1
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Zhang X, Li Z, Wang X, Hong L, Yin X, Zhang Y, Hu B, Zheng Q, Cao J. CRISPR/Cas12a integrated electrochemiluminescence biosensor for pufferfish authenticity detection based on NiCo 2O 4 NCs@Au as a coreaction accelerator. Food Chem 2024; 445:138781. [PMID: 38401312 DOI: 10.1016/j.foodchem.2024.138781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Meat adulteration has brought economic losses, health risks, and religious concerns, making it a pressing global issue. Herein, combining the high amplification efficiency of polymerase chain reaction (PCR) and the accurate recognition of CRISPR/Cas12, a sensitive and reliable electrochemiluminescence (ECL) biosensor was developed for the detection of pufferfish authenticity using NiCo2O4 NCs@Au-ABEI as nanoemitters. In the presence of target DNA, the trans-cleavage activity of CRISPR/Cas12a is activated upon specific recognition by crRNA, and then it cleaves dopamine-modified single stranded DNA (ssDNA-DA), triggering the ECL signal from the "off" to "on" state. However, without target DNA, the trans-cleavage activity of CRISPR/Cas12a is silenced. By rationally designing corresponding primers and crRNA, the biosensor was applied to specific identification of four species of pufferfish. Furthermore, as low as 0.1 % (w/w) adulterate pufferfish in mixture samples could be detected. Overall, this work provides a simple, low-cost and sensitive approach to trace pufferfish adulteration.
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Affiliation(s)
- Xiaobo Zhang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, School of Life Sciences, Dalian Minzu University, Dalian 116600, China
| | - Zhiru Li
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, School of Life Sciences, Dalian Minzu University, Dalian 116600, China
| | - Xiuwen Wang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, School of Life Sciences, Dalian Minzu University, Dalian 116600, China
| | - Lin Hong
- Dalian Inspection and Testing Certification Technical Service Center, Dalian 116021, China
| | - Xinying Yin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yan Zhang
- Standards and Quality Center of National Food and Strategic Reserves Administration, Beijing 100834, China
| | - Bing Hu
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, School of Life Sciences, Dalian Minzu University, Dalian 116600, China
| | - Qiuyue Zheng
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, School of Life Sciences, Dalian Minzu University, Dalian 116600, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, School of Life Sciences, Dalian Minzu University, Dalian 116600, China.
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2
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Hu J, Yu Y, Pan X, Yue Han, She X, Liu X, Zhang Q, Gai H, Zong C. Highly sensitive and specific detection of human papillomavirus type 16 using CRISPR/Cas12a assay coupled with an enhanced single nanoparticle dark-field microscopy imaging technique. Talanta 2024; 278:126449. [PMID: 38908140 DOI: 10.1016/j.talanta.2024.126449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
Human papillomavirus (HPV) is a prevalent sexually transmitted pathogen associated with cervical cancer. Detecting high-risk HPV (hr-HPV) infections is crucial for cervical cancer prevention, particularly in resource-limited settings. Here, we present a highly sensitive and specific sensor for HPV-16 detection based on CRISPR/Cas12a coupled with enhanced single nanoparticle dark-field microscopy (DFM) imaging techniques. Ag-Au satellites were assembled through the hybridization of AgNPs-based spherical nucleic acid (Ag-SNA) and AuNPs-based spherical nucleic acid (Au-SNA), and their disassembly upon target-mediated cleavage by the Cas12a protein was monitored using DFM for HPV-16 quantification. To enhance the cleavage efficiency and detection sensitivity, the composition of the ssDNA sequences on Ag-SNA and Au-SNA was optimized. Additionally, we explored using the SynSed technique (synergistic sedimentation of Brownian motion suppression and dehydration transfer) as an alternative particle transfer method in DFM imaging to traditional electrostatic deposition. This addresses the issue of inconsistent deposition efficiency of Ag-Au satellites and their disassembly due to their size and charge differences. The sensor achieved a remarkable limit of detection (LOD) of 10 fM, lowered by 9-fold compared to traditional electrostatic deposition methods. Clinical testing in DNA extractions from 10 human cervical swabs demonstrated significant response differences between the positive and negative samples. Our sensor offers a promising solution for sensitive and specific HPV-16 detection, with implications for cancer screening and management.
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Affiliation(s)
- Jiajia Hu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Yang Yu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Xiaoyan Pan
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Yue Han
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Xinyi She
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Xiaojun Liu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Qingquan Zhang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Hongwei Gai
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Chenghua Zong
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
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3
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He W, Li X, Li X, Guo M, Zhang M, Hu R, Li M, Ding S, Yan Y. Exploration of new ways for CRISPR/Cas12a activation: DNA hairpins without PAM and toehold and single strands containing DNA and RNA bases. J Biotechnol 2024; 391:99-105. [PMID: 38880387 DOI: 10.1016/j.jbiotec.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
The CRISPR/Cas12a system is emerging as a promising candidate for next-generation diagnostic biosensing platforms, with the discovery of new activation modes greatly expanding its applications. Here, we have identified two novel CRISPR/Cas12a system activation modes: PAM- and toehold-free DNA hairpins, and DNA-RNA hybrid strands. Utilizing a well-established real-time fluorescence method, we have demonstrated a strong correlation between DNA hairpin structures and Cas12a activation. Compared with previously reported activation modes involving single-stranded DNA and PAM-contained double-stranded DNA, the DNA hairpin activation way exhibits similar specificity and generality. Moreover, our findings indicate that increasing the number of RNA bases in DNA-RNA hybrid strands can decelerate the kinetics of Cas12a-triggered trans-cleavage of reporter probes. These newly discovered CRISPR/Cas12a activation ways hold significant potential for the development of high-performance biosensing strategies.
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Affiliation(s)
- Wen He
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinmin Li
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, PR China
| | - Minghui Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Mengxuan Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Ruiwei Hu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Menghan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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4
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Zhang D, Tian B, Ling Y, Ye L, Xiao M, Yuan K, Zhang X, Zheng G, Li X, Zheng J, Liao Y, Shu B, Gu B. CRISPR/Cas12a-Powered Amplification-Free RNA Diagnostics by Integrating T7 Exonuclease-Assisted Target Recycling and Split G-Quadruplex Catalytic Signal Output. Anal Chem 2024. [PMID: 38860917 DOI: 10.1021/acs.analchem.4c01800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Rapid and sensitive RNA detection is of great value in diverse areas, ranging from biomedical research to clinical diagnostics. Existing methods for RNA detection often rely on reverse transcription (RT) and DNA amplification or involve a time-consuming procedure and poor sensitivity. Herein, we proposed a CRISPR/Cas12a-enabled amplification-free assay for rapid, specific, and sensitive RNA diagnostics. This assay, which we termed T7/G4-CRISPR, involved the use of a T7-powered nucleic acid circuit to convert a single RNA target into numerous DNA activators via toehold-mediated strand displacement reaction and T7 exonuclease-mediated target recycling amplification, followed by activating Cas12a trans-cleavage of the linker strands inhibiting split G-Quadruplex (G4) assembly, thereby inducing fluorescence attenuation proportion to the input RNA target. We first performed step-by-step validation of the entire assay process and optimized the reaction parameters. Using the optimal conditions, T7/G4-CRISPR was capable of detecting as low as 3.6 pM target RNA, obtaining ∼100-fold improvement in sensitivity compared with the most direct Cas12a assays. Meanwhile, its excellent specificity could discriminate single nucleotide variants adjacent to the toehold region and allow species-specific pathogen identification. Furthermore, we applied it for analyzing bacterial 16S rRNA in 40 clinical urine samples, exhibiting a sensitivity of 90% and a specificity of 100% when validated by RT-quantitative PCR. Therefore, we envision that T7/G4-CRISPR will serve as a promising RNA sensing approach to expand the toolbox of CRISPR-based diagnostics.
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Affiliation(s)
- Decai Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou 510000, China
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Benshun Tian
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Yong Ling
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Long Ye
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Meng Xiao
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou 510000, China
| | - Kaixuan Yuan
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Xinqiang Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Guansheng Zheng
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Xinying Li
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Judun Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yuhui Liao
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bowen Shu
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bing Gu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou 510000, China
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5
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Tang X, Zhao S, Luo J, Wang B, Wu X, Deng R, Chang K, Chen M. Smart Stimuli-Responsive Spherical Nucleic Acids: Cutting-Edge Platforms for Biosensing, Bioimaging, and Therapeutics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310732. [PMID: 38299771 DOI: 10.1002/smll.202310732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/27/2023] [Indexed: 02/02/2024]
Abstract
Spherical nucleic acids (SNAs) with exceptional colloidal stability, multiple modularity, and programmability are excellent candidates to address common molecular delivery-related issues. Based on this, the higher targeting accuracy and enhanced controllability of stimuli-responsive SNAs render them precise nanoplatforms with inestimable prospects for diverse biomedical applications. Therefore, tailored diagnosis and treatment with stimuli-responsive SNAs may be a robust strategy to break through the bottlenecks associated with traditional nanocarriers. Various stimuli-responsive SNAs are engineered through the incorporation of multifunctional modifications to meet biomedical demands with the development of nucleic acid functionalization. This review provides a comprehensive overview of prominent research in this area and recent advancements in the utilization of stimuli-responsive SNAs in biosensing, bioimaging, and therapeutics. For each aspect, SNA nanoplatforms that exhibit responsive behavior to both internal stimuli (including sequence, enzyme, redox reactions, and pH) and external stimuli (such as light and temperature) are highlighted. This review is expected to offer inspiration and guidance strategies for the rational design and development of stimuli-responsive SNAs in the field of biomedicine.
