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Crego-Vicente B, del Olmo MD, Muro A, Fernández-Soto P. Multiplexing LAMP Assays: A Methodological Review and Diagnostic Application. Int J Mol Sci 2024; 25:6374. [PMID: 38928080 PMCID: PMC11203869 DOI: 10.3390/ijms25126374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/27/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The loop-mediated isothermal amplification (LAMP) technique is a great alternative to PCR-based methods, as it is fast, easy to use and works with high sensitivity and specificity without the need for expensive instruments. However, one of the limitations of LAMP is difficulty in achieving the simultaneous detection of several targets in a single tube, as the methodologies that allow this rely on fluorogenic probes containing specific target sequences, complicating their adaptation and the optimization of assays. Here, we summarize different methods for the development of multiplex LAMP assays based on sequence-specific detection, illustrated with a schematic representation of the technique, and evaluate their practical application based on the real-time detection and quantification of results, the possibility to visualize the results at a glance, the prior stabilization of reaction components, promoting the point-of-care use, the maximum number of specific targets amplified, and the validation of the technique in clinical samples. The various LAMP multiplexing methodologies differ in their operating conditions and mechanism. Each methodology has its advantages and disadvantages, and the choice among them will depend on specific application interests.
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Affiliation(s)
| | | | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (M.D.d.O.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (M.D.d.O.)
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2
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Jia YL, Li XQ, Wang ZX, Gao H, Chen HY, Xu JJ. Logic Signal Amplification System for Sensitive Electrochemiluminescence Detection and Subtype Identification of Cancer Cells. Anal Chem 2024; 96:7172-7178. [PMID: 38650072 DOI: 10.1021/acs.analchem.4c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Achieving sensitive detection and accurate identification of cancer cells is vital for diagnosing and treating the disease. Here, we developed a logic signal amplification system using DNA tetrahedron-mediated three-dimensional (3D) DNA nanonetworks for sensitive electrochemiluminescence (ECL) detection and subtype identification of cancer cells. Specially designed hairpins were integrated into DNA tetrahedral nanostructures (DTNs) to perform a catalytic hairpin assembly (CHA) reaction in the presence of target microRNA, forming hyperbranched 3D nanonetworks. Benefiting from the "spatial confinement effect," the DNA tetrahedron-mediated catalytic hairpin assembly (DTCHA) reaction displayed significantly faster kinetics and greater cycle conversion efficiency than traditional CHA. The resulting 3D nanonetworks could load a large amount of Ru(phen)32+, significantly enhancing its ECL signal, and exhibit detection limits for both miR-21 and miR-141 at the femtomolar level. The biosensor based on modular logic gates facilitated the distinction and quantification of cancer cells and normal cells based on miR-21 levels, combined with miR-141 levels, to further identify different subtypes of breast cancer cells. Overall, this study provides potential applications in miRNA-related clinical diagnostics.
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Affiliation(s)
- Yi-Lei Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhong-Xia Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Hang Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Liu Y, Tang Y, Bao Y, Cai K, Lu B, Zhao R, Yu C, Du Y, Li B. Iso-E-Codelock: A Rebuilding-free Electrochemical Chip with a Customizable Decoding Probe for Real-Time and Portable Pathogen Diagnostics. Angew Chem Int Ed Engl 2024; 63:e202400340. [PMID: 38497899 DOI: 10.1002/anie.202400340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/19/2024]
Abstract
In order to realize portable pathogen diagnostics with easier quantitation, digitization and integration, we develop a ready-to-use electrochemical sensing strategy (Iso-E-Codelock) for real-time detection of isothermal nucleic acid amplification. Bridged by a branched DNA as codelock, the isothermal amplicon is transduced into increased current of an electrochemical probe, holding multiple advantages of high sensitivity, high selectivity, signal-on response, "zero" background and one-pot operation. Through a self-designed portable instrument (BioAlex PHE-T), the detection can be implemented on a multichannel microchip and output real-time amplification curves just like an expensive commercial PCR machine. The microchip is a rebuilding-free and disposable component. The branch codelock probe can be customized for different targets and designs. Such high performance and flexibility have been demonstrated utilizing four virus (SARS-CoV-2, African swine fever, FluA and FluB) genes as targets, and two branch (3-way and 4-way) DNAs as codelock probes.
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Affiliation(s)
- Yichen Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yidan Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yin Bao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Kaiwei Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Rujian Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Chunxu Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
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4
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Bai D, Zhang J, Zhang Y, Yu H, Zhang L, Han X, Lv K, Wang L, Luo W, Wu Y, Zhou X, Wang W, Feng T, Xie G. A Spatially Controlled Proximity Split Tweezer Switch for Enhanced DNA Circuit Construction and Multifunctional Transduction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307421. [PMID: 38072808 DOI: 10.1002/smll.202307421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/15/2023] [Indexed: 05/03/2024]
Abstract
DNA strand displacement reactions are vital for constructing intricate nucleic acid circuits, owing to their programmability and predictability. However, the scarcity of effective methods for eliminating circuit leakages has hampered the construction of circuits with increased complexity. Herein, a versatile strategy is developed that relies on a spatially controlled proximity split tweezer (PST) switch to transduce the biomolecular signals into the independent oligonucleotides. Leveraging the double-stranded rigidity of the tweezer works synergistically with the hindering effect of the hairpin lock, effectively minimizing circuit leakage compared with sequence-level methods. In addition, the freely designed output strand is independent of the target binding sequence, allowing the PST switch conformation to be modulated by nucleic acids, small molecules, and proteins, exhibiting remarkable adaptability to a wide range of targets. Using this platform, established logical operations between different types of targets for multifunctional transduction are successfully established. Most importantly, the platform can be directly coupled with DNA catalytic circuits to further enhance transduction performance. The uniqueness of this platform lies in its design straightforwardness, flexibility, scalable intricacy, and system compatibility. These attributes pave a broad path toward nucleic acid-based development of sophisticated transduction networks, making them widely applied in basic science research and biomedical applications.
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Affiliation(s)
- Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Jianhong Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Yaoyi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Li Zhang
- Department of Forensic, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Ke Lv
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 40016, P. R. China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - You Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Xi Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Tong Feng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
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5
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Han X, Yu H, Zhang L, Weng Z, Dai L, Wang L, Song L, Wang Z, Zhao R, Wang L, Wang W, Bai D, Guo Y, Lv K, Xie G. Movable toehold for leakless self-assembly circuits. Biosens Bioelectron 2024; 245:115823. [PMID: 37979548 DOI: 10.1016/j.bios.2023.115823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/20/2023]
Abstract
Nonenzymatic self-assembly circuit utilizing hairpin substrates has been developed to be a powerful tool for information transduction, amplification and computation. However, the sensitivity, stability and application of this circuit are impeded by the presence of leakage which refers to undesired triggering in the absence of input. Herein, we proposed a movable toehold principle to suppress leakage and accelerate the catalytic reaction through removing partial hairpin toehold responsible for the leakage and transferring it to the catalyst. With movable toehold, catalytic hairpin assembly (called mtCHA) exhibited an excellent signal-to-background ratio of over 100, high robustness and improved specificity. In more complex circuit, including proximity recognition, signal amplification of small molecules (such as ATP), logic network, autocatalysis circuit and two-layer cascade circuit, mtCHA also demonstrated satisfactory performance. Our findings suggest that mtCHA holds great potential for broader applications, and the approach of repurposing harmful fragments into beneficial candidates can provide valuable insights for other chemical systems.
