1
|
Zhu L, Zhang X, Yang L, Qiu S, Liu G, Xiong X, Xiao T, Huang K, Zhu L. Label-free electrochemical sensing platform for sensitive detection of ampicillin by combining nucleic acid isothermal enzyme-free amplification circuits with CRISPR/Cas12a. Talanta 2024; 273:125950. [PMID: 38521024 DOI: 10.1016/j.talanta.2024.125950] [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: 02/04/2024] [Revised: 03/06/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
The residue of ampicillin (AMP) in food and ecological environment poses a potential harm to human health. Therefore, a reliable system for detecting AMP is in great demand. Herein, a label-free and sensitive electrochemical sensor utilizing NH2-Co-MOF as an electrocatalytic active material for methylene blue (MB) was developed for rapid and facile AMP detection by combining hybridization chain reaction (HCR), catalytic hairpin assembly (CHA) with CRISPR/Cas12a. The surface of glassy carbon electrode modified with NH2-Co-MOF was able to undergo HCR independent of the AMP, forming long dsDNA complexes to load MB, resulting in strong original electrochemical signal. The presence of AMP could trigger upstream CHA circuit to activate the CRISPR/Cas12a system, thereby achieving rapid non-specific cleavage of the trigger ssDNA of HCR on the electrode surface, hindering the occurrence of HCR and reducing the load of MB. Significant signal change triggered by the target was ultimately obtained, thus achieving sensitive detection of the AMP with a detection limit as low as 1.60 pM (S/N = 3). The proposed sensor exhibited good stability, selectivity, and stability, and achieved reliable detection of AMP in milk and livestock wastewater samples, demonstrating its promising application prospects in food safety and environmental monitoring.
Collapse
Affiliation(s)
- Li Zhu
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China
| | - Xuemei Zhang
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China
| | - Li Yang
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China
| | - Shan Qiu
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China
| | - Guoyu Liu
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China
| | - Xiaoli Xiong
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China
| | - Ting Xiao
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China
| | - Ke Huang
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China.
| | - Liping Zhu
- Sichuan Provincial Engineering Laboratory of Livestock Manure Treatment and Recycling Sichuan Normal University, Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources Ministry of Education, Sichuan Normal University, College of Chemistry and Materials Science, Chengdu, 610066, China.
| |
Collapse
|
2
|
Li D, Liang P, Ling S, Wu Y, Lv B. An optimized microRNA detection platform based on PAM formation-regulated CRISPR/Cas12a activation. Int J Biol Macromol 2024; 266:130848. [PMID: 38521316 DOI: 10.1016/j.ijbiomac.2024.130848] [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: 12/26/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
MicroRNAs (miRNAs) have emerged as biomarkers for the diagnosis and prognosis of various diseases, such as cancer. Recent advancements in CRISPR/Cas12a-based biosensors in combination with hybridization chain reaction (HCR) make it a promising approach for miRNA detection. To increase the compatibility of HCR and CRISPR/Cas12a, we compared two design strategies of hairpin DNA in HCR. The results showed that different arrangements of the protospacer sequence and protospacer adjacent motif (PAM) in the hairpin DNA could affect the sensing performance. The "PAM Formation" strategy, by which the duplex PAM sites are absent in the hairpin DNA and present in the long duplex DNA after HCR, exhibited advantages in detection sensitivity. By optimizing the probe sequences and reaction conditions, we developed a miRNA detection platform. With the same crRNA, this platform enables the identification of different miRNAs by simply replacing the loop region of the target recognition probe. In addition, the proposed platform can detect single-stranded DNA and distinguishing single or multiple base mutations in the target strand. The application of discriminating the target miRNA expression levels from different cell lines validated the reliability and practicability of the sensor platform, indicating its potential applications in early clinical accurate diagnosis of cancers.