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Affiliation(s)
- Xiaoqi Tang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Jie Luo
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Binpan Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Xianlan Wu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Ruijia Deng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
- College of Pharmacy and Laboratory Medicine, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
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6
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Liu Q, Yang M, Zhang H, Ma W, Fu X, Li H, Gao S. A colorimetric tandem combination of CRISPR/Cas12a with dual functional hybridization chain reaction for ultra-sensitive detection of Mycobacterium bovis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3220-3230. [PMID: 38717230 DOI: 10.1039/d3ay02200e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Tuberculosis caused by Mycobacterium bovis poses a global infectious threat to humans and animals. Therefore, there is an urgent need to develop a sensitive, precise, and easy-to-readout strategy. Here, a novel tandem combination of a CRISPR/Cas12a system with dual HCR (denoted as CRISPR/Cas12a-D-HCR) was constructed for detecting Mycobacterium bovis. Based on the efficient trans-cleavage activity of the active CRISPR/Cas12a system, tandem-dsDNA with PAM sites was established using two flexible hairpins, providing multiple binding sites with CRISPR/Cas12a for further amplification. Furthermore, the activation of Cas12a initiated the second hybridization chain reaction (HCR), which integrated complete G-quadruplex sequences to assemble the hemin/G-quadruplex DNAzyme. With the addition of H2O2 and ABTS, a colorimetric signal readout strategy was achieved. Consequently, CRISPR/Cas12a-D-HCR achieved a satisfactory detection linear range from 20 aM to 50 fM, and the limit of detection was as low as 2.75 aM with single mismatched recognition capability, demonstrating good discrimination of different bacterial species. Notably, the practical application performance was verified via the standard addition method, with the recovery ranging from 96.0% to 105.2% and the relative standard deviations (RSD) ranging from 0.95% to 6.45%. The proposed CRISPR/Cas12a-D-HCR sensing system served as a promising application for accurate detection in food safety and agricultural fields.
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Affiliation(s)
- Qiong Liu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Mei Yang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - He Zhang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Wenjie Ma
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Xin Fu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Huiqing Li
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Sainan Gao
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
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7
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Lei X, Cao S, Liu T, Wu Y, Yu S. Non-canonical CRISPR/Cas12a-based technology: A novel horizon for biosensing in nucleic acid detection. Talanta 2024; 271:125663. [PMID: 38232570 DOI: 10.1016/j.talanta.2024.125663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Nucleic acids are essential biomarkers in molecular diagnostics. The CRISPR/Cas system has been widely used for nucleic acid detection. Moreover, canonical CRISPR/Cas12a based biosensors can specifically recognize and cleave target DNA, as well as single-strand DNA serving as reporter probe, which have become a super star in recent years in the field of nucleic acid detection due to its high specificity, universal programmability and simple operation. However, canonical CRISPR/Cas12a based biosensors are hard to meet the requirements of higher sensitivity, higher specificity, higher efficiency, larger target scope, easier operation, multiplexing, low cost and diversified signal reading. Then, advanced non-canonical CRISPR/Cas12a based biosensors emerge. In this review, applications of non-canonical CRISPR/Cas12a-based biosensors in nucleic acid detection are summarized. And the principles, peculiarities, performances and perspectives of these non-canonical CRISPR/Cas12a based biosensors are also discussed.
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Affiliation(s)
- Xueying Lei
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Shengnan Cao
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Tao Liu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Yongjun Wu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Songcheng Yu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China.
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8
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Gong W, Zhang Y, Chen Y, Zhao X, Wang S. A dual amplified gold nanoparticle-based biosensor for ultrasensitive and selective detection of fibrin. LUMINESCENCE 2024; 39:e4764. [PMID: 38684508 DOI: 10.1002/bio.4764] [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: 02/16/2024] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Ultrasensitive, selective, and non-invasive detection of fibrin in human serum is critical for disease diagnosis. So far, the development of high-performance and ultrasensitive biosensors maintains core challenges for biosensing. Herein, we designed a novel ribbon nanoprobe for ultrasensitive detection of fibrin. The probe contains gold nanoparticles (AuNPs) that can not only link with homing peptide Cys-Arg-Glu-Lys-Ala (CREKA) to recognize fibrin but also carry long DNA belts to form G-quadruplex-based DNAzyme, catalyzing the chemiluminescence of luminol-hydrogen peroxide (H2O2) reaction. Combined with the second amplification procedure of rolling circle amplification (RCA), the assay exhibits excellent sensitivity with a detection limit of 0.04 fmol L-1 fibrin based on the 3-sigma. Furthermore, the biosensor shows high specificity on fibrin in samples because the structure of antibody-fibrin-homing peptide was employed to double recognize fibrin. Altogether, the simple and inexpensive approach may present a great potential for reliable detection of biomarkers.
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Affiliation(s)
- Wenyue Gong
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Yuanfu Zhang
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Yawei Chen
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Xue Zhao
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Shuhao Wang
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
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9
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Marpaung DSS, Sinaga AOY, Damayanti D, Taharuddin T. Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation. ANAL SCI 2024:10.1007/s44211-024-00566-y. [PMID: 38607600 DOI: 10.1007/s44211-024-00566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.
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Affiliation(s)
- David Septian Sumanto Marpaung
- Department of Biosystems Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia.
| | - Ayu Oshin Yap Sinaga
- Department of Biology, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Damayanti Damayanti
- Department of Chemical Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Taharuddin Taharuddin
- Department of Chemical Engineering, University of Lampung, Jl. Prof. Dr. Ir. Sumantri Brojonegoro No.1, Gedong Meneng, Kec. Rajabasa, Kota Bandar Lampung, Lampung, 35141, Indonesia
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10
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Tian Z, Yan H, Zeng Y. Solid-Phase Extraction and Enhanced Amplification-Free Detection of Pathogens Integrated by Multifunctional CRISPR-Cas12a. ACS APPLIED MATERIALS & INTERFACES 2024; 16:14445-14456. [PMID: 38472096 DOI: 10.1021/acsami.3c17039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Public healthcare demands effective and pragmatic diagnostic tools to address the escalating challenges in infection management in resource-limited areas. Recent advances in clustered regularly interspaced short palindromic repeat (CRISPR)-based biosensing promise the development of next-generation tools for disease diagnostics, including point-of-care (POC) testing for infectious diseases. The currently prevailing strategy of developing CRISPR/Cas-based diagnostics exploits only the target identification and trans-cleavage activity of a CRISPR-Cas12a/Cas13a system to provide diagnostic results, and they need to be combined with an additional preamplification reaction to enhance sensitivity. In contrast to this dual-function strategy, here, we present a new approach that collaboratively integrates the triple functions of CRISPR-Cas12a: target identification, sequence-specific enrichment, and signal generation. With this approach, we develop a nucleic acid assay termed Solid-Phase Extraction and Enhanced Detection Assay integrated by CRISPR-Cas12a (SPEEDi-CRISPR) that negates the need for preamplification but significantly improves the detection of limit (LOD) from the pM to fM level. Specifically, using Cas12a-coated magnetic beads, this assay combines efficient solid-phase extraction and enrichment of DNA targets enabled by the sequence-specific affinity of CRISPR-Cas12a with fluorogenic detection by activated Cas12a on beads. SPEEDi-CRISPR, for the first time, leverages the possibility of employing CRISPR/Cas12a in nucleic acid extraction and integrates the ability of both enrichment and detection of CRISPR/Cas into a single platform. Our proof-of-concept studies revealed that the SPEEDi-CRISPR assay has great specificity to distinguish HPV-18 from HPV-16, and Parvovirus B19, in addition to being able to detect HPV-18 at a concentration as low as 2.3 fM in 100 min and 4.7 fM in 60 min. Furthermore, we proved that this assay can be coupled with two point-of-care testing strategies: the smartphone-based fluorescence detector and the lateral flow assay. Overall, these results suggested that our assay could pave a new way for developing CRISPR diagnostics.
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Affiliation(s)
- Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Health Cancer Center, Gainesville, Florida 32611, United States
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11
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Ma L, Xie L, Wu Q, Yang L, Zhou Y, Cui Y, Zhang Y, Jiao B, Wang C, He Y. Integrating CRISPR-Cas12a and rolling circle-amplified G-quadruplex for naked-eye fluorescent "off-on" detection of citrus Alternaria. Int J Biol Macromol 2024; 262:129983. [PMID: 38354935 DOI: 10.1016/j.ijbiomac.2024.129983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/26/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
Alternaria is a plant pathogen that spreads globally and is prone to causing citrus brown spot disease and metabolizing mycotoxins, thus seriously hindering the development of this economic crop industry. Herein, a "label-free" and "turn on" visual fluorescent assay for citrus Alternaria based on CRISPR-Cas12a and rolling circle amplification (RCA) was described. Using ssDNA complementary to RCA primer as a trans-cleavage substrate for CRISPR-Cas12a, the two systems of CRISPR-Cas12a and RCA-amplified G-quadruplex were skillfully integrated. By using a portable light source for excitation, the positive sample produced obvious red fluorescence, while the negative sample remained almost colorless, making them easy to differentiate with the naked eye. In addition, the specificity was demonstrated by distinguishing Alternaria from other citrus disease related pathogens. Moreover, the practicality was verified by analyzing cultured Alternaria and Alternaria in actual citrus leaf and fruit samples. Therefore, this method may contribute to the on-site diagnosis of Alternaria.
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Affiliation(s)
- Lanrui Ma
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Longyingzi Xie
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Qi Wu
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Lu Yang
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Yan Zhou
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Yongliang Cui
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Yaohai Zhang
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Bining Jiao
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Chengqiu Wang
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China.
| | - Yue He
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China.
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12
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Yin Y, Wen J, Wen M, Fu X, Ke G, Zhang XB. The design strategies for CRISPR-based biosensing: Target recognition, signal conversion, and signal amplification. Biosens Bioelectron 2024; 246:115839. [PMID: 38042054 DOI: 10.1016/j.bios.2023.115839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/27/2023] [Accepted: 11/11/2023] [Indexed: 12/04/2023]
Abstract
Rapid, sensitive and selective biosensing is highly important for analyzing biological targets and dynamic physiological processes in cells and living organisms. As an emerging tool, clustered regularly interspaced short palindromic repeats (CRISPR) system is featured with excellent complementary-dependent cleavage and efficient trans-cleavage ability. These merits enable CRISPR system to improve the specificity, sensitivity, and speed for molecular detection. Herein, the structures and functions of several CRISPR proteins for biosensing are summarized in depth. Moreover, the strategies of target recognition, signal conversion, and signal amplification for CRISPR-based biosensing were highlighted from the perspective of biosensor design principles. The state-of-art applications and recent advances of CRISPR system are then outlined, with emphasis on their fluorescent, electrochemical, colorimetric, and applications in POCT technology. Finally, the current challenges and future prospects of this frontier research area are discussed.