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Affiliation(s)
- Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ling Dai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, LuZhou Key Laboratory of Nanobiosensing and Microfluidic Point-of-Care Testing, Luzhou 646000, PR China.
| | - Ke Lv
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
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6
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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Wei J, Yu M, Tan K, Shang J, He S, Xie C, Liu X, Wang F. Tailoring a Minimal Self-Replicate DNA Circuit for Highly Efficient Intracellular Imaging of microRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207961. [PMID: 36717281 DOI: 10.1002/smll.202207961] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Trace analyte detection in complex intracellular environment requires the development of simple yet robust self-sufficient molecular circuits with high signal-gain and anti-interference features. Herein, a minimal non-enzymatic self-replicate DNA circuitry (SDC) system is proposed with high-signal-gain for highly efficient biosensing in living cells. It is facilely engineered through the self-stacking of only one elementary cascade hybridization reaction (CHR), thus is encoding with more economic yet effective amplification pathways and reactants. Trigger (T) stimulates the activation of CHR for producing numerous T replica that reversely motivate new CHR reaction cycles, thus achieving the successive self-replication of CHR system with an exponentially magnified readout signal. The intrinsic self-replicate circuity design and the self-accelerated reaction format of SDC system is experimentally demonstrated and theoretically simulated. With simple circuitry configuration and low reactant complexity, the SDC amplifier enables the high-contrast and accurate visualization of microRNA (miRNA), ascribing to its robust molecular recognition and self-sufficient signal amplification, thus offering a promising strategy for monitoring these clinically significant analytes.
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Affiliation(s)
- Jie Wei
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, P. R. China
| | - Mengdi Yu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Kaiyue Tan
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jinhua Shang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Shizhen He
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chenxia Xie
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
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8
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Yu C, Zhou S, Zhao X, Tang Y, Wang L, Lu B, Meng F, Li B. Multiplex detection of clinical pathogen nucleic acids via a three-way junction structure-based nucleic acid circuit. Anal Bioanal Chem 2023; 415:2173-2183. [PMID: 36928726 PMCID: PMC10019429 DOI: 10.1007/s00216-023-04637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
Nucleic acid testing technology has made considerable progress in the last few years. However, there are still many challenges in the clinical application of multiple nucleic acid assays, such as how to ensure accurate results, increase speed and decrease cost. Herein, a three-way junction structure has been introduced to specifically translate analytes of loop-mediated isothermal amplification to a catalytic hairpin assembly. For different analyses, a well-optimized nucleic acid circuit can be directly applied to detection, through only one-component replacement, which only not avoids duplicate sequence design but also saves detection cost. Thanks to this design, multiple and logical analysis can be easily realized in a single reaction with ultra-high sensitivity and selectivity. In this paper, Mycoplasma pneumoniae and Streptococcus pneumoniae can be clearly distinguished from the clinical mixed sample with negative control or one analyte in one tube single fluorescence channel. The fair experimental results of actual clinical samples provide a strong support for the possibility of clinical application of this methodology.
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Affiliation(s)
- Chunxu Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, Jilin, China.,University of Science and Technology China, Hefei, 230026, Anhui, China
| | - Siyan Zhou
- Department of Paediatrics, The First Hospital of Jilin University, Changchun, 130021, China
| | - Xin Zhao
- Department of Paediatrics, The First Hospital of Jilin University, Changchun, 130021, China
| | - Yidan Tang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, Jilin, China
| | - Lina Wang
- Department of Paediatrics, The First Hospital of Jilin University, Changchun, 130021, China
| | - Baiyang Lu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, Jilin, China.
| | - Fanzheng Meng
- Department of Paediatrics, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, Jilin, China. .,University of Science and Technology China, Hefei, 230026, Anhui, China.
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9
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Zhou XM, Zhuo Y, Yuan R, Chai YQ. Target-mediated self-assembly of DNA networks for sensitive detection and intracellular imaging of APE1 in living cells. Chem Sci 2023; 14:2318-2324. [PMID: 36873854 PMCID: PMC9977452 DOI: 10.1039/d2sc06968g] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
Herein, giant DNA networks were assembled from two kinds of functionalized tetrahedral DNA nanostructures (f-TDNs) for sensitive detection and intracellular imaging of apurinic/apyrimidinic endonuclease 1 (APE1) as well as gene therapy in tumor cells. Impressively, the reaction rate of the catalytic hairpin assembly (CHA) reaction on f-TDNs was much faster than that of the conventional free CHA reaction owing to the high local concentration of hairpins, spatial confinement effect and production of giant DNA networks, which significantly enhanced the fluorescence signal to achieve sensitive detection of APE1 with a limit of 3.34 × 10-8 U μL-1. More importantly, the aptamer Sgc8 assembled on f-TDNs could enhance the targeting activity of the DNA structure to tumor cells, allowing it to endocytose into cells without any transfection reagents, which could achieve selective imaging of intracellular APE1 in living cells. Meanwhile, the siRNA carried by f-TDN1 could be accurately released to promote tumor cell apoptosis in the presence of endogenous target APE1, realizing effective and precise tumor therapy. Benefiting from the high specificity and sensitivity, the developed DNA nanostructures provide an excellent nanoplatform for precise cancer diagnosis and therapy.
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Affiliation(s)
- Xue-Mei Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
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10
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Wang Y, Zhu Z, Yu C, Wu R, Zhu J, Li B. Lego-Like Catalytic Hairpin Assembly Enables Controllable DNA-Oligomer Formation and Spatiotemporal Amplification in Single Molecular Signaling. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206283. [PMID: 36436946 DOI: 10.1002/smll.202206283] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/14/2022] [Indexed: 06/16/2023]
Abstract
While the solid-state nanopore shows increasing potential during sensitive and label-free single molecular analysis, target concentration and signal amplification method is in urgent need. In this article, a solution via designing a model nucleic acid circuit reaction that can produce "Y" shape-structure three-way DNA oligomers with controllable size and polymerization degree is proposed. Such a so-called lego-like three-way catalytic hairpin assembly (LK-3W-CHA) can provide both concentration amplification (via CHA circuit) and programmable size control (via lego-like building mode) to enhance spatiotemporal resolution in single molecular sensing of solid-state nanopore. Oligomers containing 1-4 DNA three-way junctions (Y monomers, Y1-Y4) are designed in proof-of-concept experiments and applications. When the oligomers are applied to direct translocation measurements, Y2-Y4 can significantly increase the signal resolution and stability than that of Y1. Meanwhile, Y1 to Y4 can be used as the tags on the long DNA carrier to provide very legible secondary signals for specific identification, multiple assays, and information storage. Compared with other possible tags, Y1-Y4 provides higher signal density and amplitude, and quasi-linear "inner reference" for each other, which may provide more systematic, reliable, and controllable experimental results.
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Affiliation(s)
- Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhentong Zhu
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Chunmiao Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jinbo Zhu
- Cavendish Lab, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
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11
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Li L, Fang X, Le J, Zheng Y, Tan X, Jiang Z, Li H, Xu J, Xu H. Highly sensitive detection and intracellular imaging of MicroRNAs based on target-triggered cascade catalytic hairpin assembly. Talanta 2022; 250:123753. [DOI: 10.1016/j.talanta.2022.123753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 11/30/2022]
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12
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Tan K, Zhang Q, Wang Q, Gong X, Yu S, Li R, Liu X, Wang F. Functional Zeolitic Imidazolate Framework for Robust l-Deoxyribozyme-Based Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204858. [PMID: 36216588 DOI: 10.1002/smll.202204858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Programmable chiral biocatalysis represents a promising therapeutic strategy for its high stereospecific control over various biotransformations (e.g., chiral Aβ isomerization) of living entities yet is rarely explored. With an extraordinary resistance to nuclease digestion, the non-natural left-handed deoxyribozyme (l-DNAzyme) therapy is constrained by inefficient delivery/release and insufficient cofactors supply. Herein, an efficient adenosine triphosphate (ATP)-stimulated disassembly of l-histidine (l-His)-integrated ZIF-8 (l-His-ZIF-8) is reported for sustaining the l-DNAzyme-amplified photodynamic therapy. This self-sufficient l-therapeutic platform can intelligently release the l-DNAzyme probe and simultaneously supply l-His DNAzyme cofactors via endogenous ATP. Then, the intrinsic microRNA-21 catalyzes the generation of robust l-DNAzyme via the catalytic hybridization reaction for activating the photosensitizer with multiplied guaranteed therapeutic operation. This l-therapeutic strategy opens up great prospects for more precise diagnosis and customized gene silencing-based therapy.
