including enzyme-responsive drug delivery and cell-specific targeting. We report that quantum dot DNA hydrogels can be used for delivery of doxorubicin, an anticancer drug, to increase potency 9-fold against cancer cells. This approach also demonstrated high biocompatibility, trackability, and in vivo therapeutic efficacy in mice bearing xenografted breast cancer tumors. This work paves the way for the development of new tunable biotemplated nanomaterials with multiple synergistic functionalities for biomedical applications. The development of nanomaterials for imaging and drug delivery has been of great interest to the field. Here, the authors synthesized multifunctional enzyme-responsive hydrogels with self-assembling quantum dots for nucleic acid and drug delivery as well as having imaging capability.
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Affiliation(s)
- Libing Zhang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada, M5S 3M2
| | - Sae Rin Jean
- Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, Ontario, Canada, M5S 3H6
| | - Sharif Ahmed
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada, M5S 3M2
| | - Peter M Aldridge
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G9
| | - Xiyan Li
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G4
| | - Fengjia Fan
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G4
| | - Edward H Sargent
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G4.
| | - Shana O Kelley
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada, M5S 3M2. .,Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, Ontario, Canada, M5S 3H6. .,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3G9. .,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada, M5S 1A8.
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37
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Massey M, Medintz IL, Ancona MG, Algar WR. Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR. ACS Sens 2017; 2:1205-1214. [PMID: 28787151 DOI: 10.1021/acssensors.7b00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.
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Affiliation(s)
- Melissa Massey
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | | | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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38
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Fan D, Wang E, Dong S. A DNA-based parity generator/checker for error detection through data transmission with visual readout and an output-correction function. Chem Sci 2017; 8:1888-1895. [PMID: 28553479 PMCID: PMC5424811 DOI: 10.1039/c6sc04056j] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/26/2016] [Indexed: 12/19/2022] Open
Abstract
During any type of binary data transmission, the occurrence of bit errors is an inevitable and frequent problem suffered. These errors, which have fatal effects on the correct logic computation, especially in sophisticated logic circuits, can be checked through insertion of a parity generator (pG) at the transmitting end and a parity checker (pC) at the receiving end. Herein, taking even pG/pC as a model device, we constructed the first DNA-based molecular parity generator/checker (pG/pC) for error detection through data transmission, on a universal single-strand platform according to solely DNA hybridization. Compared with previous pG/pC systems, the distinct advantage of this one is that it can present not only fluorescence signals but also visual outputs, which can be directly recognized by the naked eye, using DNA inputs modulated split-G-quadruplex and its DNAzyme as signal reporters, thus greatly extending its potential practical applications. More importantly, an "Output-Correction" function was introduced into the pC for the first time, in which all of the erroneous outputs can be adequately corrected to their normal states, guaranteeing the regular operation of subsequent logic devices. Furthermore, through negative logic conversion towards the constructed even pG/pC, the odd pG/pC with equal functions was obtained. Furthermore, this system can also execute multi-input triggered concatenated logic computations with dual output-modes, which largely fulfilled the requirements of complicated computing.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin , 130022 China .
- University of Chinese Academy of Sciences , Beijing , 100039 China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin , 130022 China .
- University of Chinese Academy of Sciences , Beijing , 100039 China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin , 130022 China .