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Affiliation(s)
- Yao Yin
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jialin Wen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Mei Wen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiaoyi Fu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Guoliang Ke
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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13
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Fu X, Sun J, Yu B, Ye Y, Sheng L, Ji J, Zheng J, Fan M, Shao J, Sun X. Investigating enzyme kinetics and fluorescence sensing strategy of CRISPR/Cas12a for foodborne pathogenic bacteria. Anal Chim Acta 2024; 1290:342203. [PMID: 38246741 DOI: 10.1016/j.aca.2024.342203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
Foodborne pathogenic bacteria are widespread in various foods, whose cross-contamination and re-contamination are critical influences on food safety. Rapid, accurate, and sensitive detection of foodborne pathogenic bacteria remains a topic of concern. CRISPR/Cas12a can recognize double-stranded DNA directly, showing great potential in nucleic acid detection. However, few studies have investigated the cleavage properties of CRISPR/Cas12a. In this study, the trans-cleavage properties of LbCas12a and AsCas12a were investigated to construct the detection methods for foodborne pathogenic bacteria. The highly sensitive fluorescent strategies for foodborne pathogens were constructed by analyzing the cleavage rates and properties of substrates at different substrate concentrations. Cas12a was activated in the presence of foodborne pathogenic target sequence was present, resulting in the cleavage of a single-stranded reporter ssDNA co-labelled by fluorescein quencher and fluorescein. The sensitivity and specificity of the Cas12a fluorescent strategy was investigated with Salmonella and Staphylococcus aureus as examples. The results showed that AsCas12a was slightly more capable of trans-cleavage than LbCas12a. The detection limits of AsCas12a for Salmonella and Staphylococcus aureus were 24.9 CFU mL-1 and 1.50 CFU mL-1, respectively. In all the seven bacteria, Staphylococcus aureus and Salmonella were accurately discriminated. The study provided a basis for constructing and improving the CRISPR/Cas12a fluorescence strategies. The AsCas12a-based detection strategy is expected to be a promising method for field detection.
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Affiliation(s)
- XuRan Fu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - JiaDi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Bingqian Yu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Yongli Ye
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Lina Sheng
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jian Ji
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jiayu Zheng
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Minghong Fan
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Jingdong Shao
- Comprehensive Technology Center of Zhangjiagang Customs, Zhangjiagang, Jiangsu, 215600, PR China
| | - XiuLan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
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14
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Li Y, Cai M, Zhang W, Liu Y, Yuan X, Han N, Li J, Jin S, Ding C. Cas12a-based direct visualization of nanoparticle-stabilized fluorescence signal for multiplex detection of DNA methylation biomarkers. Biosens Bioelectron 2024; 244:115810. [PMID: 37924654 DOI: 10.1016/j.bios.2023.115810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
The CRISPR-Cas12a RNA-guided complexes hold immense promise for nucleic acid detection. However, limitations arise from their specificity in detecting off-targets and the stability of the signal molecules. Here, we have developed a platform that integrates multiplex amplification and nanomolecular-reporting signals, allowing us to detect various clinically relevant nucleic acid targets with enhanced stability, sensitivity, and visual interpretation. Through the electrostatic co-assembly of the Oligo reporter with oppositely charged nanoparticles, we observed a significant enhancement in its stability in low-pollution environments, reaching up to a threefold increase compared to the original version. Additionally, the fluorescence efficiency was expanded by three orders of magnitude, broadening the detection range considerably. Utilizing a multiplex strategy, this assay can accomplish simultaneous detection of multiple targets and single-point indication detection of nine specific targets. This significant advancement heightened the sensitivity of disease screening and improved the accuracy of diagnosing disease-related changes. We tested this assay in a colorectal cancer model, demonstrating that it can identify DNA methylation features at the aM-level within 40-60 min. Validation using clinical samples yielded consistent results with qPCR and bisulfite sequencing, affirming the assay's reliability and potential for clinical applications.
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Affiliation(s)
- Yu Li
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Miaomiao Cai
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Wenwen Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Ying Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaoqing Yuan
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Na Han
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jing Li
- Yinchuan Hospital of Traditional Chinese Medicine, Ningxia, 750001, China
| | - Shengnan Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chunming Ding
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
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15
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Li Y, Liu Y, Tang X, Qiao J, Kou J, Man S, Zhu L, Ma L. CRISPR/Cas-Powered Amplification-Free Detection of Nucleic Acids: Current State of the Art, Challenges, and Futuristic Perspectives. ACS Sens 2023; 8:4420-4441. [PMID: 37978935 DOI: 10.1021/acssensors.3c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
CRISPR/Cas system is becoming an increasingly influential technology that has been repositioned in nucleic acid detection. A preamplification step is usually required to improve the sensitivity of CRISPR/Cas-based detection. The striking biological features of CRISPR/Cas, including programmability, high sensitivity and sequence specificity, and single-base resolution. More strikingly, the target-activated trans-cleavage could act as a biocatalytic signal transductor and amplifier, thereby empowering it to potentially perform nucleic acid detection without a preamplification step. The reports of such work are on the rise, which is not only scientifically significant but also promising for futuristic end-user applications. This review started with the introduction of the detection methods of nucleic acids and the CRISPR/Cas-based diagnostics (CRISPR-Dx). Next, we objectively discussed the pros and cons of preamplification steps for CRISPR-Dx. We then illustrated and highlighted the recently developed strategies for CRISPR/Cas-powered amplification-free detection that can be realized through the uses of ultralocalized reactors, cascade reactions, ultrasensitive detection systems, or others. Lastly, the challenges and futuristic perspectives were proposed. It can be expected that this work not only makes the researchers better understand the current strategies for this emerging field, but also provides insight for designing novel CRISPR-Dx without a preamplification step to win practicable use in the near future.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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16
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Jiang Y, Qian X, Zheng M, Deng K, Li C. Enhancement and inactivation effect of CRISPR/Cas12a via extending hairpin activators for detection of transcription factors. Mikrochim Acta 2023; 191:43. [PMID: 38114763 DOI: 10.1007/s00604-023-06123-0] [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: 07/24/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023]
Abstract
An enhancement effect for the activation of CRISPR/Cas12a (CRISPR = clustered regularly interspaced short palindromic repeats; Cas = CRISPR-associated) was discovered. That was, a hairpin model with dangling 5' end complementary to crRNA (CRISPR RNA) greatly improved the activity of CRISPR/Cas12a after extention of two random sequences. But, the corresponding intact hairpin without PAM (protospacer adjacent motif) or suboptimal PAM sequences was completely inactive to CRISPR/Cas12a because of the superhigh stability of intact hairpin. According to the finding, a CRISPR/Cas12a-based strategy coupled with a signal reported system was designed for transcription factors detection. By using mono-labeled ssDNA (single-stranded DNA) as reporter and two newly synthesized N-C (nitrogen-doped carbon) nanosheets as scavenger to eliminate the fluorescent background, the strategy realized the detection of NF-ĸB p50 (p50 subunit of nuclear factor kappa-B) with a linear detection range of 0.8 - 2000.0 pM and a LOD of 0.5 pM. The discovery of "enhancement and inactivation effect" not only deepened insight into CRISPR/Cas12a but also broadened the practical application of CRISPR/Cas systems for the molecular detection and disease diagnostics.
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Affiliation(s)
- Yu Jiang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
- Hunan Province College Key Laboratory of Molecular Design and Green Chemistry, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Xinmei Qian
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
- Hunan Province College Key Laboratory of Molecular Design and Green Chemistry, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Mingyu Zheng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
| | - Keqin Deng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China.
| | - Chunxiang Li
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China.
- Hunan Province College Key Laboratory of Molecular Design and Green Chemistry, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China.
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17
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Wang C, Xie Y, Song X, Chao Z, Wu K, Fang Y, Zhao H, Ju H, Liu Y. A NIR Programmable In Vivo miRNA Magnifier for NIR-II Imaging of Early Stage Cancer. Angew Chem Int Ed Engl 2023; 62:e202312665. [PMID: 37903741 DOI: 10.1002/anie.202312665] [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: 08/28/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Aberrant expressions of biomolecules occur much earlier than tumor visualized size and morphology change, but their common measurement strategies such as biopsy suffer from invasive sampling process. In vivo imaging of slight biomolecule expression difference is urgently needed for early cancer detection. Fluorescence of rare earth nanoparticles (RENPs) in second near-infrared (NIR-II) region makes them appropriate tool for in vivo imaging. However, the incapacity to couple with signal amplification strategies, especially programmable signal amplification strategies, limited their application in lowly expressed biomarkers imaging. Here we develop a 980/808 nm NIR programmed in vivo microRNAs (miRNAs) magnifier by conjugating activatable DNAzyme walker set to RENPs, which achieves more effective NIR-II imaging of early stage tumor than size monitoring imaging technique. Dye FD1080 (FD1080) modified substrate DNA quenches NIR-II downconversion emission of RENPs under 808 nm excitation. The miRNA recognition region in DNAzyme walker is sealed by a photo-cleavable strand to avoid "false positive" signal in systemic circulation. Upconversion emission of RENPs under 980 nm irradiation activates DNAzyme walker for miRNA recognition and amplifies NIR-II fluorescence recovery of RENPs via DNAzyme catalytic reaction to achieve in vivo miRNA imaging. This strategy demonstrates good application potential in the field of early cancer detection.
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Affiliation(s)
- Caixia Wang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuxin Xie
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xuefang Song
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zhicong Chao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Kun Wu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hongxia Zhao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
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18
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Li T, Cheng N. Sensitive and Portable Signal Readout Strategies Boost Point-of-Care CRISPR/Cas12a Biosensors. ACS Sens 2023; 8:3988-4007. [PMID: 37870387 DOI: 10.1021/acssensors.3c01338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Point-of-care (POC) detection is getting more and more attention in many fields due to its accuracy and on-site test property. The CRISPR/Cas12a system is endowed with excellent sensitivity, target identification specificity, and signal amplification ability in biosensing because of its unique trans-cleavage ability. As a result, a lot of research has been made to develop CRISPR/Cas12a-based biosensors. In this review, we focused on signal readout strategies and summarized recent sensitivity-improving strategies in fluorescence, colorimetric, and electrochemical signaling. Then we introduced novel portability-improving strategies based on lateral flow assays (LFAs), microfluidic chips, simplified instruments, and one-pot design. In the end, we also provide our outlook for the future development of CRISPR/Cas12a biosensors.
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Affiliation(s)
- Tong Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Nan Cheng
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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19
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Chen HR, Zhang S, Chen T, Yang WG, Su ML, Fu GY, Yi WJ, Yuan R, Xu SC, Liang WB. Ultrasensitive quantitation of Paraquat based on a small molecule-induced dual-cycle amplification strategy. Biosens Bioelectron 2023; 240:115640. [PMID: 37651947 DOI: 10.1016/j.bios.2023.115640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Paraquat (PQ) is a typical biotoxic small molecule. Knowledge of how to directly introduce it into cyclic amplification rather than transform it into a secondary target is lacking in current analytical methods. Considering the urgent need for trace pesticide residue detection and the inherent defects of small molecule analysis, a CRISPR/Cas12a-driven small molecule-induced dual-cycle strategy was developed based on the immune competition method. The key to signal amplification is the mutual activation and acceleration between Cycle 1 triggered by the small molecule and Cycle 2 driven by CRISPR/Cas12a. Impressively, small molecules have been successfully incorporated into the dual-cycle strategy, which achieves a low detection limit (3.1 pg/mL) and a wide linear range (from 10 pg/mL to 50 μg/mL). Moreover, the designed biosensor was successfully employed to evaluate the PQ residual level in real samples and showed effective implementation for the bioanalysis of small molecule targets and pesticide residue-related food safety.