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Affiliation(s)
- Kaiyue Tan
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Qingqing Zhang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Qing Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xue Gong
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Shanshan Yu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Ruomeng Li
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430072, China
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13
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Li H, Lu H, Tang Y, Wang H, Xiao Y, Li B. A Rebuilding‐Free Nucleic Acid Detection Strategy Enables Ultrasensitive Genotyping, N‐in‐1 Logic Screening and Accurate Multiplex Assay of Dangerous Pathogens. Angew Chem Int Ed Engl 2022; 61:e202209496. [DOI: 10.1002/anie.202209496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Huan Li
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin, 130022 China
- University of Science and Technology of China Hefei Anhui 230026 China
| | - Huiying Lu
- School of Life Sciences Northeast Normal University Changchun Jilin, 130024 China
| | - Yidan Tang
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin, 130022 China
| | - Huaning Wang
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin, 130022 China
- University of Science and Technology of China Hefei Anhui 230026 China
| | - Yao Xiao
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin, 130022 China
- University of Science and Technology of China Hefei Anhui 230026 China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin, 130022 China
- University of Science and Technology of China Hefei Anhui 230026 China
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14
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Li H, Lu H, Tang Y, Wang H, Xiao Y, Li B. A Rebuilding‐Free Nucleic Acid Detection Strategy Enables Ultrasensitive Genotyping, N‐in‐1 Logic Screening and Accurate Multiplex Assay of Dangerous Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Huan Li
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry 130022 Changchun CHINA
| | - Huiying Lu
- Northeast Normal University School of Life Sciences CHINA
| | - Yidan Tang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry 5625 Remin StreetChangchun 130022 Changchun CHINA
| | - Huaning Wang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry CHINA
| | - Yao Xiao
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry CHINA
| | - Bingling Li
- Changchun Institute of Applied Chemistry, Chinese Academy of Science State Key Lab of Electroanalytical Chemistry 5625 Renmin Street 130022 Changchun CHINA
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15
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Wang Y, Chen Y, Wan Y, Hong C, Shang J, Li F, Liu X, Wang F. An Autocatalytic DNA Circuit Based on Hybridization Chain Assembly for Intracellular Imaging of Polynucleotide Kinase. ACS APPLIED MATERIALS & INTERFACES 2022; 14:31727-31736. [PMID: 35786848 DOI: 10.1021/acsami.2c08523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polynucleotide kinase (PNK) plays an essential role in various cellular events by regulating phosphorylation processes, and abnormal homeostasis of PNK could cause many human diseases. Herein, we proposed an autocatalytic hybridization system (AHS) through the elaborate integration of hybridization chain assembly (HCA) and catalytic DNA assembly (CDA) that enables a highly efficient positive feedback amplification. The PNK-targeting AHS biosensor is composed of three modules: a recognition module, an HCA amplification module, and a CDA autocatalytic module. In the presence of PNK, the recognition module could transform the PNK input into an exposed nucleic acid initiator (I). Then the initiator strand I could trigger the autonomous HCA process in the amplification module, and the resulted HCA products could reassemble the split CDA trigger strand T, subsequently inducing the CDA process in the autocatalytic module to form abundant DNA duplex products. Consequently, the embedded initiator strand I was liberated from the CDA duplex product to autonomously trigger the new rounds of HCA circuit. The rational integration and cooperative cross-activation between the HCA and CDA module could prominently accelerate the reaction and realize the exponential amplification efficiency by initiator regeneration. As a result, the self-sustainable AHS amplifier could implement the sensitive detection of PNK in vitro and in biological samples and further fulfill accurate monitoring of the intracellular PNK activity and the effective screening of PNK inhibitors. This work paves a way for exploiting highly efficient artificial DNA circuits to analyze low-abundance biomarkers, holding great potential in biochemical research and clinical diagnosis.
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Affiliation(s)
- Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yeqing Wan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Chen Hong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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16
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Zheng C, Hu X, Sun S, Zhu L, Wang N, Zhang J, Huang G, Wang Y, Huang X, Wang L, Shen Z. Hairpin allosteric molecular beacons-based cascaded amplification for effective detection of lung cancer-associated microRNA. Talanta 2022; 244:123412. [DOI: 10.1016/j.talanta.2022.123412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/07/2022] [Accepted: 03/25/2022] [Indexed: 12/25/2022]
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17
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He JY, Deng HL, Shang X, Yang CL, Zuo SY, Yuan R, Liu HY, Xu WJ. Modulating the Fluorescence of Silver Nanoclusters Wrapped in DNA Hairpin Loops via Confined Strand Displacement and Transient Concatenate Ligation for Amplifiable Biosensing. Anal Chem 2022; 94:8041-8049. [PMID: 35617342 DOI: 10.1021/acs.analchem.2c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It is intriguing to modulate the fluorescence emission of DNA-scaffolded silver nanoclusters (AgNCs) via confined strand displacement and transient concatenate ligation for amplifiable biosensing of a DNA segment related to SARS-CoV-2 (s2DNA). Herein, three stem-loop structural hairpins for signaling, recognizing, and assisting are designed to assemble a variant three-way DNA device (3WDD) with the aid of two linkers, in which orange-emitting AgNC (oAgNC) is stably clustered and populated in the closed loop of a hairpin reporter. The presence of s2DNA initiates the toehold-mediated strand displacement that is confined in this 3WDD for repeatable recycling amplification, outputting numerous hybrid DNA-duplex conformers that are implemented for a transient "head-tail-head" tandem ligation one by one. As a result, the oAgNC-hosted hairpin loops are quickly opened in loose coil motifs, bringing a significant fluorescence decay of multiple clusters dependent on s2DNA. Demonstrations and understanding of the tunable spectral performance of a hairpin loop-wrapped AgNC via switching 3WDD conformation would be highly beneficial to open a new avenue for applicable biosensing, bioanalysis, or clinical diagnostics.
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Affiliation(s)
- Jia-Yang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hui-Lin Deng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xin Shang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chun-Li Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Si-Yu Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hong-Yan Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wen-Ju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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18
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Zhao R, Yu C, Lu B, Li B. Coupling nucleic acid circuitry with the CRISPR-Cas12a system for universal and signal-on detection. RSC Adv 2022; 12:10374-10378. [PMID: 35425009 PMCID: PMC8977996 DOI: 10.1039/d2ra01332k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
We report a universal and signal-on HCR based detection platform via innovatively coupling the CRISPR-Cas12a system with HCR. By using this CRISPR-HCR pathway, we can detect different targets by only changing the crRNA. The CRISPR-HCR platform coupling with an upstream amplifier can achieve a practical sensitivity as low as ∼aM of ASFV gene in serum.