- University of Chinese Academy of Sciences , Beijing , 100039 China
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39
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Fan D, Zhu X, Dong S, Wang E. Tyramine Hydrochloride Based Label-Free System for Operating Various DNA Logic Gates and a DNA Caliper for Base Number Measurements. Chemphyschem 2017; 18:1767-1772. [DOI: 10.1002/cphc.201601291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Indexed: 01/13/2023]
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 P.R. China
| | - Xiaoqing 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 P.R. China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 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
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
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40
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Fan D, Wang E, Dong S. Exploiting Polydopamine Nanospheres to DNA Computing: A Simple, Enzyme-Free and G-Quadruplex-Free DNA Parity Generator/Checker for Error Detection during Data Transmission. ACS APPLIED MATERIALS & INTERFACES 2017; 9:1322-1330. [PMID: 27990820 DOI: 10.1021/acsami.6b14317] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular logic devices with various functions play an indispensable role in molecular data transmission/processing. However, during any kinds of data transmission, a constant and unavoidable circumstance is the appearance of bit errors, which have serious effects on the regular logic computation. Fortunately, these errors can be detected via plugging a parity generator (pG) at the transmitting terminal and a parity checker (pC) at the receiving terminal. Herein, taking advantage of the efficient adsorption/quenching ability of polydopamine nanospheres toward fluorophore-labeled single-stranded DNA, we explored this biocompatible nanomaterial to DNA logic computation and constructed the first simple, enzyme-free, and G-quadruplex-free DNA pG/pC for error detection through data transmission. Besides, graphene oxide (GO) was innovatively introduced as the "corrective element" to perform the output-correction function of pC. All the erroneous outputs were corrected to normal conditions completely, ensuring the regular operation of later logic computing. The total operation of this non-G4 pG/pC system (error checking/output-correction) could be completed within 1 h (about 1/3 of previous G4 platform) in a simpler and more efficient way. Notably, the odd pG/pC with analogous functions was also achieved through negative logic conversion to the fabricated even one. Furthermore, the same system could also perform three-input concatenated logic computation (XOR-INHIBIT), enriching the complexity of PDs-based logic computation.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
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41
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Li Z, He X, Luo X, Wang L, Ma N. DNA-Programmed Quantum Dot Polymerization for Ultrasensitive Molecular Imaging of Cancer Cells. Anal Chem 2016; 88:9355-9358. [PMID: 27649276 DOI: 10.1021/acs.analchem.6b02864] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inorganic nanocrystals, such as quantum dots (QDs), hold great promise as molecular imaging contrast agents because of their superior optical properties. However, the molecular imaging sensitivity of these probes is far from optimized due to the lack of efficient and general method for molecular engineering of nanocrystal into effective bioprobes for signal-amplified imaging. Herein, we develop a strategy to boost the molecular imaging sensitivity of QDs over the limit by copolymerizing QDs and cell-binding aptamers into linear QD-aptamer polymers (QAPs) through DNA-programmed hybridization chain reaction. We show that the cancer cells treated with QAPs exhibit much stronger photoluminescence (PL) signal than those treated with QD-aptamer monomers (QAMs) because of multivalent binding and multi-QD-based signal amplification. The enhanced cell binding and imaging capacity of QAPs significantly improves imaging-based discrimination between different cancer cell types. This approach adds a new dimension for engineering inorganic nanoparticles into effective bioprobes for biomedical applications.
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Affiliation(s)
- Zhi Li
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou, 215123, P. R. China
| | - Xuewen He
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou, 215123, P. R. China
| | - Xucheng Luo
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou, 215123, P. R. China
| | - Li Wang
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou, 215123, P. R. China
| | - Nan Ma
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou, 215123, P. R. China
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42
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Ge L, Wang W, Sun X, Hou T, Li F. Versatile and Programmable DNA Logic Gates on Universal and Label-Free Homogeneous Electrochemical Platform. Anal Chem 2016; 88:9691-9698. [DOI: 10.1021/acs.analchem.6b02584] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Lei Ge
- College of Chemistry
and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People’s Republic of China
| | - Wenxiao Wang
- College of Chemistry
and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People’s Republic of China
| | - Ximei Sun
- College of Chemistry
and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People’s Republic of China
| | - Ting Hou
- College of Chemistry
and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People’s Republic of China
| | - Feng Li
- College of Chemistry
and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People’s Republic of China
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43
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Xiao Z, Zhu H, Xin A, Li Y, Ling L. Triplex DNA logic gate based upon switching on/off their structure by Ag(+)/cysteine. Analyst 2016; 140:7322-6. [PMID: 26359516 DOI: 10.1039/c5an01371b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The formation of intramolecular triplex DNA can be regulated by Ag(+) and Cys (cysteine), which switch off/on the fluorescence of the oligonucleotides, 5'-TAMRA-TTC TCT TCC TCT TCC TTC TGA CGA CAG TTG ACT CTT CCT TCT CCT TCT CTT-BHQ-2-3' (Oligo 1) and 3'-GAA GGA AGA GGA AGA GAA-5' (Oligo 2). Based on this principle, sensors for Ag(+) and Cys are developed. The sensor for Ag(+) has a linear range of 2.5 nM-40 nM and a detection limit of 1.8 nM, whereas the sensor for Cys has a linear range of 10.0 nM-120.0 nM and a detection limit of 8.2 nM. Furthermore, the fluorescence is reversible with the alternate addition of Ag(+) and Cys. We constructed a DNA logic gate using Ag(+) and Cys as the input, and the fluorescence intensity as the output. The DNA logic gate is simple; moreover, it has a fast response and good reversibility.