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Affiliation(s)
- Hao-Ran Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Shun Zhang
- Center of Laboratory Medicine, Chongqing Prevention and Treatment Center for Occupational Diseases, Chongqing Key Laboratory of Prevention and Treatment for Occupational Diseases and Poisoning, Chongqing, 400060, PR China; Zybio Inc., Chongqing, 400039, PR China
| | - Tao Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Wei-Guo Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ming-Li Su
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Guan-Yan Fu
- Center of Laboratory Medicine, Chongqing Prevention and Treatment Center for Occupational Diseases, Chongqing Key Laboratory of Prevention and Treatment for Occupational Diseases and Poisoning, Chongqing, 400060, PR China
| | | | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Shang-Cheng Xu
- Center of Laboratory Medicine, Chongqing Prevention and Treatment Center for Occupational Diseases, Chongqing Key Laboratory of Prevention and Treatment for Occupational Diseases and Poisoning, Chongqing, 400060, PR China.
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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20
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Yin Y, Xie W, Xiong M, Gao Y, Liu Q, Han D, Ke G, Zhang XB. FINDER: A Fluidly Confined CRISPR-Based DNA Reporter on Living Cell Membranes for Rapid and Sensitive Cancer Cell Identification. Angew Chem Int Ed Engl 2023; 62:e202309837. [PMID: 37710395 DOI: 10.1002/anie.202309837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
The accurate, rapid, and sensitive identification of cancer cells in complex physiological environments is significant in biological studies, personalized medicine, and biomedical engineering. Inspired by the naturally confined enzymes on fluid cell membranes, a fluidly confined CRISPR-based DNA reporter (FINDER) was developed on living cell membranes, which was successfully applied for rapid and sensitive cancer cell identification in clinical blood samples. Benefiting from the spatial confinement effect for improved local concentration, and membrane fluidity for higher collision efficiency, the activity of CRISPR-Cas12a was, for the first time, found to be significantly enhanced on living cell membranes. This new phenomenon was then combined with multiple aptamer-based DNA logic gate for cell recognition, thus a FINDER system capable of accurate, rapid and sensitive cancer cell identification was constructed. The FINDER rapidly identified target cells in only 20 min, and achieved over 80 % recognition efficiency with only 0.1 % of target cells presented in clinical blood samples, indicating its potential application in biological studies, personalized medicine, and biomedical engineering.
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Affiliation(s)
- Yao Yin
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo / Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Wei Xie
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo / Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Mengyi Xiong
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo / Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Yingying Gao
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo / Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Qin Liu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo / Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Da Han
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo / Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Xiao-Bing Zhang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo / Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
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21
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Alon DM, Mittelman K, Stibbe E, Countryman S, Stodieck L, Doraisingam S, Leal Martin DM, Hamo ER, Pines G, Burstein D. CRISPR-based genetic diagnostics in microgravity. Biosens Bioelectron 2023; 237:115479. [PMID: 37459685 DOI: 10.1016/j.bios.2023.115479] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 08/13/2023]
Abstract
Monitoring astronauts' health during space missions poses many challenges, including rapid assessment of crew health conditions. Sensitive genetic diagnostics are crucial for examining crew members and the spacecraft environment. CRISPR-Cas12a, coupled with isothermal amplification, has proven to be a promising biosensing system for rapid, on-site detection of genomic targets. However, the efficiency and sensitivity of CRISPR-based diagnostics have never been tested in microgravity. We tested the use of recombinase polymerase amplification (RPA) coupled with the collateral cleavage activity of Cas12a for genetic diagnostics onboard the International Space Station. We explored the detection sensitivity of amplified and unamplified target DNA. By coupling RPA with Cas12a, we identified targets in attomolar concentrations. We further assessed the reactions' stability following long-term storage. Our results demonstrate that CRISPR-based detection is a powerful tool for on-site genetic diagnostics in microgravity, and can be further utilized for long-term space endeavors to improve astronauts' health and well-being.
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Affiliation(s)
- Dan Mark Alon
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv, 6997801, Israel; Department of Entomology, Agricultural Research Organization - the Volcani Center, 68 HaMaccabim Rd, Rishon LeZion, 7505101, Israel
| | - Karin Mittelman
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Eytan Stibbe
- The Ramon Foundation, Kaplan 1, Tel Aviv, 6473402, Israel
| | | | - Louis Stodieck
- BioServe Space Technologies, University of Colorado Boulder, CO, 80309, USA
| | | | | | | | - Gur Pines
- Department of Entomology, Agricultural Research Organization - the Volcani Center, 68 HaMaccabim Rd, Rishon LeZion, 7505101, Israel.
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv, 6997801, Israel.
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22
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Yang F, Li S, Bi X, Yuan R, Xiang Y. Multicolor-Encoded DNA Framework Enables Specific and Amplified In Situ Detection of the Mitochondrial Apoptotic Signaling Pathway. Anal Chem 2023; 95:12514-12520. [PMID: 37553880 DOI: 10.1021/acs.analchem.3c02462] [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: 08/10/2023]
Abstract
Monitoring the molecular activation networks of cellular processes through fluorescence imaging to accurately elucidate the signaling pathways of mitochondrial apoptosis and the regulation of upstream and downstream molecules remains a current major challenge. In this work, a multicolor-encoded tetrahedral DNA framework (meTDF) carrying two pairs of catalytic hairpins is synthesized to monitor the intracellular upstream manganese superoxide dismutase (MnSOD) mRNA and the downstream cytochrome c (Cyt c) molecules for specific and sensitive detection of the mitochondrial apoptotic signaling pathway. These two types of molecules can trigger catalytic hairpin assembly (CHA) reactions with accelerated reaction kinetics for the hairpin pairs confined on meTDF to show highly amplified fluorescence for sensitive and simultaneous detection of MnSOD mRNA and Cyt c with detection limits of 3.7 pM and 0.23 nM in vitro, respectively. Moreover, the high stability and biocompatibility of the designed meTDF can facilitate efficient delivery of the probes into cells to monitor intracellular MnSOD mRNA and Cyt c for specific detection of the mitochondrial apoptosis pathway regulated by different drugs. With the successful demonstration of their robust capability, the meTDF nanoprobes can thus open new opportunities for detecting cell apoptotic mechanisms for studying the corresponding apoptotic signaling pathways and for screening potential therapeutic drugs.
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Affiliation(s)
- Fang Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Shunmei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xin Bi
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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23
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Ivanov AV, Safenkova IV, Zherdev AV, Wan Y, Dzantiev BB. Comparison of Single-Stranded DNA Probes Conjugated with Magnetic Particles for Trans-Cleavage in Cas12a-Based Biosensors. BIOSENSORS 2023; 13:700. [PMID: 37504099 PMCID: PMC10376970 DOI: 10.3390/bios13070700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Biosensors based on endonuclease Cas12 provide high specificity in pathogen detection. Sensitive detection using Cas12-based assays can be achieved using trans-cleaved DNA probes attached to simply separated carriers, such as magnetic particles (MPs). The aim of this work was to compare polyA, polyC, and polyT single-stranded (ss) DNA with different lengths (from 10 to 145 nt) as trans-target probes were immobilized on streptavidin-covered MPs. Each ssDNA probe was labeled using fluorescein (5') and biotin (3'). To compare the probes, we used guide RNAs that were programmed for the recognition of two bacterial pathogens: Dickeya solani (causing blackleg and soft rot) and Erwinia amylovora (causing fire blight). The Cas12 was activated by targeting double-stranded DNA fragments of D. solani or E. amylovora and cleaved the MP-ssDNA conjugates. The considered probes demonstrated basically different dependencies in terms of cleavage efficiency. PolyC was the most effective probe when compared to polyA or polyT probes of the same length. The minimal acceptable length for the cleavage follows the row: polyC < polyT < polyA. The efficiencies of polyC and polyT probes with optimal length were proven for the DNA targets' detection of D. solani and E. amylovora. The regularities found can be used in Cas12a-based detection of viruses, bacteria, and other DNA/RNA-containing analytes.
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Affiliation(s)
- Aleksandr V Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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24
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Fu R, Xianyu Y. Gold Nanomaterials-Implemented CRISPR-Cas Systems for Biosensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300057. [PMID: 36840654 DOI: 10.1002/smll.202300057] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/04/2023] [Indexed: 05/25/2023]
Abstract
Due to their superiority in the simple design and precise targeting, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have attracted significant interest for biosensing. On the one hand, CRISPR-Cas systems have the capacity to precisely recognize and cleave specific DNA and RNA sequences. On the other hand, CRISPR-Cas systems such as orthologs of Cas9, Cas12, and Cas13 exhibit cis-cleavage or trans-cleavage activities after recognizing the target sequence. Owing to the cleavage activities, CRISPR-Cas systems can be designed for biosensing by degrading tagged nucleic acids to produce detectable signals. To meet the requirements of point-of-care detection and versatile signal readouts, gold nanomaterials with excellent properties such as high extinction coefficients, easy surface functionalization, and biocompatibility are implemented in CRISPR-Cas-based biosensors. In combination with gold nanomaterials such as gold nanoparticles, gold nanorods, and gold nanostars, great efforts are devoted to fabricating CRISPR-Cas-based biosensors for the detection of diverse targets. This review focuses on the current advances in gold nanomaterials-implemented CRISPR-Cas-based biosensors, particularly the working mechanism and the performance of these biosensors. CRISPR-Cas systems, including CRISPR-Cas9, CRISPR-Cas12a, and CRISPR-Cas13a are discussed and highlighted. Meanwhile, prospects and challenges are also discussed in the design of biosensing strategies based on gold nanomaterials and CRISPR-Cas systems.