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Affiliation(s)
- Rujian Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Chunxu Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
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19
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Tang Y, Qi L, Liu Y, Guo L, Zhao R, Yang M, Du Y, Li B. CLIPON: A CRISPR-Enabled Strategy that Turns Commercial Pregnancy Test Strips into General Point-of-Need Test Devices. Angew Chem Int Ed Engl 2022; 61:e202115907. [PMID: 35064613 DOI: 10.1002/anie.202115907] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Indexed: 12/24/2022]
Abstract
Desirable biosensing assays need to be sensitive, specific, cost-effective, instrument-free, and versatile. Herein we report a new strategy termed CLIPON (CRISPR and Large DNA assembly Induced Pregnancy strips for signal-ON detection) that can deliver these traits. CLIPON integrates a commercial pregnancy test strip (PTS) with four biological elements: the human chorionic gonadotropin (hCG), CRISPR-Cas12a, crRNA and cauliflower-like large-sized DNA assemblies (CLD). CLIPON uses the Cas12a/crRNA complex both to recognize a target of interest and to release CLD-bound hCG so that target presence can translate into a colorimetric signal on the PTS. We demonstrate the versatility of CLIPON through sensitive and specific detection of HPV genomic DNA, SARS-CoV-2 genomic RNA and adenosine. We also engineer a cell phone app and a hand-held microchip to achieve signal quantification. CLIPON represents an attractive option for biosensing and point-of-care diagnostics.
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Affiliation(s)
- Yidan Tang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Lijuan Qi
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yichen Liu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Lulu Guo
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Rujian Zhao
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Meiting Yang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Yan Du
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
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20
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Tang Y, Qi L, Liu Y, Guo L, Zhao R, Yang M, Du Y, Li B. CLIPON: A CRISPR‐Enabled Strategy that Turns Commercial Pregnancy Test Strips into General Point‐of‐Need Test Devices. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yidan Tang
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Lijuan Qi
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Yichen Liu
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Lulu Guo
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Rujian Zhao
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Meiting Yang
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Yan Du
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
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22
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Xue W, Zhang Q, Chang Y, Brennan JD, Li Y, Liu M. Quantifying DNA damage on paper sensors via controlled template-independent DNA polymerization. Chem Sci 2022; 13:6496-6501. [PMID: 35756503 PMCID: PMC9172109 DOI: 10.1039/d1sc04268h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/13/2021] [Indexed: 11/21/2022] Open
Abstract
Terminal deoxynucleotidyl transferase (TdT) catalyzes template-independent DNA synthesis in a well-controllable mode on paper, allowing absolute quantification of polymetric labeling of a single 3′-OH present on genomic DNA.
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Affiliation(s)
- Wei Xue
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, Dalian University of Technology, Dalian, 116024, China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, Dalian University of Technology, Dalian, 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, Dalian University of Technology, Dalian, 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
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23
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Liao Y, Gao J, Huang W, Yuan R, Xu W. LAMP-H +-responsive electrochemical ratiometric biosensor with minimized background signal for highly sensitive assay of specific short-stranded DNA. Biosens Bioelectron 2022; 195:113662. [PMID: 34571484 DOI: 10.1016/j.bios.2021.113662] [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: 08/02/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 11/02/2022]
Abstract
Herein, the sequence-specific short-stranded biomarker DNA (hDNA, 21-nt) is acted as targeting out-primer to implement the loop-mediated isothermal amplification for releasing hydrogen ions (LAMP-H+). Using LAMP-H+ as signaling transducer, we report a highly sensitive electrochemical ratiometric biosensor for hDNA with minimized background signal, which is achieved via magnetic separation using AuNPs-modified Fe3O4 (Au@Fe3O4) as micro-reactor. In Au@Fe3O4, a double-stranded complex of a pH-responsible strand (I*) and a substrate strand (S*) is bound via Au-N bonds, where the treatment with LAMP-H+ leads to I* folding into i-motif conformation and S* dehybridization. The S* further hybridizes a catalytic strand (C*) to assemble Mg2+-DNAzymes that are cleaved by Mg2+, releasing C* for repeated formation and robust nicking of Mg2+-DNAzymes. The resultant output fuel strands (F*) are introduced in a modified electrode to drive the strand displacement of two hairpins individually labeled with two electron mediators. Through F*-mediated recycled amplification, the ratio of their electrochemical currents changed in opposite is highly sensitive to the varied hDNA down to 2.1 fM. By integrating LAMP-H+-stimulated i-motif switching with Mg2+-DNAzyme cleavage, this logic transduction of LAMP-H+(i-motif/Mg2+-DNAzyme)F* efficiently minimizes the inherent background of traditional LAMP-based assays. Resultantly, our electrochemical ratiometric strategy would be applicable to diverse short-stranded DNAs or even RNAs as targeting primers of LAMP.
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Affiliation(s)
- Yumeng Liao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Jiaxi Gao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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24
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Yu J, Liu J, Ma CB, Qi L, Du Y, Hu X, Jiang Y, Zhou M, Wang E. Signal-On Electrochemical Detection for Drug-Resistant Hepatitis B Virus Mutants through Three-Way Junction Transduction and Exonuclease III-Assisted Catalyzed Hairpin Assembly. Anal Chem 2021; 94:600-605. [PMID: 34920663 DOI: 10.1021/acs.analchem.1c03451] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The present detection method for hepatitis B virus (HBV) drug-resistant mutation has a high misdiagnosis rate and usually needs to meet stringent requirements for technology and equipment, leading to complex and time-consuming manipulation and drawback of high costs. Herein, with the purpose of developing cost-effective, highly efficient, and handy diagnosis for HBV drug-resistant mutants, we propose an electrochemical signal-on strategy through the three-way junction (3WJ) transduction and exonuclease III (Exo III)-assisted catalyzed hairpin assembly (CHA). To achieve single-copy gene detection, loop-mediated nucleic acid isothermal amplification (LAMP), one of the highly promising and compatible techniques to revolutionize point-of-care genetic detection, is first adopted for amplification. The rtN236T mutation, an error encoded by codon 236 of the reverse transcriptase region of HBV DNA, was employed as the model gene target. Under the optimized conditions, it allows end-point transduction from HBV drug-resistant mutants-genomic information to electrochemical signals with ultrahigh sensitivity, specificity, and signal-to-noise ratio, showing the lowest detection concentration down to 2 copies/μL. Such a method provides a possibly new principle for ideal in vitro diagnosis, supporting the construction of a clinic HBV diagnosis platform with high accuracy and generalization. Moreover, it is not restricted by specific nucleic acid sequences but can be applied to the detection of various disease genes, laying the foundation for multiple detection.
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Affiliation(s)
- Jiaxue Yu
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, National & Local United Engineering Laboratory for Power Batteries, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Jingju Liu
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, National & Local United Engineering Laboratory for Power Batteries, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Chong-Bo Ma
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, National & Local United Engineering Laboratory for Power Batteries, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Lijuan Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Xintong Hu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Ming Zhou
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, National & Local United Engineering Laboratory for Power Batteries, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
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25
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Zhu D, Ma Z, Wang Z, Wei Q, Li X, Wang J, Su S, Zuo X, Fan C, Chao J, Wang L. Modular DNA Circuits for Point-of-Care Colorimetric Assay of Infectious Pathogens. Anal Chem 2021; 93:13861-13869. [PMID: 34506117 DOI: 10.1021/acs.analchem.1c02597] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Accurate, specific, and inexpensive detection of multiple infectious pathogens simultaneously is a significant goal for human health and safety. Herein we present a rationally designed modular DNA circuit for point-of-care (POC) detection of a variety of infectious pathogens based on nucleic acid isothermal amplification technology and DNAzyme-mediated colorimetric readout. A modular DNA circuit was constructed with a fixed module and a flexible module and was rationally designed according to genetic targets. On this basis, the platform could detect multiple genetic targets corresponding to infectious pathogens simultaneously. Signal amplification properties of the DNA circuit and the peroxidase-like DNAzyme enable the detection limits to reach the picomolar level. By urea treatment and magnetic separation, the fixed module can be reused at least five times, which makes this assay more economical and environmentally friendly. The detection of genetic infectious pathogens should be accomplished in 2 h with naked-eye observation and may provide an efficient tool for POC analysis of multiple infectious pathogens, especially in resource-poor areas.