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Affiliation(s)
- Zhiyou Xiao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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44
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Fratto BE, Lewer JM, Katz E. An Enzyme-Based Half-Adder and Half-Subtractor with a Modular Design. Chemphyschem 2016; 17:2210-7. [PMID: 27037520 DOI: 10.1002/cphc.201600173] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 01/01/2023]
Abstract
A half-adder and a half-subtractor have been realized using enzymatic reaction cascades performed in a flow cell device. The individual cells were modified with different enzymes and assembled in complex networks to perform logic operations and arithmetic functions. The modular design of the logic devices allowed for easy re-configuration, enabling them to perform various functions. The final output signals, represented by redox species [Fe(CN)6 ](3-/4-) or NADH/NAD(+) , were analyzed optically to derive the calculation results. These output signals might be applicable in the future for actuation processes, for example, substance release activated by logically processed signals.
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Affiliation(s)
- Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Jessica M Lewer
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699, USA.
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45
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The Effect of Basepair Mismatch on DNA Strand Displacement. Biophys J 2016. [PMID: 27074674 DOI: 10.1016/j.bpj.2016.02.027.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality.
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46
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Broadwater DWB, Kim HD. The Effect of Basepair Mismatch on DNA Strand Displacement. Biophys J 2016; 110:1476-1484. [PMID: 27074674 PMCID: PMC4833772 DOI: 10.1016/j.bpj.2016.02.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 02/02/2016] [Accepted: 02/09/2016] [Indexed: 01/31/2023] Open
Abstract
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality.
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Affiliation(s)
- D W Bo Broadwater
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
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47
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Label-free DNA Y junction for bisphenol A monitoring using exonuclease III-based signal protection strategy. Biosens Bioelectron 2016; 77:277-83. [DOI: 10.1016/j.bios.2015.09.042] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/20/2022]
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48
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Yang G, Zhang Y, Xia H, Zou G, Zhang Q. Multiconfigurable logic gate operation in 1D polydiacetylene microtube waveguide. RSC Adv 2016. [DOI: 10.1039/c6ra07564a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Reversible electrical modulation of waveguiding in a 1D viologen-modified PDA microtube based on fluorescence resonance energy transfer. By applying a voltage, the emission at the tip of the VFPDA microtube was decreased (−1.5 V), or was returned to original values (1.5 V).
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Affiliation(s)
- Guang Yang
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- Key Laboratory of Optoelectronic Science and Technology in Anhui Province
- University of Science and Technology of China
- Hefei
| | - Yan Zhang
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- Key Laboratory of Optoelectronic Science and Technology in Anhui Province
- University of Science and Technology of China
- Hefei
| | - Hongyan Xia
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- Key Laboratory of Optoelectronic Science and Technology in Anhui Province
- University of Science and Technology of China
- Hefei
| | - Gang Zou
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- Key Laboratory of Optoelectronic Science and Technology in Anhui Province
- University of Science and Technology of China
- Hefei
| | - Qijin Zhang
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- Key Laboratory of Optoelectronic Science and Technology in Anhui Province
- University of Science and Technology of China
- Hefei
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49
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He X, Zeng T, Li Z, Wang G, Ma N. Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA-Programmed Nanoparticle Disassembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509726] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xuewen He
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Tao Zeng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Zhi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Ganglin Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Nan Ma
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
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50
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He X, Zeng T, Li Z, Wang G, Ma N. Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA-Programmed Nanoparticle Disassembly. Angew Chem Int Ed Engl 2015; 55:3073-6. [PMID: 26694689 DOI: 10.1002/anie.201509726] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 11/26/2015] [Indexed: 12/19/2022]
Abstract
Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low-abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal-to-background ratio of conventional molecular imaging probes. Herein, we report a class of DNA-templated gold nanoparticle (GNP)-quantum dot (QD) assembly-based probes for catalytic imaging of cancer-related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA-programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non-catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells.
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Affiliation(s)
- Xuewen He
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Tao Zeng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Zhi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Ganglin Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Nan Ma
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China.
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