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Affiliation(s)
- Ruijie Fu
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yunlei Xianyu
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P. R. China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, P. R. China
- Ningbo Research Institute, Zhejiang University, Ningbo, Zhejiang, 315100, P. R. China
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25
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Tian Z, Yan H, Zeng Y. Solid-Phase Extraction and Enhanced Amplification-Free Detection of Pathogens Integrated by Dual-Functional CRISPR-Cas12a. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.28.23289279. [PMID: 37162995 PMCID: PMC10168481 DOI: 10.1101/2023.04.28.23289279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Public healthcare demands effective and pragmatic diagnostic tools to address the escalating challenges in infection management in resource-limited areas. Recent advance in CRISPR-based biosensing promises the development of next-generation tools for disease diagnostics, including point-of-care (POC) testing for infectious diseases. Currently prevailing strategy of developing CRISPR assays exploits only the non-specific trans-cleavage function of a CRISPR-Cas12a/Cas13a system for detection and combines it with an additional pre-amplification reaction to enhance the sensitivity. In contrast to this single-function strategy, here we present a new approach that collaboratively integrates the dual functions of CRISPR-Cas12a: sequence-specific binding and trans-cleavage activity. With this approach, we developed a POC nucleic acid assay termed Solid-Phase Extraction and Enhanced Detection assay Integrated by CRISPR-Cas12a (SPEEDi-CRISPR) that negates the need for preamplification but significantly improves the detection of limit (LOD) from the pM to fM level. Specifically, using Cas12a-coated magnetic beads, this assay combines efficient solid-phase extraction and enrichment of DNA targets enabled by the sequence-specific affinity of CRISPR-Cas12a with the fluorogenic detection by the activated Cas12a on beads. Our proof-of-concept study demonstrated that the SPEEDi-CRISPR assay affords an improved detection sensitivity for human papillomavirus (HPV)-18 with a LOD of 2.3 fM and excellent specificity to discriminate HPV-18 from HPV-16, Parvovirus B19, and scramble HPV-18. Furthermore, this robust assay was readily coupled with a portable smartphone-based fluorescence detector and a lateral flow assay for quantitative detection and visualized readout, respectively. Overall, these results should suggest that our dual-function strategy could pave a new way for developing the next-generation CRISPR diagnostics and that the SPEEDi-CRISPR assay provides a potentially useful tool for point-of-care testing.
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26
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Wang X, Mu X, Li J, Liu G, Zhao S, Tian J. A novel nanoparticle surface-constrained CRISPR-Cas12a 3D DNA walker-like nanomachines for sensitive and stable miRNAs detection. Anal Chim Acta 2023; 1251:340950. [PMID: 36925314 DOI: 10.1016/j.aca.2023.340950] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/01/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023]
Abstract
The CRISPR-Cas system has broad prospects as a new type of nucleic acid signal amplification technology based on the trans-cleavage activity of Cas12a to single-stranded DNA, but the trans-cleavage reaction efficiency is relatively low in solution. In order to overcome this negative factor, a new 3D DNA nanomachine whose CRISPR-Cas12a is limited to the surface of nanoparticles is used for sensitive and stable detection of miRNA. By loading Cas12a activator onto spherical nucleic acid (SNA), the CRISPR-Cas12a activator system on the surface of Au nanoparticles (AuNPs) acts as a walker to carry out continuous recognition-walking-cutting reaction on the surface of AuNPs, which enhances the trans-cleavage activity of Cas12a to SNAs. Benefiting from the confinement effect of spherical nucleic acids surface, a 3D DNA nanomachine has been developed for the detection of miRNA-21, which has achieved high sensitivity and accuracy, and the detection limit is able to reach 8.0 pM. This new 3D DNA walker-like nanomachine provided another insight for future bioanalysis and early clinical diagnoses of disease and liquid biopsy.
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Affiliation(s)
- Xin Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Xiaomei Mu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Jinshen Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Guang Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Jianniao Tian
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
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27
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Liu Z, Quan L, Ma F, Yang M, Jiang X, Chen X. Determination of adenosine by CRISPR-Cas12a system based on duplexed aptamer and molecular beacon reporter linked to gold nanoparticles. Mikrochim Acta 2023; 190:173. [PMID: 37020072 PMCID: PMC10075494 DOI: 10.1007/s00604-023-05748-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/13/2023] [Indexed: 04/07/2023]
Abstract
Adenosine as a potential tumor marker is of great value for clinical disease diagnosis. Since the CRISPR-cas12a system is only capable of recognizing nucleic acid targets we expanded the CRISPR-cas12a system to determine small molecules by designing a duplexed aptamer (DA) converting g-RNA recognition of adenosine to recognition of aptamer complementary DNA strands (ACD). To further improve the sensitivity of determination, we designed a molecule beacon (MB)/gold nanoparticle (AuNP)-based reporter, which has higher sensitivity than traditional ssDNA reporter. In addition, the AuNP-based reporter enables more efficient and fast determination. The determination of adenosine under 488-nm excitation can be realized within 7 min, which is more than 4 times faster than traditional ssDNA reporter. The linear determination range of the assay to adenosine was 0.5-100 μM with the determination limit of 15.67 nM. The assay was applied to recovery determination of adenosine in serum samples with satisfactory results. The recoveries were between 91 and 106% and the RSD values of different concertation were below 4.8%. This sensitive, highly selective, and stable sensing system is expected to play a role in the clinical determination of adenosine and other biomolecules.
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Affiliation(s)
- Zhenhua Liu
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | | | - Fanghui Ma
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Minghui Yang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, 410083, China.
| | - Xinyu Jiang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China.
| | - Xiang Chen
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, 410083, China.
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410000, China.
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28
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Zhan X, Zhou J, Jiang Y, An P, Luo B, Lan F, Ying B, Wu Y. DNA tetrahedron-based CRISPR bioassay for treble-self-amplified and multiplex HPV-DNA detection with elemental tagging. Biosens Bioelectron 2023; 229:115229. [PMID: 36947920 DOI: 10.1016/j.bios.2023.115229] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/26/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
Sensitive quantification of multiple analytes of interest is of great significance for clinical diagnosis. CRISPR Cas platforms offer a strategy for improving the specificity, sensitivity, and speed of nucleic acid-based diagnostics, while their multiplex analysis capability is still limited and challenging. Herein, we develop a novel DNA Tetrahedron (DTN)-supported biosensor based on the spatially separated CRISPR Cas self-amplification strategy and multiple-metal-nanoparticle tagging coupled with inductively coupled plasma mass spectrometry (ICP-MS) detection to improve the sensitivity and feasibility of the platform for multiplex detection of HPV-DNA (HPV-16, HPV-18 and HPV-52). Given target DNA induces robust trans-cleavage activity of the Cas12a/crRNA duplex, and the surrounding corresponding single-stranded DNA (ssDNA) linker are cleaved into short fragments that are unable to bond metal-nanoparticle probes (197Au, 107Ag, 195Pt) onto DTN modified magnetic beads probe (MBs-DTN), resulting in obvious ICP-MS signal change. Of note, compared with ssDNA functionalized MBs, a higher Signal-to-Noise Ratio was obtained by using MBs-DTN in our system, further amplifying the signal by regulating probes on the surface of MBs. As expected, the HPV-DNA could be detected with detection limits as low as 218 fM and be multiplexed assayed at one test with high accuracy and specificity by this proposed strategy. Furthermore, we demonstrated that the HPV-DNA in cervical swab samples could be detected, showing high consistency with DNA sequencing results. We believe that this work provides a promising option in designing CRISPR based multiplex detection system for high sensitivity, good specificity, and clinical molecular diagnostics.
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Affiliation(s)
- Xiaohui Zhan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yujia Jiang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Peng An
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Bin Luo
- Analytical and Testing Center, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, People's Republic of China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, People's Republic of China.
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29
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Guo Y, Guo L, Su Y, Xiong Y. CRISPR-Cas system manipulating nanoparticles signal transduction for cancer diagnosis. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2023; 15:e1851. [PMID: 36199268 DOI: 10.1002/wnan.1851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/30/2022] [Accepted: 08/10/2022] [Indexed: 11/05/2022]
Abstract
Early diagnosis of cancer is important to improve the survival rate and relieve patient pain. Sensitive detection of cancer related biomarkers in body fluids is a critical approach for the early diagnosis of cancer. The clustered regularly interspaced short palindromic repeat-associated protein (CRISPR-Cas) system has emerged as a molecular manipulation technology because of its simple detection procedure, high base resolution, and isothermal signal amplification. Recently, various nanomaterials with unique optical and electrical characteristics have been introduced as the novel signal transducers to enhance the detection performance of CRISPR-Cas-based nanosensors. This review summarizes the working mechanisms of the CRISPR-Cas system for biosensing. It also enumerates the strategies of CRISPR-manipulated nanosensors based on various signal models for cancer diagnosis, including colorimetric, fluorescence, electrochemical, electrochemiluminescence, pressure, and other signals. Finally, the prospects and challenges of CRISPR-Cas-based nanosensors for cancer diagnostic are also discussed. This article is categorized under: Diagnostic Tools > Biosensing.
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Affiliation(s)
- Yuqian Guo
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
| | - Liang Guo
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang, People's Republic of China
| | - Yu Su
- School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China.,School of Food Science and Technology, Nanchang University, Nanchang, People's Republic of China
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30
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Ivanov AV, Safenkova IV, Biketov SF, Zherdev AV, Dzantiev BB. Engineering of DNA Structures Attached to Magnetic Particles for Effective Trans- and Cis-Cleavage in Cas12-Based Biosensors. Int J Mol Sci 2023; 24:ijms24054484. [PMID: 36901914 PMCID: PMC10003267 DOI: 10.3390/ijms24054484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Sequence-specific endonuclease Cas12-based biosensors have rapidly evolved as a strong tool to detect nucleic acids. Magnetic particles (MPs) with attached DNA structures could be used as a universal platform to manipulate the DNA-cleavage activity of Cas12. Here, we propose nanostructures of trans- and cis-DNA targets immobilized on the MPs. The main advantage of the nanostructures is a rigid double-stranded DNA adaptor that distances the cleavage site from the MP surface to ensure maximum Cas12 activity. Adaptors with different lengths were compared by detecting the cleavage by fluorescence and gel electrophoresis of the released DNA fragments. The length-dependent effects for cleavage on the MPs' surface were found both for cis- and trans-targets. For trans-DNA targets with a cleavable 15-dT tail, the results showed that the optimal range of the adaptor length was 120-300 bp. For cis-targets, we varied the length and location of the adaptor (at the PAM or spacer ends) to estimate the effect of the MP's surface on the PAM-recognition process or R-loop formation. The sequential arrangement of an adaptor, PAM, and a spacer was preferred and required the minimum adaptor length of 3 bp. Thus, with cis-cleavage, the cleavage site can be located closer to the surface of the MPs than with trans-cleavage. The findings provide solutions for efficient Cas12-based biosensors using surface-attached DNA structures.