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Affiliation(s)
- Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Zihao Ma
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Zichun Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Qingyun Wei
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Xiaojian Li
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jingjing Wang
- Hebei Provincial Key Laboratory of Ophthalmology, Hebei Provincial Eye Hospital, Xingtai 054001, China
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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26
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Yin X, Chen B, He M, Hu B. A Homogeneous Multicomponent Nucleic Acid Enzyme Assay for Universal Nucleic Acid Detection by Single-Particle Inductively Coupled Plasma Mass Spectrometry. Anal Chem 2021; 93:4952-4959. [PMID: 33689302 DOI: 10.1021/acs.analchem.0c05444] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS) has great potential for sensitive analysis of nucleic acids; however, it usually requires separation of target-induced nanoparticle reporters, and the sequence of probes on nanoparticle reporters has to be tuned for each target accordingly. Here, we developed a homogeneous multicomponent nucleic acid enzyme (MNAzyme) assay for universal nucleic acid detection. The two components of MNAzyme contain target recognition sites, substrate binding sites, and a catalytic core. Only in the presence of a specific nucleic acid target, the MNAzyme will assemble to trigger its nucleic acid enzyme activity and cleave its substrate (Linker DNA). The Linker DNA could link gold nanoparticle (AuNP) probes to form a larger assembled particle, while the cleavage of Linker DNA will disturb the linkage between probes, inducing a smaller assembled particle. The assembled particles with different sizes could be differentiated and sensitively detected in SP-ICP-MS, which also enables the tolerance of a complex matrix. By simply altering the sequences of the target recognition sites in MNAzyme, we applied the assay for two types of nucleic acids (long strand DNA and short strand RNA), malaria DNA and miRNA-10b. With increasing the target concentration, the signal intensity of each assembled particle decreases, but the frequency of assembled particle pulse increases. Both targets could be quantitatively detected from 0.1 to 25 pmol L-1 with high specificity in serum samples. The developed MNAzyme-SP-ICP-MS assay possesses simple operation in a homogeneous reaction, easy tunability for multiple types of nucleic acid targets, and good compatibility with clinic samples.
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Affiliation(s)
- Xiao Yin
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Beibei Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Man He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bin Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
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27
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Lv WY, Li CH, Li YF, Zhen SJ, Huang CZ. Hierarchical Hybridization Chain Reaction for Amplified Signal Output and Cascade DNA Logic Circuits. Anal Chem 2021; 93:3411-3417. [DOI: 10.1021/acs.analchem.0c04483] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wen Yi Lv
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chun Hong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yuan Fang Li
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
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28
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Li H, Tang Y, Song D, Lu B, Guo L, Li B. Establishment of Dual Hairpin Ligation-Induced Isothermal Amplification for Universal, Accurate, and Flexible Nucleic Acid Detection. Anal Chem 2021; 93:3315-3323. [PMID: 33538577 DOI: 10.1021/acs.analchem.1c00007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Isothermal amplifications have found their potentials in applications of portable nucleic acid diagnostics. However, there are still several certain deficiencies existing in the current amplification methods, including high false-positive signals, limited range of targets, difficult primer design, and so forth. Here, we report an effective solution via the development of dual hairpin ligation-induced isothermal amplification (DHLA) consisting of (1) the formation of a dual hairpin probe (DHP) based on sequence specific hybridization and ligation and (2) exponential isothermal amplification of DHP in the presence of polymerase and primers. Taking both microRNA and virus RNA as model targets, DHLA is proven to be accurate, flexible, and applicable to most deoxyribonucleic acid and ribonucleic acid targets ranging from ∼20 to hundreds of nt. The detection limit is down to the ∼aM level without a false-positive signal. More importantly, the whole detection can be directly applied to a new target via a slight change in the DHP sequence, without redesigning the primer set. This unique property not only simplifies the process for new reaction development but also enables flexible multiprobe strategies to achieve antidegradation analysis.
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Affiliation(s)
- Huan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yidan Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Defeng Song
- Department of General Surgery, China-Japan Union Hospital of JiLin University, Changchun, Jilin 130021, P. R. China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Lulu Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
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29
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Cui H, Wu W, Xu H, Cao H, Hong N, Cheng L, Liao F, Jiang Y, Ma G, Fan H. A homogeneous strategy of target-triggered catalytic hairpin assembly for thrombin signal amplification. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Wang X, Tao Z. Expanding the analytical applications of nucleic acid hybridization using junction probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4931-4938. [PMID: 33043948 DOI: 10.1039/d0ay01605e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nucleic acid hybridization is crucial in target recognition with respect to in vitro and in vivo nucleic acid biosensing. Conventional linear probes and molecular beacons encounter challenges in multiplexing and specific recognition of intractable nucleic acids. Advances in nucleic acid nanotechnologies have resulted in a set of novel structural probes: junction probes (JPs), which make full use of the advantages of specificity, stability, programmability and predictability of Watson-Crick base pairing. In recent years, junction probes have been regularly implemented in constructing systems related to biosensing, synthetic biology and gene regulation. Herein, we summarize the latest advances in JP designs as potential nucleic acid biosensing systems and their expansive applications, and provide some general guidelines for developing JP based sensing strategies for implementation of such systems.
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Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China.
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31
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Lu J, Liang S, Tan L, Hu K, Zhao S, Tian J. Sensitive detection of microRNA using a label-free copper nanoparticle system with polymerase-based signal amplification. Anal Bioanal Chem 2020; 412:7179-7185. [PMID: 32785774 DOI: 10.1007/s00216-020-02850-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 11/25/2022]
Abstract
The abnormal expression of microRNAs (miRNAs) has been reported in many diseases, so it is of great interest to develop simple and accurate methods for the detection and analysis of miRNA expression. We have developed a novel biosensor to detect miRNAs. This method is based on a polymeric double-stranded DNA (dsDNA) copper nanoparticle (CuNP) template that is synthesised by a polymerase. When Cu2+ and ascorbic acid are added to the system, the dsDNA template (which is rich in A-T bases) promotes the formation of CuNPs, resulting in high fluorescence intensity. This system provides sensitive analysis of miRNA expression with a limit of detection down to 17.8 pmol/L, due to significant changes in the fluorescence signal of the system before and after the addition of the target. The linear range between F0-F and concentration of miR-122 is 80.0 pmol/L to 4.50 nmol/L, and the recovery rate in spiked HepG2 cell lysates is 93.33-102.53%. This method expands the applications of fluorescent DNA-CuNPs in the field of biosensor analysis, and can be used to detect and analyse any miRNA marker by changing the target recognition sequence. Graphical abstract A label-free dsDNA-CuNP-based and enzyme-assisted signal amplification method for microRNA is constructed.
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Affiliation(s)
- Jiangnan Lu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Shuping Liang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Li Tan
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Kun Hu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Shulin Zhao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Jianniao Tian
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China.
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32
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Tian Z, Peng P, Wang H, Zheng J, Shi L, Li T. Aptamer-Braked Multi-hairpin Cascade Circuits for Logic-Controlled Label-Free In Situ Bioimaging. Anal Chem 2020; 92:10357-10364. [PMID: 32600028 DOI: 10.1021/acs.analchem.0c00583] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As a common hairpin-based amplification strategy, catalytic-hairpin assembly (CHA) has been widely used to construct various DNA circuits for biosensing and imaging. However, the hairpin substrates can potentially react without catalysts and result in circuit leakage, which may be quite severe in a CHA reaction consisting of three or four hairpins due to the formation of stable three-/four-way junction product. To circumvent this problem, here we introduce a well-designed ATP aptamer as a DNA brake into a four-hairpin cascade circuit, where the triggering toehold is blocked by the aptamer brake and thus the circuit leakage decreases dramatically. Such an aptamer-braked DNA circuit is then employed to build an AND logic gate in response to multiple external stimuli in acidic cell membrane microenvironments. Induced by a bimolecular i-motif that binds thioflavin T (ThT), the dimerization of a four-way junction in situ assembled on the cell surface is accomplished, enabling the logic-controlled cell membrane imaging in a label-free manner. Our design would be applicable to other hairpin-based amplification strategies and may find more applications in the construction of multiresponsive DNA cascade circuits in complex living systems.