Collapse
Affiliation(s)
- Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Pengda Liang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Shen Ling
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yapeng Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Bei Lv
- Key Lab of Innovative Applications of Bioresources and Functional Molecules of Jiangsu Province, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing 210013, China.
| |
Collapse
|
3
|
Zhu F, Zhao Q. CRISPR/Cas12a linked sandwich aptamer assay for sensitive detection of thrombin. Anal Chim Acta 2024; 1287:342106. [PMID: 38182384 DOI: 10.1016/j.aca.2023.342106] [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: 08/25/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Thrombin is a serine protease and hemostasis regulator with multiple functions and recognized as an important biomarker for diseases, and sensitive detection of thrombin is of significance for clinical diagnostics and disease monitoring. Recently, the target-triggered nonspecific single-stranded deoxyribonuclease activity of CRISPR/Cas system is discovered, making it become a powerful tool in assay developments due to the ease of signal amplification. In the short period of development, many CRISPR based nucleic acid detection methods have already played a critical role in clinical diagnostics. However, the application of CRISPR/Cas system for protein biomarkers remains limited. RESULTS Here we describe a CRISPR/Cas12a linked sandwich aptamer assay for detection of thrombin, which was based on the formation of a sandwich complex of target by using a capture aptamer or antibody coated on the microplate and a well-designed detection DNA strand. The detection DNA strand contained an anti-thrombin aptamer and an active DNA of Cas12a, thus the sandwich complex was labeled with the active DNA. The active DNA triggered activity of Cas12a in indiscriminately cleaving fluorophore and quencher labeled DNA reporters, causing significant fluorescence increase. Our method enabled sensitive detection of thrombin down to 10 pM, and it showed high selectivity for thrombin. The assay exhibited good performance in diluted serum samples, demonstrating the applicability for thrombin analysis in the real media. SIGNIFICANCE This assay combines the merits of high affinity of aptamer, trans-cleavage activity of Cas12a, high selectivity of sandwich format analysis, and high-throughput detection of microplate assay, and it shows promise in applications.
Collapse
Affiliation(s)
- Fengxi Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China.
| |
Collapse
|
4
|
Qi L, Liu J, Liu S, Liu Y, Xiao Y, Zhang Z, Zhou W, Jiang Y, Fang X. Ultrasensitive Point-of-Care Detection of Protein Markers Using an Aptamer-CRISPR/Cas12a-Regulated Liquid Crystal Sensor (ALICS). Anal Chem 2024; 96:866-875. [PMID: 38164718 DOI: 10.1021/acs.analchem.3c04492] [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: 01/03/2024]
Abstract
Despite extensive efforts, point-of-care testing (POCT) of protein markers with high sensitivity and specificity and at a low cost remains challenging. In this work, we developed an aptamer-CRISPR/Cas12a-regulated liquid crystal sensor (ALICS), which achieved ultrasensitive protein detection using a smartphone-coupled portable device. Specifically, a DNA probe that contained an aptamer sequence for the protein target and an activation sequence for the Cas12a-crRNA complex was prefixed on a substrate and was released in the presence of target. The activation sequence of the DNA probe then bound to the Cas12a-crRNA complex to activate the collateral cleavage reaction, producing a bright-to-dark optical change in a DNA-functionalized liquid crystal interface. The optical image was captured by a smartphone for quantification of the target concentration. For the two model proteins, SARS-CoV-2 nucleocapsid protein (N protein) and carcino-embryonic antigen (CEA), ALICS achieved detection limits of 0.4 and 20 pg/mL, respectively, which are higher than the typical sensitivity of the SARS-CoV-2 test and the clinical CEA test. In the clinical sample tests, ALICS also exhibited superior performances compared to those of the commercial ELISA and lateral flow test kits. Overall, ALICS represents an ultrasensitive and cost-effective platform for POCT, showing a great potential for pathogen detection and disease monitoring under resource-limited conditions.