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Affiliation(s)
- Aleksandr V. Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence: ; Tel./Fax: +7-495-954-2804
| | - Sergey F. Biketov
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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31
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Choi HK, Yoon J. Nanotechnology-Assisted Biosensors for the Detection of Viral Nucleic Acids: An Overview. BIOSENSORS 2023; 13:208. [PMID: 36831973 PMCID: PMC9953881 DOI: 10.3390/bios13020208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/21/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
The accurate and rapid diagnosis of viral diseases has garnered increasing attention in the field of biosensors. The development of highly sensitive, selective, and accessible biosensors is crucial for early disease detection and preventing mortality. However, developing biosensors optimized for viral disease diagnosis has several limitations, including the accurate detection of mutations. For decades, nanotechnology has been applied in numerous biological fields such as biosensors, bioelectronics, and regenerative medicine. Nanotechnology offers a promising strategy to address the current limitations of conventional viral nucleic acid-based biosensors. The implementation of nanotechnologies, such as functional nanomaterials, nanoplatform-fabrication techniques, and surface nanoengineering, to biosensors has not only improved the performance of biosensors but has also expanded the range of sensing targets. Therefore, a deep understanding of the combination of nanotechnologies and biosensors is required to prepare for sanitary emergencies such as the recent COVID-19 pandemic. In this review, we provide interdisciplinary information on nanotechnology-assisted biosensors. First, representative nanotechnologies for biosensors are discussed, after which this review summarizes various nanotechnology-assisted viral nucleic acid biosensors. Therefore, we expect that this review will provide a valuable basis for the development of novel viral nucleic acid biosensors.
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Affiliation(s)
- Hye Kyu Choi
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jinho Yoon
- Department of Biomedical-Chemical Engineering, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi-do, Republic of Korea
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32
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Li H, Xie Y, Chen F, Bai H, Xiu L, Zhou X, Guo X, Hu Q, Yin K. Amplification-free CRISPR/Cas detection technology: challenges, strategies, and perspectives. Chem Soc Rev 2023; 52:361-382. [PMID: 36533412 DOI: 10.1039/d2cs00594h] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rapid and accurate molecular diagnosis is a prerequisite for precision medicine, food safety, and environmental monitoring. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)-based detection, as a cutting-edged technique, has become an immensely effective tool for molecular diagnosis because of its outstanding advantages including attomolar level sensitivity, sequence-targeted single-base specificity, and rapid turnover time. However, the CRISPR/Cas-based detection methods typically require a pre-amplification step to elevate the concentration of the analyte, which may produce non-specific amplicons, prolong the detection time, and raise the risk of carryover contamination. Hence, various strategies for target amplification-free CRISPR/Cas-based detection have been developed, aiming to minimize the sensitivity loss due to lack of pre-amplification, enable detection for non-nucleic acid targets, and facilitate integration in portable devices. In this review, the current status and challenges of target amplification-free CRISPR/Cas-based detection are first summarized, followed by highlighting the four main strategies to promote the performance of target amplification-free CRISPR/Cas-based technology. Furthermore, we discuss future perspectives that will contribute to developing more efficient amplification-free CRISPR/Cas detection systems.
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Affiliation(s)
- Huimin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Yi Xie
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Fumin Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Huiwen Bai
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, 220 South 33rd St., Philadelphia, Pennsylvania, USA
| | - Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Xiaonong Zhou
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
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Wang B, Wang M, Peng F, Fu X, Wen M, Shi Y, Chen M, Ke G, Zhang XB. Construction and Application of DNAzyme-based Nanodevices. Chem Res Chin Univ 2023; 39:42-60. [PMID: 36687211 PMCID: PMC9841151 DOI: 10.1007/s40242-023-2334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Menghui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaoyi Fu
- Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, 310022 P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Yuyan Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Mei Chen
- College of Materials Science and Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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Alon DM, Partosh T, Burstein D, Pines G. Rapid and sensitive on-site genetic diagnostics of pest fruit flies using CRISPR-Cas12a. PEST MANAGEMENT SCIENCE 2023; 79:68-75. [PMID: 36073293 PMCID: PMC10086973 DOI: 10.1002/ps.7173] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/22/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Bactrocera zonata, a major fruit pest species, is gradually spreading west from its native habitat in East Asia. In recent years it has become a significant threat to the Mediterranean area, with the potential of invading Europe, the Americas, and Australia. To prevent it spreading, monitoring efforts in cultivation sites and border controls are carried out. Despite these efforts, and due to morphological similarities between B. zonata and other pests in relevant developmental stages, the monitoring process is challenging, time-consuming, and requires external assistance from professional laboratories. CRISPR-Cas12a genetic diagnostics has been rapidly developing in recent years and provides an efficient tool for the genetic identification of pathogens, viruses, and other genetic targets. Here we design a CRISPR-Cas12a detection assay that differentially detects two major pest species, B. zonata and Ceratitis capitata. RESULTS We demonstrate the specificity and high sensitivity of this method. Identification of target pests was done using specific and universal primers on pooled samples, enabling differentiation of pests with high certainty. We also demonstrate reaction stability over time for future on-site applications. DISCUSSION Our easy-to-use and affordable assay employs a simple DNA extraction technique together with isothermal amplification and Cas12a-based detection. This method is highly modular, and the presented target design method can be applied to a wide array of pests. This approach can be easily adapted to fit local threats and requires minimal training of operators in border controls and other relevant locations, reshaping pest control and making state-of-the-art technologies available worldwide, including in developing countries. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Dan Mark Alon
- Department of EntomologyAgricultural Research Organization—The Volcani CenterRishon LeZionIsrael
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life ScienceTel Aviv UniversityTel AvivIsrael
| | - Tamir Partosh
- Department of EntomologyAgricultural Research Organization—The Volcani CenterRishon LeZionIsrael
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life ScienceTel Aviv UniversityTel AvivIsrael
| | - Gur Pines
- Department of EntomologyAgricultural Research Organization—The Volcani CenterRishon LeZionIsrael
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35
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Green CM, Spangler J, Susumu K, Stenger DA, Medintz IL, Díaz SA. Quantum Dot-Based Molecular Beacons for Quantitative Detection of Nucleic Acids with CRISPR/Cas(N) Nucleases. ACS NANO 2022; 16:20693-20704. [PMID: 36378103 DOI: 10.1021/acsnano.2c07749] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Strategies utilizing the CRISPR/Cas nucleases Cas13 and Cas12 have shown great promise in the development of highly sensitive and rapid diagnostic assays for the detection of pathogenic nucleic acids. The most common approaches utilizing fluorophore-quencher molecular beacons require strand amplification strategies or highly sensitive optical setups to overcome the limitations of the readout. Here, we demonstrate a flexible strategy for assembling highly luminescent and colorimetric quantum dot-nucleic acid hairpin (QD-HP) molecular beacons for use in CRISPR/Cas diagnostics. This strategy utilizes a chimeric peptide-peptide nucleic acid (peptide-PNA) to conjugate fluorescently labeled DNA or RNA hairpins to ZnS-coated QDs. QDs are particularly promising alternatives for molecular beacons due to their greater brightness, strong UV absorbance with large emission offset, exceptional photostability, and potential for multiplexing due to their sharp emission peaks. Using Förster resonance energy transfer (FRET), we have developed ratiometric reporters capable of pM target detection (without nucleotide amplification) for both target DNA and RNA, and we further demonstrated their capabilities for multiplexing and camera-phone detection. The flexibility of this system is imparted by the dual functionality of the QD as both a FRET donor and a central nanoscaffold for arranging nucleic acids and fluorescent acceptors on its surface. This method also provides a generalized approach that could be applied for use in other CRISPR/Cas nuclease systems.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Joseph Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
- Jacobs Corporation, Hanover, Maryland21076, United States
| | - David A Stenger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
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36
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Yi Y, Han Y, Cheng X, Zhang Z, Sun Y, Zhang K, Xu JJ. Three-Dimensional Surface-Enhanced Raman Scattering Platform with Hotspots Built by a Nano-mower for Rapid Detection of MRSA. Anal Chem 2022; 94:17205-17211. [PMID: 36446023 DOI: 10.1021/acs.analchem.2c03834] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the greatest threats to human health due to its strong drug resistance, wide distribution range, and high infection rate. Rapid identification of MRSA strains is very important for accurate diagnosis and early treatment of MRSA infections. Here, we introduced an Exo III-assisted nanomotor mower to build 3D hotspots for rapid detection of MRSA by surface-enhanced Raman scattering (SERS). As the bacteria bound to the aptamer, two trigger chains were released from the double-stranded structure, and the nano-mowers were activated by opening a hairpin probe on gold nanoparticles (AuNPs). With the continued cleavage of Exo III and cyclic release of the trigger chain, multiple hairpin DNAs on the AuNPs were cleaved to increase the motor power. The resulting nano-mower continued slicing protective DNA from larger AuNPs, exposing the AuNPs. Without the protection of DNA, Mg2+ in the buffer induced spontaneous aggregation of the AuNPs, and a large number of hotspots were formed for SERS measurements. Under optimal conditions, MRSA can be detected within 40 min, and the concentration of MRSA showed a good linear relationship with the SERS intensity at 1342 cm-1, with a limit of detection as low as 1 CFU/mL and a wide linear range (100 to 107 CFU/mL). This strategy creates a rapid bacterial detection method that performs well on actual samples utilizing portable Raman spectroscopy instruments, with potential applications in food detection, water detection, clinical treatment, and diagnosis.