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Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Jiao Zheng
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
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33
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Zhu L, Zhang M, Ye J, Yan M, Zhu Q, Huang J, Yang X. Ratiometric Electrochemiluminescent/Electrochemical Strategy for Sensitive Detection of MicroRNA Based on Duplex-Specific Nuclease and Multilayer Circuit of Catalytic Hairpin Assembly. Anal Chem 2020; 92:8614-8622. [PMID: 32452205 DOI: 10.1021/acs.analchem.0c01949] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this study, we proposed a ratiometric electrochemiluminescent (ECL)/electrochemical (EC) biosensor based on duplex-specific nuclease (DSN)-assisted target recycling and multilayer catalytic hairpin assembly (CHA) amplification cascades for the detection of microRNA (miRNA). The DSN-assisted target recycling transformed miRNAs into a large number of ssDNA, which then catalyzed a multilayer CHA amplification cascade to produce numerous long dsDNA duplexes Hn/Hn+1 (n = 2, 4, 6, ...). Then the Hn/Hn+1 displaced the ferrocene (Fc)-labeled ssDNA (Sx+1, x = 1, 3, 5, ...) to hybridize with the Sx sequence on the gold electrode surface. Consequently, a great number of long Sx/Hn/Hn+1 duplexes were immobilized for binding Ru(phen)32+ to obtain an amplified ECL signal. Meanwhile, the EC signal of Fc was reduced, and the quenching effect of Fc to ECL signal also decreased. By measuring the ratio of the ECL signal of Ru(phen)32+ to the EC signal of Fc, quantitative analysis of miRNA-499 with high accuracy and reproducibility was obtained. The ratiometric biosensor shows high sensitivity and a wide linear range of 6 orders of magnitude. With the help of DSN-assisted target recycling, this strategy can be easily extended to detect other miRNAs without redesigning the CHA cascade system. The proposed "hybrid" ratiometric ECL/EC strategy enriches the ratiometric sensors and can find extensive applications in bioanalysis, especially for multiplex detection.
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Affiliation(s)
- Liping Zhu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Mengqian Zhang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jing Ye
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Mengxia Yan
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | - Qiuju Zhu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | - Xiurong Yang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
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34
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Tang Y, Li H, Li B. Homogeneous and universal transduction of various nucleic acids to an off-shelf device based on programmable toehold switch sensing. Chem Commun (Camb) 2020; 56:2483-2486. [PMID: 32002523 DOI: 10.1039/c9cc09154h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Through a rational construction of an RNA toehold switch sensor, the glucometer-based detection of nucleic acids was innovatively simplified into a completely homogeneous and label-free process. Compared with traditional strategies that rely on multiple operations such as chemical conjugation and bead separation, this new strategy is more robust, user-friendly, reagent-saving, and reproducible, and can be universally adapted for use on extensive target species, e.g. herein, the real-world pathogen genes.
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Affiliation(s)
- Yidan Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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Li H, Tang Y, Li B. Homogeneous and Universal Detection of Various Targets with a Dual-Step Transduced Toehold Switch Sensor. Chembiochem 2020; 21:1418-1422. [PMID: 31913537 DOI: 10.1002/cbic.201900749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Indexed: 12/13/2022]
Abstract
Toehold switch sensors represent a class of new advances that allow specific targets to trigger in situ expression of a protein reporter. Although they offer unique advantages of a label-free nature and high portability, they generally require repeated sequence design, high expenditure, and laborious optimization of toehold switch sequences according to different targets. To simplify the sensing process further and to improve its practicability, we innovatively introduce a dual-step pre-transduction upon traditional toehold switch sensor. Through two successive toehold-mediated strand-displacement reactions that are initiated, respectively, by a linear and an associative trigger, different DNAs, RNAs, or ligands of functional nucleic acids can be generally transduced into the input of one high-performance toehold switch sensor. This advance greatly increases the target range. Furthermore, the whole process is signal-on, homogeneous, and free of any requirements for complicated operations such as probe labeling, separation, and reconstruction of the toehold switch, being promising and practical even in portable or point-of-care assays.
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Affiliation(s)
- Huan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yidan Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
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Liu J, Zhan Z, Liang T, Xie G, Aguilar ZP, Xu H. Dual-signal amplification strategy: Universal asymmetric tailing-PCR triggered rolling circle amplification assay for fluorescent detection of Cronobacter spp. in milk. J Dairy Sci 2020; 103:3055-3065. [PMID: 32037161 DOI: 10.3168/jds.2019-17590] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/08/2019] [Indexed: 01/19/2023]
Abstract
Cronobacter spp. are important opportunistic foodborne pathogens in powdered infant formula that cause many serious diseases in neonates and infants. In this study, a novel assay based on dual signal amplification strategy was developed by coupling asymmetric tailing PCR (AT-PCR) with rolling circle amplification (RCA) for the detection of Cronobacter spp. in milk. The tailing single-stranded DNA was generated through AT-PCR and used to initiate RCA, generating tandem repetitive G-quadruplex sequences. In the presence of the fluorescence dye thioflavin T that could intercalate into the G-quadruplex structures, the fluorescence signal was detected with a microplate reader. The AT-PCR coupled with RCA assay was specific for Cronobacter spp. detection because of the highly specific primers chosen for the AT-PCR. The limits of detection were 4.3 × 101 cfu/mL in pure culture and 4.5 × 102 cfu/mL in spiked milk, respectively. The fixed sequences designed in the hairpin DNA allowed this AT-PCR coupled with RCA assay to serve as a universal platform for the detection of other pathogens by modifying the specificity of the PCR primers.
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Affiliation(s)
- Ju Liu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Zhongxu Zhan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China; Jiangxi Institute for Food Control, Nanchang, 330001, PR China
| | - Taobo Liang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Guoyang Xie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | | | - Hengyi Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China.
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One-tube smart genetic testing via coupling isothermal amplification and three-way nucleic acid circuit to glucometers. Anal Chim Acta 2020; 1106:191-198. [PMID: 32145848 PMCID: PMC7094703 DOI: 10.1016/j.aca.2020.01.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 11/23/2022]
Abstract
Urgent demand for portable diagnosis has promoted a new sensing strategy that uses personal glucometer (PGM) to detect non-glucose targets. Even though great progresses have been achieved in terms of target range and sensing principle, issues such as low final signal-to-background ratio and hard-to-realize one-tube smart analysis still exist and challenge real-world applications in gene detection. Here we propose a practical solution via coupling isothermal amplification (i.e. LAMP) and three-way amplifiable catalytic hairpin assembly (i.e. CHA) to a PGM. It allows direct transduction from genomic information to commercial portable devices with all of ultra-high sensitivity, specificity and enhanced signal-to-noise ratio. Compared with previous report without signal amplification, the introduction of CHA has successfully improved the signal amplitude by at least 12.5 folds. More importantly, through importing an effective three-way junction based transduction, we also innovatively develop a one-tube logical or multiplex analysis strategy in PGM based detection. Totally four situations of two foodborne bacteria genes, in Cronobacter sakazakii (ompA) and Escherichia coli (malB), could be directly readout using the final PGM signals, with the lowest detection amount down to less than 100 molecular copies (6.6 × 10-18 M). It is believed such a LAMP-CHA-PGM method has been already sensitive, specific, and of great potential for practically portable gene diagnostics.