Collapse
Affiliation(s)
- Lubin Qi
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Jie Liu
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Songlin Liu
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Yang Liu
- Department of Orthopedics, Second Affiliated Hospital of Shandong First Medical University, Taian 271000, PR China
| | - Yating Xiao
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, PR China
| | - Zhen Zhang
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Science, Beijing 100190, PR China
| | - Wei Zhou
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Yifei Jiang
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Xiaohong Fang
- Hangzhou Institute of Medicine (HIM), Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, PR China
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Science, Beijing 100190, PR China
| |
Collapse
|
5
|
Talebian S, Dehghani F, Weiss PS, Conde J. Evolution of CRISPR-enabled biosensors for amplification-free nucleic acid detection. Trends Biotechnol 2024; 42:10-13. [PMID: 37516612 DOI: 10.1016/j.tibtech.2023.07.004] [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: 05/31/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
CRISPR biosensors enable rapid and accurate detection of nucleic acids without resorting to target amplification. Specifically, these systems facilitate the simultaneous detection of multiple nucleic acid targets with single-base specificity. This is an invaluable asset that can ultimately facilitate accurate diagnoses of biologically complex diseases.
Collapse
Affiliation(s)
- Sepehr Talebian
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia; Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia.
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia; Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia
| | - Paul S Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - João Conde
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Kalkan AK, Palaz F, Sofija S, Elmousa N, Ledezma Y, Cachat E, Rios-Solis L. Improving recombinant protein production in CHO cells using the CRISPR-Cas system. Biotechnol Adv 2023; 64:108115. [PMID: 36758652 DOI: 10.1016/j.biotechadv.2023.108115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
Collapse
Affiliation(s)
- Ali Kerem Kalkan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Environmental Engineering Department, Gebze Technical University, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Semeniuk Sofija
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nada Elmousa
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Yuri Ledezma
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; Biology Department, Faculty of Pure and Natural Sciences, Universidad Mayor de San Andrés, Bolivia
| | - Elise Cachat
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK; UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Leonardo Rios-Solis
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
| |
Collapse
|
8
|
Suliman Maashi M. CRISPR/Cas-based Aptasensor as an Innovative Sensing Approaches for Food Safety Analysis: Recent Progresses and New Horizons. Crit Rev Anal Chem 2023:1-19. [PMID: 36940173 DOI: 10.1080/10408347.2023.2188955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Food safety is one of the greatest public problems occurring around the world. Chemical, physical, and microbiological hazards could lead to food safety problems, which might occur at all stages of the supply chain. To tackle food safety problems and protect consumer health, specific, accurate, and rapid diagnosis techniques meeting various requirements are the imperative measures to ensure food safety. CRISPR-Cas system, a novel emerging technology, is effectively repurposed in (bio)sensing and has shown a tremendous capability to develop on-site and portable diagnostic methods with high specificity and sensitivity. Among numerous existing CRISPR/Cas systems, CRISPR/Cas13a and CRISPR/Cas12a are extensively employed in the design of biosensors, owing to their ability to cleave both non-target and target sequences. However, the specificity limitation in CRISPR/Cas has hindered its progress. Nowadays, nucleic acid aptamers recognized for their specificity and high-affinity characteristics for their analytes are incorporated into CRISPR/Cas systems. With the benefits of reproducibility, high durability, portability, facile operation, and cost-effectiveness, CRISPR/Cas-based aptasensing approaches are an ideal choice for fabricating highly specific point-of-need analytical tools with enhanced response signals. In the current study, we explore some of the most recent progress in the CRISPR/Cas-mediated aptasensors for detecting food risk factors including veterinary drugs, pesticide residues, pathogens, mycotoxins, heavy metals, illegal additives, food additives, and other contaminants. The nanomaterial engineering support with CRISPR/Cas aptasensors is also signified to achieve a hopeful perspective to provide new straightforward test kits toward trace amounts of different contaminants encountered in food samples.