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Affiliation(s)
- Yang Yi
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Yunxiang Han
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Xi Cheng
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Zhe Zhang
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Yudie Sun
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Kui Zhang
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma'anshan, Anhui 243032, P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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37
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Simultaneous ultrasensitive ADP and ATP quantification based on CRISPR/Cas12a integrated ZIF-90@Ag3AuS2@Fe3O4 nanocomposites. Biosens Bioelectron 2022; 218:114784. [DOI: 10.1016/j.bios.2022.114784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 11/19/2022]
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38
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Gao H, Feng M, Li F, Zhang K, Zhang T, Zhang Z, Yang C, Deng R, Zhang J, Jiang P. G-Quadruplex DNAzyme-Substrated CRISPR/Cas12 Assay for Label-Free Detection of Single-Celled Parasitic Infection. ACS Sens 2022; 7:2968-2977. [PMID: 36206316 DOI: 10.1021/acssensors.2c01104] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Early diagnosis of parasitic diseases can dramatically alleviate medical, economic, and social burdens. Herein, we report a sensitive and label-free assay for diagnosing single-celled parasitic infections using G-quadruplex (G4) DNAzyme as a reporter for CRISPR/Cas12. The substitution of a fluorescent DNA reporter with G4 DNAzyme increased the sensitivity for detecting Leishmania donovani (L. donovani) by 5 times and obviated the need for using chemically labeled DNA probes. The G4 DNAzyme-substrated CRISPR/Cas12 (GsubCas12) assay yielded a limit of detection of 3.1 parasites in the detection of cultured L. donovani and was further applied to analyze L. donovani in infected mice. The results showed that the GsubCas12 assay could positively detect L. donovani in spleen samples from infected mice about 2 weeks after low-dose inoculation, nearly 2 weeks earlier than that of parasitological analysis. GsubCas12 assay is promising as a diagnostic tool for parasitic infection in resource-limited regions.
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Affiliation(s)
- Hua Gao
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Miaomiao Feng
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Feng Li
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Ting Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Zifang Zhang
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Chengyun Yang
- Center of Disease Control and Prevention of Henan Province, Zhengzhou 450016, P. R. China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Junrong Zhang
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Peng Jiang
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
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Du Y, Han D, An Z, Wang J, Gao Z. CRISPR/dCas9-surface-enhanced Raman scattering for the detection of drug resistance gene macB. Mikrochim Acta 2022; 189:394. [PMID: 36155855 DOI: 10.1007/s00604-022-05460-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/09/2022] [Indexed: 10/14/2022]
Abstract
Antibiotics have brought many benefits to public health systems worldwide since their first use in the last century, yet with their overuse in clinical treatment and livestock farming, new public health issues have arisen. Previously, we found in our experiments that the levels of macB genes in bovine raw milk ranked among the top of many drug resistance genes. In this paper, we present an analysis of regularly interspaced clustered short palindromic repeats (CRISPR) combined with surface-enhanced Raman scattering (SERS) technology for the detection of the drug resistance gene macB. The analysis was accomplished through the collaboration of the CRISPR system's ability to specifically identify genes and the more sensitive performance of the SERS. The analysis detects the drug resistance gene macB and does not yet require complex steps such as nucleic acid amplification. This method may prove to be an effective method for accurate detection of the drug-resistant gene macB, thus enabling more effective prevention of contamination of drug-resistant genes in food hygiene.
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Affiliation(s)
- Yuwan Du
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, People's Republic of China
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, People's Republic of China
| | - Zhaoxia An
- Public Health and Preventive Medicine, Hebei University, Hebei, 71000, People's Republic of China
| | - Jiang Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, People's Republic of China.
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, People's Republic of China.
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40
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Li J, Tang L, Li T, Li K, Zhang Y, Ni W, Xiao MM, Zhao Y, Zhang ZY, Zhang GJ. Tandem Cas13a/crRNA-Mediated CRISPR-FET Biosensor: A One-for-All Check Station for Virus without Amplification. ACS Sens 2022; 7:2680-2690. [PMID: 36073895 DOI: 10.1021/acssensors.2c01200] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The path toward field-effect transistor (FET) application from laboratory to clinic has delivered a compelling push in the biomedical domain, yet ultrasensitive and timely pathogen identification without PCR remains a long-lasting challenge. Herein, we create a generic check station termed "CRISPR-FET", first incorporating the CRISPR/Cas13a system within the FET modality, for accelerated and unamplified detection of viral RNA. Unlike conventional FETs bearing target-specific receptors, this sensor holds three unique advancements: (i) an ingenious sensing mechanism is used, which converts the signal of a large-sized analyte into an on-chip cleavage response of an immobilized CRISPR reporter, enabling signal generation events to occur all within the Debye length; (ii) the multipurpose inspection of the CoV ORF1ab, CoV N gene, and HCV RNA unveils the potential for "one-for-all" scalable FET-based molecular diagnostics; and (iii) it is shown that Cas13a-crRNAs targeting different sites of the viral genome can be deployed in tandem to amplify the FET response, empowering the detection limit down to 1.56 aM, which is a world-record level of sensitivity in the FET for direct viral gene sensing. Notably, a brilliant clinical applicability was made in distinguishing HCV-infected patients from normal controls. Overall, this study sheds new insights into FET-based nucleic acid sensing technology and invokes a vision for its possible future roles in diagnosis of various viral diseases.
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Affiliation(s)
- Jiahao Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Lina Tang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Tingxian Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Kun Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Yulin Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Wei Ni
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, China
| | - Meng-Meng Xiao
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan 411105, P. R. China
| | - Youyun Zhao
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, China
| | - Zhi-Yong Zhang
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan 411105, P. R. China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
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41
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Rational fabrication of a DNA walking nanomachine on graphene oxide surface for fluorescent bioassay. Biosens Bioelectron 2022; 211:114349. [DOI: 10.1016/j.bios.2022.114349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/22/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
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42
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Pasparakis G. Recent developments in the use of gold and silver nanoparticles in biomedicine. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1817. [PMID: 35775611 PMCID: PMC9539467 DOI: 10.1002/wnan.1817] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/18/2022]
Abstract
Gold and silver nanoparticles (NPs) are widely used in the biomedical research both in the therapeutic and the sensing/diagnostics fronts. Both metals share some common optical properties with surface plasmon resonance being the most widely exploited property in therapeutics and diagnostics. Au NPs exhibit excellent light‐to‐heat conversion efficiencies and hence have found applications primarily in precision oncology, while Ag NPs have excellent antibacterial properties which can be harnessed in biomaterials' design. Both metals constitute excellent biosensing platforms owing to their plasmonic properties and are now routinely used in various optical platforms. The utilization of Au and Ag NPs in the COVID‐19 pandemic was rapidly expanded mostly in biosensing and point‐of‐care platforms and to some extent in therapeutics. In this review article, the main physicochemical properties of Au and Ag NPs are discussed with selective examples from the recent literature. This article is categorized under:Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Diagnostic Tools > In Vitro Nanoparticle‐Based Sensing Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
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Affiliation(s)
- George Pasparakis
- Department of Chemical Engineering University of Patras Patras Greece
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43
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Liao K, Peng W, Qian B, Nan W, Shan Y, Zeng D, Tang F, Wu X, Chen Y, Xue F, Dai J. A highly adaptable platform powered by CRISPR-Cas12a to diagnose lumpy skin disease in cattle. Anal Chim Acta 2022; 1221:340079. [PMID: 35934339 DOI: 10.1016/j.aca.2022.340079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022]
Abstract
Lumpy skin disease (LSD) in cattle, a transboundary viral disease of cattle once restricted to Africa, has been spreading to many European and Asian countries in the past decade with huge economic losses. This emerging worldwide threat to cattle warrants the development of diagnostic methods for accurate disease screening of suspected samples to effectively control the spread of LSD. In this study, we integrated pre-amplification and three kinds of sensor systems with CRISPR and therefore established an LSD diagnosis platform with highly adaptable and ultra-sensitive advantages. It was the first CRISPR-powered platform that could identify lumpy skin disease virus from vaccine strains of goat pox virus and sheep pox virus. Its limit of detection (LOD) was one copy/reaction after introducing PCR or recombinase-aided amplification (RAA). Moreover, this platform achieved a satisfactory overall agreement in clinical diagnoses of 50 samples and its reproducibility and accuracy were superior to other qPCR methods we tested. The whole diagnostic procedure, from DNA extraction to the results, could complete in 5 h with a total cost of 1.7-9.6 $/test. Overall, this CRISPR-powered platform provided a novel diagnostic tool for portable, ultra-sensitive, rapid, and highly adaptable disease screening of LSD and may be an effective method to control this transboundary disease's spread.
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Affiliation(s)
- Kai Liao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanqing Peng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingxu Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenlong Nan
- Laboratory of Diagnostics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China
| | - Yuping Shan
- Lianyungang Animal Husbandry and Veterinary Station, Lianyungang, Jiangsu, 222003, China
| | - Dexin Zeng
- Technology Center of Hefei Customs, Hefei, 230022, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Wu
- Laboratory of Diagnostics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China
| | - Yiping Chen
- Laboratory of Diagnostics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China.
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; China Pharmaceutical University, Nanjing, 211198, China
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44
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Wu C, Chen Z, Li C, Hao Y, Tang Y, Yuan Y, Chai L, Fan T, Yu J, Ma X, Al-Hartomy OA, Wageh S, Al-Sehemi AG, Luo Z, He Y, Li J, Xie Z, Zhang H. CRISPR-Cas12a-Empowered Electrochemical Biosensor for Rapid and Ultrasensitive Detection of SARS-CoV-2 Delta Variant. NANO-MICRO LETTERS 2022; 14:159. [PMID: 35925472 PMCID: PMC9352833 DOI: 10.1007/s40820-022-00888-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/17/2022] [Indexed: 05/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The gold standard method for the diagnosis of SARS-CoV-2 depends on quantitative reverse transcription-polymerase chain reaction till now, which is time-consuming and requires expensive instrumentation, and the confirmation of variants relies on further sequencing techniques. Herein, we first proposed a robust technique-methodology of electrochemical CRISPR sensing with the advantages of rapid, highly sensitivity and specificity for the detection of SARS-CoV-2 variant. To enhance the sensing capability, gold electrodes are uniformly decorated with electro-deposited gold nanoparticles. Using DNA template identical to SARS-CoV-2 Delta spike gene sequence as model, our biosensor exhibits excellent analytical detection limit (50 fM) and high linearity (R2 = 0.987) over six orders of magnitude dynamic range from 100 fM to 10 nM without any nucleic-acid-amplification assays. The detection can be completed within 1 h with high stability and specificity which benefits from the CRISPR-Cas system. Furthermore, based on the wireless micro-electrochemical platform, the proposed biosensor reveals promising application ability in point-of-care testing.
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Affiliation(s)
- Chenshuo Wu
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Zhi Chen
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China.
- Hospital of Guangzhou Medical University, Qingyuan city People's Hospital, Qingyuan, 511518, People's Republic of China.
| | - Chaozhou Li
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yabin Hao
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Shenzhen Han's Tech Limited Company, Shenzhen, 518000, People's Republic of China
| | - Yuxuan Tang
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Hospital of Guangzhou Medical University, Qingyuan city People's Hospital, Qingyuan, 511518, People's Republic of China
| | - Yuxuan Yuan
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Luxiao Chai
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Taojian Fan
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Jiangtian Yu
- Shenzhen International Institute for Biomedical Research, Shenzhen, 518116, People's Republic of China
| | - Xiaopeng Ma
- Department of Respiratory, Shenzhen Children's Hospital, Shenzhen, 518038, People's Republic of China
| | - Omar A Al-Hartomy
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - S Wageh
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Abdullah G Al-Sehemi
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Zhiguang Luo
- Zhongmin (Shenzhen) Intelligent Ecology Co., Ltd, Shenzhen, 518055, People's Republic of China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, People's Republic of China
| | - Jingfeng Li
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China.