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A rapid, adaptative DNA biosensor based on molecular beacon-concatenated dual signal amplification strategies for ultrasensitive detection of p53 gene and cancer cells. Talanta 2019; 210:120638. [PMID: 31987215 DOI: 10.1016/j.talanta.2019.120638] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 11/23/2022]
Abstract
The cancer diagnosis with single level of biomarkers suffers from limitation of insufficient accuracy. Hence, developing sensitive, rapid and adaptative analytical strategies for double-level biomarkers are essential for improving the accuracy of clinical cancer diagnosis at early stage. Herein, a DNA biosensor was established based on the catalytic hairpin assembly-mediated Y-junction nicking enzyme assisted signal amplification (CHA-YNEASA) circuits, where the two circuits were concatenated by molecular beacon (MB). In absence of target, both the CHA and YNEASA circuits were effectively hindered because of MB's outstanding ability to control signal background. In presence of target, the initiated CHA circuits made enzyme recognition sequences in close proximity to the assisted sequences to open MB, leading to further trigger the YNEASA circuits. Due to the unique design of dual signal amplification strategies, CHA-YNEASA circuits significantly shorten the reaction time, and improve signal-to-background ratio as well as facilitate the analysis process. It was demonstrated that a high sensitivity with limit of detection (LOD) of 0.9 pM for p53 gene detection was obtained just within 23 min by the proposed DNA biosensor. Moreover, mismatched p53 gene at nucleic acid level was effectively discriminated and strong anti-interference capability was achieved. Noticeably, the DNA biosensor was adaptative for designing a cytosensor at cell level using hairpin DNA, containing MUC1 aptamer and initiation strand of CHA-YNEASA circuits, as switch based on modularity principle. The cytosensor is able to measure MUC1 positive breast cancer cells (MCF-7) with the LOD as low as 100 cells/mL. Excellent specificity for MUC1 negative cells, and good anti-interference capability in 10% fetal bovine serum (FBS) were observed by the cytosensor. Therefore, the proposed DNA biosensor is a sensitive, rapid, adaptative platform for detection of double-level biomarkers, offering novel strategy applied for clinical cancer diagnosis.
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Dong Q, Liu Q, Guo L, Li D, Shang X, Li B, Du Y. A signal-flexible gene diagnostic strategy coupling loop-mediated isothermal amplification with hybridization chain reaction. Anal Chim Acta 2019; 1079:171-179. [PMID: 31387708 PMCID: PMC7094597 DOI: 10.1016/j.aca.2019.06.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/03/2019] [Accepted: 06/23/2019] [Indexed: 12/20/2022]
Abstract
Recent study proves that the combination of loop mediated isothermal nucleic acid amplification (LAMP) with one-step strand displacement (OSD) is of great help to improve the sequence specificity during genetic detection. However, because OSD is incapable of signal amplification, the signal-to-noise ratio or the observable signal change may be usually not significant enough to satisfy practical usage. With the purpose to overcome this challenge, herein a more advanced and practical sensing principle is developed with the OSD replaced by an amplifiable nucleic acid circuit, hybridization chain reaction (HCR). The very contagious norovirus (NoV) was employed as the model target. Compared with LAMP-OSD, the LAMP-HCR can detect as few as 30 copies of NoV gene in 2% fecal samples with significantly enlarged signal change and signal-to-background ratio. Therefore, more reliable detection is achieved. Moreover, due to the high compatibility of HCR, the final LAMP-HCR products can be flexibly transduced into different types of readouts, including fluorescence, flow cytometer (FCM) and even a personal glucose meter (PGM). This further enlarges the operating environments for the detection from hospital labs, bedsides, to potential off-the-shelf devices in local pharmacies. Especially when using FCM or PGM, with the assistance of magnetic beads (MBs), the detection shows even higher tolerance capability to complicated biological matrices.
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Affiliation(s)
- Qing Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Changchun University of Science and Technology, Changchun, Jilin, 130022, China
| | - Quanyi Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Lulu Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Dan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
| | - Xudong Shang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China.
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China.
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Li X, Yin F, Xu X, Liu L, Xue Q, Tong L, Jiang W, Li C. A facile DNA/RNA nanoflower for sensitive imaging of telomerase RNA in living cells based on "zipper lock-and-key" strategy. Biosens Bioelectron 2019; 147:111788. [PMID: 31671380 DOI: 10.1016/j.bios.2019.111788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 01/03/2023]
Abstract
The sensitive imaging of telomerase RNA (TR) in living cells is crucial for improved guidance in cancer clinical diagnosis because its expression level is closely related to malignant diseases. The efficient delivery of multiple nucleic acid probes to target cells is critical for nucleic acid-based methods to successfully image low-abundance TR in living cells. While novel nanomaterials enhance delivery efficiency, uncontrolled loading and slow intracellular release remain major challenges for multiple-probe delivery. Here, we designed a facile DNA/RNA nanoflower (NF) to perform the controlled loading of multiple probes and rapid intracellular release based on the "zipper lock-and-key" strategy. First, a long RNA generated by rolling circle transcription acts as both the "smart zipper lock" and the delivery carrier to alternately lock multiple functional DNAs through DNA-RNA base pairing, and the resulting RNA/DNA hybrids self-assemble into packed NFs. The functional DNAs include the fluorescence molecular beacon H1 for TR recognition, H2 for hybrid chain reaction (HCR) and DNA-cholesterol for size control. After NF internalization by the cells, the intracellular RNase H acts as the "key" to specifically open the DNA/RNA NFs by cleaving the RNA in the DNA/RNA hybrid, releasing high amounts of H1 and H2 in a confined space and thereby facilitating the HCR amplification analysis of cytoplasmic TR. With the addition of a DNA-nuclear localization peptide component in the same NF, nuclear TR can also be sensitively detected. Compared with the regular H1/H2 mixture, the DNA/RNA NFs produced a higher-contrast fluorescence signal. This indicated that the proposed strategy allowed the side arms of H1/H2 to be sealed into the RNA sequence-programmed "zipper lock" by controlled loading, avoiding mutual nonspecific H1/H2 hybridization. In addition, due to the fast kinetics of the RNase endonuclease reaction, the loaded H1/H2 was quickly released. Furthermore, the strategy was successfully used to assay the expression levels of TR in HeLa, HepG2 and HL-7702 cells, demonstrating that this approach holds the potential for the sensitive detection of low-abundance biomarkers in living cells.
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Affiliation(s)
- Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, PR China; Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Fei Yin
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, PR China
| | - Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Liqi Liu
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, PR China
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, PR China
| | - Lin Tong
- Department of Biomedical Engineering, Florida International University, Miami, FL, 33174, USA
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Chenzhong Li
- Department of Biomedical Engineering, Florida International University, Miami, FL, 33174, USA.
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42
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Zhao Y, Fang X, Chen F, Bai M, Fan C, Zhao Y. Locus-patterned sequence oriented enrichment for multi-dimensional gene analysis. Chem Sci 2019; 10:8421-8427. [PMID: 31803421 PMCID: PMC6844269 DOI: 10.1039/c9sc02496d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/22/2019] [Indexed: 11/21/2022] Open
Abstract
Multi-dimensional gene analysis provides in-depth insights into gene sequence, locus variations and molecular abundance, whereas it is vulnerable to the perturbation of complex reaction networks and always compromises on the discrimination of analogous sequences. Here, we present a sequence oriented enrichment method patterned by the prescribed locus without crosstalk between concurrent reactions. Energetically favourable structures of nucleic acid probes are theoretically derived and oriented to a specific gene locus. We designed a pair of universal probes for multiple conserved loci to avoid side reactions from undesired interactions among increased probe sets. Furthermore, competitive probes were customized to sink analogues for differentiating the reaction equilibrium and kinetics of sequence enrichment from the target, so variant loci can be synchronously identified with nucleotide-level resolution. Thus, the gene locus guides sequence enrichment and combinatorial signals to create unique codes, which provides access to multidimensional and precise information for gene decoding.
