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Reed MA, Gerasimova YV. Single-tube isothermal label-free fluorescent sensor for pathogen detection based on genetic signatures. Front Chem 2022; 10:951279. [PMID: 36118306 PMCID: PMC9475119 DOI: 10.3389/fchem.2022.951279] [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: 05/23/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
We report on a single-tube biosensor for real-time detection of bacterial pathogens with multiplex capabilities. The biosensor consists of two DNA probes, which bind to the complementary fragment of a bacterial RNA to form a three-way junction (3WJ) nucleic acid structure. One of the probes encodes a fluorescent light-up RNA aptamer under T7 promoter. It allows for generation of multiple aptamer copies due to elongation and transcription of the 3WJ structure in the presence of the complementary target. The aptamer coordinates and thereby enhances fluorescence of a cognate fluorogenic dye, allowing for fluorescent detection of the RNA target. Multiple aptamer copies can be produced from a single target-dependent 3WJ structure allowing for amplification and visual observation of the signal. The limit of detection depended on the assay time and was found to be 1.7 nM or 0.6 nM for 30-min or 60-min assay, respectively, when N-methylmesoporphyrin IX (NMM) was used as a fluorescent indicator. The sensor is excellent in analyzing folded RNA targets and differentiating between closely related sequences due to the multicomponent character of the target-interrogating probe. Response to unamplified samples of total bacterial RNA from Mycobacterium tuberculosis complex or Escherichia coli was observed with excellent selectivity within 30 min under isothermal conditions at 50°C in a one-tube one-step assay. Several bacterial species can be detected in multiplex by utilizing biosensors with the template strands encoding different light-up aptamers. The isothermal one-tube-one-step format of the assay and the possibility to monitor the signal visually makes it amenable to use in a point-of-care scenario.
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Xu R, Cheng Y, Li X, Zhang Z, Zhu M, Qi X, Chen L, Han L. Aptamer-based signal amplification strategies coupled with microchips for high-sensitivity bioanalytical applications: A review. Anal Chim Acta 2022; 1209:339893. [DOI: 10.1016/j.aca.2022.339893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023]
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Lee S, Kim H, Kim HY, Park HG. Target-induced transcription of a light-up RNA aptamer to construct a novel method for alkaline phosphatase assay. Chem Commun (Camb) 2021; 57:12341-12344. [PMID: 34735558 DOI: 10.1039/d1cc04787f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We herein developed a novel method for alkaline phosphatase (ALP) assay based on the target-induced transcription of a light-up RNA aptamer, consequently producing a highly enhanced fluorescence signal upon specifically binding to the corresponding dye. Using this strategy, we successfully determined the ALP activity down to 0.018 U L-1 (dynamic linear range of 0.04-4 U L-1) with excellent selectivity.
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Affiliation(s)
- Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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Woo J, Kim JH, Kim S, Park KS. Promoter engineering improves transcription efficiency in biomolecular assays. Chem Commun (Camb) 2021; 57:1619-1622. [PMID: 33458724 DOI: 10.1039/d0cc07797f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We identified a novel 12 bp promoter that significantly increased transcription efficiency. Unlike the standard 20 bp promoter, which contains both recognition and initiation regions, the new promoter contains only a recognition region and is more suitable for diagnostic applications due to its smaller size. This promoter effectively produced different light-up RNA aptamers via transcription. Moreover, we used the promoter to analyze RNase H activity and achieved a detection limit of 0.009 U mL-1, which was significantly better than that achieved via previous methods. We propose that the new promoter may serve as a key component in various diagnostic applications.
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Affiliation(s)
- Jisu Woo
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Guo Z, Qin Y, Chen P, Hu J, Zhou Y, Zhao X, Liu Z, Fei Y, Jiang X, Wu X. Hyperboloid-Drum Microdisk Laser Biosensors for Ultrasensitive Detection of Human IgG. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000239. [PMID: 32510822 DOI: 10.1002/smll.202000239] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 05/25/2023]
Abstract
Whispering gallery mode (WGM) microresonators have been used as optical sensors in fundamental research and practical applications. The majority of WGM sensors are passive resonators that require complex systems, thereby limiting their practicality. Active resonators enable the remote excitation and collection of WGM-modulated fluorescence spectra, without requiring complex systems, and can be used as alternatives to passive microresonators. This paper demonstrates an active microresonator, which is a microdisk laser in a hyperboloid-drum (HD) shape. The HD microdisk lasers are a combination of a rhodamine B-doped photoresist and a silica microdisk. These HD microdisk lasers can be utilized for the detection of label-free biomolecules. The biomolecule concentration can be as low as 1 ag mL-1 , whereas the theoretical detection limit of the biosensor for human IgG in phosphate buffer saline is 9 ag mL-1 (0.06 aM ). Additionally, the biosensors are able to detect biomolecules in an artificial serum, with a theoretical detection limit of 9 ag mL-1 (0.06 aM ). These results are approximately four orders of magnitude more sensitive than those for the typical active WGM biosensors. The proposed HD microdisk laser biosensors show enormous detection potential for biomarkers in protein secretions or body fluids.
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Affiliation(s)
- Zhihe Guo
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra Precision Optical Manufacturing, Fudan University, Shanghai, 200433, China
| | - Yingchun Qin
- National Laboratory of Solid State Microstructures and College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210093, China
| | - Peizong Chen
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, 200433, China
| | - Jinliang Hu
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra Precision Optical Manufacturing, Fudan University, Shanghai, 200433, China
| | - Yi Zhou
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra Precision Optical Manufacturing, Fudan University, Shanghai, 200433, China
| | - Xuyang Zhao
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra Precision Optical Manufacturing, Fudan University, Shanghai, 200433, China
| | - Zhiran Liu
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra Precision Optical Manufacturing, Fudan University, Shanghai, 200433, China
| | - Yiyan Fei
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra Precision Optical Manufacturing, Fudan University, Shanghai, 200433, China
| | - Xiaoshun Jiang
- National Laboratory of Solid State Microstructures and College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210093, China
| | - Xiang Wu
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra Precision Optical Manufacturing, Fudan University, Shanghai, 200433, China
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