- Shenzhen International Institute for Biomedical Research, Shenzhen, 518116, People's Republic of China.
| | - Zhongjian Xie
- Shenzhen International Institute for Biomedical Research, Shenzhen, 518116, People's Republic of China.
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518038, People's Republic of China.
| | - Han Zhang
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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45
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Zeng M, Ke Y, Zhuang Z, Qin C, Li LY, Sheng G, Li Z, Meng H, Ding X. Harnessing Multiplex crRNA in the CRISPR/Cas12a System Enables an Amplification-Free DNA Diagnostic Platform for ASFV Detection. Anal Chem 2022; 94:10805-10812. [PMID: 35857897 DOI: 10.1021/acs.analchem.2c01588] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-associated (Cas) protein systems have been increasingly incorporated in nucleic-acid diagnosis. CRISPR/Cas12a can cleave single-stranded DNA (ssDNA) after being guided to the target double-stranded DNA (dsDNA) with crRNA, making it a specific tool for dsDNA detection. Assisted by nucleic acid preamplification, CRISPR/Cas12a enables dsDNA detection at the attomolar level. However, such mandatory preamplification in CRISPR/Cas12a also accompanies the extra step of transferring preamplification products into the CRISPR/Cas12a system, which is not only cumbersome and time-consuming but also induces the risk of cross-contamination. Herein, we demonstrate a multiplex-crRNA strategy to enhance the sensitivity of the CRISPR/Cas12a system without any preamplification. This multiplex-crRNA strategy harnesses multiple sequences of crRNA which target different regions of the same dsDNA substrate in the same CRISPR/Cas12a system. Therefore, detection signals are accumulated without amplification, which augments the conventional detection limit. For application demonstration, the B646L gene from the African swine fever virus (ASFV), which is a dsDNA virus, is exemplified. The detection limit of the multiplex-crRNA system can be improved to ∼1 picomolar (pM) without amplification, which is ∼64 times stronger than the conventional single-crRNA system. The multiplex-crRNA system presented in this study, with slight modifications, can be generalized to other biosensing settings where preamplification is not readily available.
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Affiliation(s)
- Muchu Zeng
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China.,Zhejiang University─University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang 324400, PR China.,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Yuqing Ke
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Zhiyi Zhuang
- School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, PR China
| | - Chao Qin
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200040, PR China
| | - Lai Yan Li
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Gaoyuan Sheng
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Zhuoru Li
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - He Meng
- Shanghai Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200040, PR China
| | - Xianting Ding
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China.,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
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46
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Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res 2022; 50:8377-8391. [PMID: 35822842 PMCID: PMC9371913 DOI: 10.1093/nar/gkac578] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Danila Moscone
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Aakash Saha
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Ida Treglia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte Sant'Angelo, Ed. 7, Via Cintia 26, 80126 Naples, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
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47
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Sun Y, Fang L, Yi Y, Feng A, Zhang K, Xu JJ. Multistage nucleic acid amplification induced nano-aggregation for 3D hotspots-improved SERS detection of circulating miRNAs. J Nanobiotechnology 2022; 20:285. [PMID: 35710556 PMCID: PMC9205088 DOI: 10.1186/s12951-022-01500-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Circulating miRNAs in the blood can regulate disease development and thus indicate disease states via their various expression levels. For these reasons, circulating miRNAs constitute useful biomarkers, and an approach to the accurate detection of circulating miRNAs is attractive in the diagnosis and treatment of diseases. However, methods for clinical detecting of circulating miRNA that take both sensitivity and practicality into account are still needed. Therefore, we aimed herein to solve some inherent problems in the actual detection using a robust surface-enhanced Raman scattering (SERS) platform with integrated nucleic acid amplification and nanoparticle aggregation to construct 3D hotspots for improving performance of analyzing circulating miRNAs. After target recognition and initial signal amplification by DNAzyme, we observed that release triggered an open hairpin DNA on gold nanoparticles (AuNPs), which then promote AuNP aggregation, causing the accumulation of a large number of hotspots in three-dimention. The SERS biosensor achieved a better performance than the sandwich-type separation detection, with a low detection limit (0.37 fM) and a broad linear range (1 fM–10 nM) in liquids. This SERS platform can be used as a powerful tool for the detection of circulating miRNAs, and it can be used to improve the sensitivity and accuracy of various clinical-disease diagnoses.
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Affiliation(s)
- Yudie Sun
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma 'anshan, 243032, An-hui, People's Republic of China
| | - La Fang
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma 'anshan, 243032, An-hui, People's Republic of China
| | - Yang Yi
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma 'anshan, 243032, An-hui, People's Republic of China
| | - Aobo Feng
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma 'anshan, 243032, An-hui, People's Republic of China
| | - Kui Zhang
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma Xiang Road, Ma 'anshan, 243032, An-hui, People's Republic of China.
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nan-Jing University, Nanjing, 210023, People's Republic of China
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48
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A CRISPR-Cas12a-powered magnetic relaxation switching biosensor for the sensitive detection of Salmonella. Biosens Bioelectron 2022; 213:114437. [PMID: 35696867 DOI: 10.1016/j.bios.2022.114437] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/10/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022]
Abstract
Magnetic relaxation switching (MRS) biosensors are attractive in the field of food safety owing to their simplicity and high signal-to-noise ratio. But they are less in sensitivity and stability caused by the insufficient crosslinking or non-specific binding of magnetic nanoparticles (MNPs) with targets. To address this problem, the CRISPR-Cas12a system was introduced into an MRS biosensor for the first time, to precisely control the binding of two types of MNPs with sizes of 130 nm (MNP130) and 30 nm (MNP30), for the sensitive detection of Salmonella. Delicately, the biosensor was designed based on the different magnetic properties of the two sizes of MNPs. The target Salmonella activated the collateral cleavage activity of the CRISPR-Cas12a system, which inhibited the binding of the two sizes of MNPs, resulting in an increase of unbound MNP30. After separating MNP130-MNP30 complexes and MNP130 from MNP30, the free MNP30 left in solution acted as transverse relaxation time (T2) signal reporters for Salmonella detection. Under optimized conditions, the CRISPR-MRS biosensor presented a limit of detection of 1.3 × 102 CFU mL-1 for Salmonella, which is lower than most MRS biosensor analogues. It also showed satisfactory specificity and performed well in spiked chicken meat samples. This biosensing strategy not only extends the reach of the CRISPR-Cas12a system in biosensors but also offers an alternative for pathogen detection with satisfactory sensitivity.
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49
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Li YY, Li HD, Fang WK, Liu D, Liu MH, Zheng MQ, Zhang LL, Yu H, Tang HW. Amplification of the Fluorescence Signal with Clustered Regularly Interspaced Short Palindromic Repeats-Cas12a Based on Au Nanoparticle-DNAzyme Probe and On-Site Detection of Pb 2+ Via the Photonic Crystal Chip. ACS Sens 2022; 7:1572-1580. [PMID: 35482449 DOI: 10.1021/acssensors.2c00516] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although great headway has been made in DNAzyme-based detection of Pb2+, its adaptability, sensitivity, and accessibility in complex media still need to be improved. For this, we introduce new ways to surmount these hurdles. First, a spherical nucleic acid (SNA) fluorescence probe (Au nanoparticles-DNAzyme probe) is utilized to specifically identify Pb2+ and its suitability for precise detection of Pb2+ in complex samples due to its excellent nuclease resistance. Second, the sensitivity of Pb2+ detection is greatly enhanced via the use of a clustered regularly interspaced short palindromic repeats-Cas12a with target recognition accuracy to amplify the fluorescent signal upon the trans cleavage of the SNA (signal probe), and the limit of detection reaches as low as 86 fM. Third, we boost the fluorescence on photonic crystal chips with a bionic periodic arrangement by employing a straightforward detection device (smartphone and portable UV lamp) to achieve on-site detection of Pb2+ with the limit of detection as low as 24 pM. Based on the abovementioned efforts, the modified Pb2+ fluorescence sensor has the advantages of higher sensitivity, better specificity, accessibility, less sample consumption, and so forth. Moreover, it can be applied to accurately detect Pb2+ in complex biological or environmental samples, which is of great promise for widespread applications.
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Affiliation(s)
- Yu-Yao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Hao-Dong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, People’s Republic of China
| | - Wen-Kai Fang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Da Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Meng-Han Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Ming-Qiu Zheng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Li-Ling Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - He Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Hong-Wu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
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50
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Luo T, Li J, He Y, Liu H, Deng Z, Long X, Wan Q, Ding J, Gong Z, Yang Y, Zhong S. Designing a CRISPR/Cas12a- and Au-Nanobeacon-Based Diagnostic Biosensor Enabling Direct, Rapid, and Sensitive miRNA Detection. Anal Chem 2022; 94:6566-6573. [PMID: 35451838 DOI: 10.1021/acs.analchem.2c00401] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Direct, rapid, sensitive, and selective detection of nucleic acids in complex biological fluids is crucial for medical early diagnosis. We herein combine the trans-cleavage ability of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a with Au-nanobeacon to establish a CRISPR-based biosensor, providing rapid miRNA detection with high speed and attomolar sensitivity. In this strategy, we first report that the trans-cleavage activity of CRISPR/cas12a, which was previously reported to be triggered only by target ssDNA or dsDNA, can be activated by the target miRNA directly. Therefore, this method is direct, i.e., does not need the conversion of miRNA into its complementary DNA (cDNA). Meanwhile, as compared to the traditional ssDNA reporters and molecular beacon (MB) reporters, the Au-nanobeacon reporters exhibit improved reaction kinetics and sensitivity. In this assay, the miRNA-21 could be detected with very high sensitivity in only 5 min. Finally, the proposed strategy enables rapid, sensitive, and selective miRNA determination in complex biological samples, providing a potential tool for medical early diagnosis.
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Affiliation(s)
- Tong Luo
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiacheng Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yao He
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Hui Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhiwei Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Xi Long
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Qingqing Wan
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiacheng Ding
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zan Gong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yanjing Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Shian Zhong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
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