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Affiliation(s)
- Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Xiaoxing Fang
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering , Institute of Molecular Medicine , Renji Hospital , School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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43
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Yang F, Cheng Y, Cao Y, Zhang Y, Dong H, Lu H, Zhang X. MicroRNA Triggered DNA “Nano Wheel” for Visualizing Intracellular microRNA via Localized DNA Cascade Reaction. Anal Chem 2019; 91:9828-9835. [DOI: 10.1021/acs.analchem.9b01487] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Fan Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Yaru Cheng
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Yu Cao
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Yiyi Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Haifeng Dong
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Huiting Lu
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Xueji Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
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Zhu Z, Wu R, Li B. Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit. Chem Sci 2019; 10:1953-1961. [PMID: 30881624 PMCID: PMC6385554 DOI: 10.1039/c8sc04875d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 12/18/2022] Open
Abstract
Recent advances have proven that using solid-state nanopores is a promising single molecular technique to enrich the DNA assembly signaling library. Other than using them for distinguishing structures, here we innovatively adapt solid-state nanopores for use in analyzing assembly mixtures, which is usually a tougher task for either traditional characterization techniques or nanopores themselves. A trigger induced DNA step polymerization (SP-CHA), producing three-way-DNA concatemers, is designed as a model. Through counting and integrating the translocation-induced current block when each concatemer passes through a glass conical glass nanopore, we propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the "base-pair distribution" of SP-CHA concatemer mixtures. Due to the higher sensitivity, a number of super long concatemers that were previously difficult to detect via gel electrophoresis are also revealed. These ultra-concatemers, longer than 2 kbp, could provide a much enhanced signal-to-noise ratio for nanopores and are thus believed to be more accurate indicators for the existence of a trigger, which may be of benefit for further applications, such as molecular machines or biosensors.
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Affiliation(s)
- Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
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Yang L, Wu Q, Chen Y, Liu X, Wang F, Zhou X. Amplified MicroRNA Detection and Intracellular Imaging Based on an Autonomous and Catalytic Assembly of DNAzyme. ACS Sens 2019; 4:110-117. [PMID: 30562005 DOI: 10.1021/acssensors.8b01000] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abnormal microRNAs (miRNAs) expression is demonstrated to associate with various important biological processes, including tumorigenesis, metastasis, and progression. Given the low miRNA expression at the earlier stage of diseases, its amplified detection still requires more efforts. Inspired by the two-stage arithmetic amplifier of electric devices, we reported an autonomous and catalytic assembly of DNAzyme strategy by integrating a DNAzyme biocatalyst and catalytic hairpin assembly (CHA) circuit. Here the catalytically inactive DNAzyme subunits were respectively grafted into these metastable CHA hairpin reactants that were kinetically impeded without false cross-hybridizations. The target catalyzed the nonenzymatic CHA-mediated successive assembly of dumbbell-like bis-DNAzyme nanostructures, leading to the efficient DNAzyme-mediated cleavage of fluorophore/quencher-modified substrate and to the generation of an amplified fluorescence signal. The present CHA-DNAzyme amplifier can be employed as a versatile and general sensing platform for analyzing other analytes (e.g., miRNA) by introducing a sensing module into the present system. Moreover, the homogeneous CHA-DNAzyme method could realize the sensitive intracellular miRNA imaging in living cells, which is attributed to the inherently synergistic amplification property between DNAzyme and CHA reactions. Given the attractive analytical features of the autonomous CHA-DNAzyme system, the present strategy shows great promise for analyzing additional different analytes in clinical research fields.
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Affiliation(s)
- Lei Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuqi Chen
- Key Laboratory of Biomedical Polymers (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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46
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Cui YX, Feng XN, Li XY, Zhang YP, Tang AN, Kong DM. Trifunctional integrated DNA-based universal sensing platform for detection of diverse biomolecules in one-pot isothermal exponential amplification mode. Chem Commun (Camb) 2019; 55:7603-7606. [DOI: 10.1039/c9cc03758f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Template constructed with only a short single-stranded DNA is necessary; it is first recognized by the target enzyme, then multiple amplification cycles are initiated, achieving ultra-high sensitivity by a one-pot isothermal reaction.
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Affiliation(s)
- Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Xue-Nan Feng
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
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47
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Cai S, Yang D, Tian X, Ye J, Xu M, Abdullah Al-Maskri AA, Jung C, Zeng S. A novel helper qPCR system for platinum detection via Pt-DNA coordination. Anal Chim Acta 2018; 1050:154-160. [PMID: 30661583 DOI: 10.1016/j.aca.2018.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/30/2018] [Accepted: 11/02/2018] [Indexed: 11/26/2022]
Abstract
A novel real-time polymerase chain reaction (qPCR) platform for the simple and robust detection of platinum is described for the first time. Compared with conventional qPCR, a helper template, which is related to the active template for performing qPCR, was introduced in our helper qPCR system. Several guanine (G) bases were introduced in the helper template to obtain a platinum-responsive on/off switch based on G-Pt-G coordination. Because of the helper template, a slight change in platinum concentration would significantly change the signal in the qPCR. This novel helper qPCR technique easily detects platinum with high sensitivity (1 ng/mL) and selectivity over other metal ions. Therefore, it will be a promising technique for the detection of platinum in biomedical and environmental samples.
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Affiliation(s)
- Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dan Yang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xueke Tian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Mingcheng Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Cheulhee Jung
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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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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49
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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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50
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Wang H, Li C, Liu X, Zhou X, Wang F. Construction of an enzyme-free concatenated DNA circuit for signal amplification and intracellular imaging. Chem Sci 2018; 9:5842-5849. [PMID: 30079197 PMCID: PMC6050587 DOI: 10.1039/c8sc01981a] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
A rationally and modularly engineered two-layered CHA–HCR circuit was constructed for amplified biosensing and bioimaging with high performance.
Nucleic acid circuits have shown promising potential for amplified detection of biomarkers with interest in biologically important engineering applications. In this work, by properly integrating two signal amplification approaches, catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR), a concatenated CHA–HCR system was established as an isothermal enzyme-free amplification strategy for highly sensitive and selective nucleic acid assay. The target catalyzes the self-assembly of CHA hairpin substrates into dsDNA products, where the split segments of HCR trigger are successively connected to drive the subsequent autonomous cross-opening of HCR hairpins, leading to the construction of HCR tandem copolymeric dsDNA nanowires. The resulting HCR copolymer brings a fluorophore donor/acceptor pair into close proximity that allows an efficient generation of FRET readout signal. Moreover, the optimized CHA–HCR circuit, upon the incorporation of an auxiliary sensing module, can be converted into a universal sensing platform for detecting cancerous biomarkers (e.g., a well-known oncogene miR-21) through a convenient easy-to-integrate procedure. The concatenated CHA–HCR amplifier enables accurate intracellular miRNA imaging in living cells, which is especially suitable for in situ amplified detection of lowly expressed endogenous analytes. The inherent synergistically accelerated recognition and hybridization features of CHA–HCR circuit contribute to the amplified detection of endogenous RNAs in living cells. The flexible and programmable nature of the homogeneous CHA–HCR system provides a versatile and robust toolbox for a wide range of research fields, such as in vivo bioimaging, clinical diagnosis and environmental monitoring.
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Affiliation(s)
- Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Chunxiao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education , College of Chemistry and Molecular Sciences , Wuhan University , 430072 Wuhan , China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
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