1
|
Yang R, Xie S, Zhou B, Guo M, Fan J, Su F, Ji Z, Chen Y, Li B. Postamplifying Cas12a Activation through Hybridization Chain Reaction-Triggered Fluorescent Nanocluster Formation for Ultrasensitive Nucleic Acid Detection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:9890-9899. [PMID: 38353672 DOI: 10.1021/acsami.3c18732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
CRISPR/Cas12a-based biosensing is advancing rapidly; however, achieving sensitive and cost-effective reporting of Cas12a activation remains a challenge. In response, we have developed a label-free system capable of postamplifying Cas12a activation by integrating hybridization chain reaction (HCR) and DNA-copper nanoclusters (DNA-CuNCs). The trans-cleavage of Cas12a triggers a silenced HCR, leading to the in situ assembly of fluorescent DNA-CuNCs, allowing for the turn-on reporting of Cas12a activation. Without preamplification, this assay can detect DNA with a detection limit of 5 fM. Furthermore, when coupled with preamplification, the system achieves exceptional sensitivity, detecting the monkeypox virus (MPXV) plasmid at 1 copy in human serum. In a MPXV pseudovirus-based validation test, the obtained results are in agreement with those obtained by qPCR, reinforcing the robustness of this method. Our study represents the first effort to manipulate DNA-CuNC formation on HCR for highly sensitive and cost-effective reporting of Cas12a, resulting in an efficient synthetic biology-enabled sensing platform for biosafety applications.
Collapse
Affiliation(s)
- Runlin Yang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Siying Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
- School of Public Health, Xiamen University, Xiamen 361102, China
| | - Bin Zhou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Mingming Guo
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Jun Fan
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Fengli Su
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Zhirun Ji
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Yue Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing 211166, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|
2
|
Ji Z, Zhou B, Shang Z, Liu S, Li X, Zhang X, Li B. Active CRISPR-Cas12a on Hydrophilic Metal-Organic Frameworks: A Nanobiocomposite with High Stability and Activity for Nucleic Acid Detection. Anal Chem 2023. [PMID: 37413791 DOI: 10.1021/acs.analchem.3c00400] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
CRISPR-Cas12a is an accurate and responsive biosensing technique, but its limited stability has restricted its widespread applications. To address this, we propose a strategy using metal-organic frameworks (MOFs) to protect Cas12a from harsh environments. After screening multiple candidate MOFs, it was found that hydrophilic MAF-7 is highly compatible with Cas12a, and the as-formed Cas12a-on-MAF-7 (COM) not only retains high enzymatic activity but also possesses excellent tolerance to heat, salt, and organic solvents. Further investigation showed that COM can serve as an analytical component for nucleic acid detection, resulting in an ultrasensitive assay for SARS-CoV-2 RNA detection with a detection limit of 1 copy. This is the first successful attempt to create an active Cas12a nanobiocomposite that functions as a biosensor without the need for shell deconstruction or enzyme release.
Collapse
Affiliation(s)
- Zhirun Ji
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bin Zhou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Zhaoyang Shang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Sirui Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xue Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|
3
|
Anbiaee G, Khoshbin Z, Zahraee H, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Exonuclease-based aptasensors: Promising for food safety and diagnostic aims. Talanta 2023; 259:124500. [PMID: 37001398 DOI: 10.1016/j.talanta.2023.124500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023]
Abstract
As of today's requirement, developing cost-effective smart sensing tools with ultrahigh sensitivity for food safety insurance is of special importance. For this purpose, aptamer-based biosensors (aptasensors) powered by the superiorities of the recycling signal amplification strategies have been expanded especially. Target recycling supported by enzymes is an appealing approach for implementing signal amplification. As the supreme biocatalyst enzymes, exonucleases can inaugurate signal improvement by involving a single target in a process would result in appreciable repeating cycles of the cleavage of the phosphodiester bonds between the building blocks of the nucleic acid strands, and also, their terminals. Although there are diverse substances for catalyzing amplification strategies, including nanoparticles, carbon-based nanocomposites, and quantum dots (QDs), exonucleases are of superiority over them by simplifying the amplification process with no need for the complicated pre-treatment processes. The outstanding selectivity and great sensitivity of the aptasensors tuned by amplification potency of exonucleases nominate them as the promising sensing tools for label-free, ease-of-use, cost-effective, and real-time diagnosis of diverse targets. Here, we summarize the achievements and perspectives in the scientific branch of aptasensor design for the qualitative monitoring of diverse targets by cooperation of exonucleases with the conspicuous potential for the signal amplification. Finally, some results are expressed to provide a comprehensive viewpoint for developing novel nuclease-based aptasensors in the future.
Collapse
Affiliation(s)
- Ghasem Anbiaee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
4
|
Zhao F, Wang P, Wang H, Liu S, Sohail M, Zhang X, Li B, Huang H. CRISPR/Cas12a-mediated ultrasensitive and on-site monkeypox viral testing. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2105-2113. [PMID: 37066613 DOI: 10.1039/d2ay01998a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spread of the monkeypox virus (MPXV) from Central and West Africa to previously non-endemic regions has caused a global panic. In this context, the rapid, specific, and ultrasensitive detection of MPXV is crucial to contain its spread, though such technology has seldom been reported. Herein, we proposed an MPXV assay combining recombinase-aided amplification (RAA) and CRISPR/Cas12a. This assay targeted the highly conserved MPXV F3L gene and demonstrates a low detection limit (LOD) of 101 copies per μL. By leveraging the high specificity nature of RAA and CRISPR/Cas12a, we rationally optimized probes and conditions to achieve high selectivity that differentiates MPXV from other orthopox viruses and current high-profile viruses. To facilitate on-site screening of potential MPXV carriers, a kit integrating lateral flow strips was developed, enabling naked-eye MPXV detection with a LOD of 104 copies per μL. Our RAA-Cas12a-MPXV assay was able to detect MPXV without the need for sophisticated operation and expensive equipment. We believe that this assay can be rapidly deployed in emerging viral outbreaks for on-site surveillance of MPXV.
Collapse
Affiliation(s)
- Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Haoxuan Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Sirui Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| |
Collapse
|
5
|
Ma X, Suo T, Zhao F, Shang Z, Chen Y, Wang P, Li B. Integrating CRISPR/Cas12a with strand displacement amplification for the ultrasensitive aptasensing of cadmium(II). Anal Bioanal Chem 2023; 415:2281-2289. [PMID: 36952025 DOI: 10.1007/s00216-023-04650-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/26/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
Cadmium ion (Cd(II)) is a pernicious environmental pollutant that has been shown to contaminate agricultural lands, accumulate through the food chain, and seriously threaten human health. At present, Cd(II) monitoring is dependent on centralized instruments, necessitating the development of rapid and on-site detection platforms. Against this backdrop, the present study reports on the development of a fluorometric aptasensor designed to target Cd(II), which is achieved through the integration of strand displacement amplification (SDA) and CRISPR/Cas12a. In the absence of Cd(II), the aptamer initiates SDA, resulting in the generation of a profusion of ssDNA that activates Cas12a, leading to a substantial increase in fluorescence output. Conversely, the presence of Cd(II) curtails the SDA efficiency, culminating in a significant reduction in fluorescence output. The proposed approach has been demonstrated to enable the selective detection of Cd(II) at concentrations of 60 pM, with the performance of the aptasensor validated in real water and rice samples. The proposed platform based on aptamer-target interaction holds immense promise as a signal-amplified and precise method for the detection of Cd(II) and has the potential to transform current hazard detection practices in food samples.
Collapse
Affiliation(s)
- Xiaochen Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing, 100101, China
| | - Tiying Suo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
- Nanjing Jiangbei New Area Biopharmaceutical Public Platform Co., Ltd., Nanjing, 211899, China
| | - Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Zhaoyang Shang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yue Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, 211166, China.
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| |
Collapse
|