Collapse
Affiliation(s)
- Marwah Suliman Maashi
- Medical Laboratory Science Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Regenerative Medicine Unit at King Fahad Medical Research Centre, Jeddah, Saudi Arabia
| |
Collapse
|
9
|
Zhou B, Yang R, Sohail M, Kong X, Zhang X, Fu N, Li B. CRISPR/Cas14 provides a promising platform in facile and versatile aptasensing with improved sensitivity. Talanta 2023; 254:124120. [PMID: 36463799 DOI: 10.1016/j.talanta.2022.124120] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/13/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
CRISPR is reshaping biosensing technology due to its programmability, sensitivity, and specificity. Most current CRISPR-based biosensors are developed based on Cas12 and Cas13, while the biosensing potentials of the newly discovered Cas14 have not been fully elucidated yet. Herein, a fluorometric biosensor named HARRY (highly sensitive aptamer-regulated Cas14 R-loop for bioanalysis) was developed. The diblock ssDNA is designed to contain the activator sequence of Cas14 and the aptamer sequence of specific targets. In the absence of targets, the ssDNA activates Cas14a, then the Cas14a trans-cleavages the fluorescent reporter, causing fluorescence enhancement. In the presence of the targets, ssDNA-target assembly is formed via aptamer interaction, resulting in the inhibition of Cas14a activation. HARRY can detect ATP, Cd2+, histamine, aflatoxin B1, and thrombin with detection limits at the low-nanomolar level, which shows improvement compared with Cas12a-based aptasensors in sensitivity and versatility. We reasoned that the improvement is derived from the ssDNA specificity of Cas14a and found that the detection limit of HARRY is correlated to the binding affinities of aptamers. This study unlocks the potential of Cas14a in versatile aptasensing, which may inspire the development of CRISPR-based biosensors from the Cas14a branch.
Collapse
Affiliation(s)
- Bin Zhou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, China
| | - Runlin Yang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, China
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China; College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoxue Kong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Ninghua Fu
- Department of Chemistry, Tsinghua University, Beijing, 100084, China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| |
Collapse
|
10
|
Zhu Y, Wu J, Zhou Q. Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection. Biosens Bioelectron 2023; 230:115282. [PMID: 37028002 DOI: 10.1016/j.bios.2023.115282] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
In addition to carrying and transmitting genetic material, some DNA molecules have specific binding ability or catalytic function. DNA with this special function is collectively referred to as functional DNA (fDNA), such as aptamer, DNAzyme and so on. fDNA has the advantages of simple synthetic process, low cost and low toxicity. It also has high chemical stability, recognition specificity and biocompatibility. In recent years, fDNA biosensors have been widely investigated as signal recognition elements and signal transduction elements for the detection of non-nucleic acid targets. However, the main problem of fDNA sensors is their limited sensitivity to trace targets, especially when the affinity of fDNA to the targets is low. To further improve the sensitivity, various nucleic acid signal amplification strategies (NASAS) are explored to improve the limit of detection of fDNA. In this review, we will introduce four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and the corresponding design principles. The principle and application of these fDNA sensors integrated with signal amplification strategies for detection of non-nucleic acid targets are summarized. Finally, the main challenges and application prospects of NASAS integrated fDNA biosensing system are discussed.
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Huang D, Shen P, Xu C, Xu Z, Cheng D, Zhu X, Fang M, Wang Z, Xu Z. Dual nucleases-assisted cyclic amplification using polydopamine nanospheres-based biosensors for one-pot detection of microRNAs. Biosens Bioelectron 2023; 222:114957. [PMID: 36463653 DOI: 10.1016/j.bios.2022.114957] [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: 09/20/2022] [Revised: 10/27/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
The accurate detection of microRNAs (miRNAs) is essential in the early diagnosis and treatment of cancers. Existing miRNA detection methods represented by nucleic acid amplification (NAA) techniques, such as qRT-PCR, suffer from the small size of miRNAs and lead to limited practicability. CRISPR Cas13a system, another valuable toolbox for nucleic acid detection, relies heavily on the behaviors of accompanying isothermal NAA techniques, which prompts similar deficiencies in miRNA detection. In this study, a dual nucleases-assisted cyclic amplification (DUNCAN) strategy has been established to replace NAA techniques for one-pot detection of miRNAs. The DUNCAN strategy contained an initial reaction based on CRISPR Cas13a for target recognition, and an accompanied cyclic reaction using DNA probes protected by polydopamine nanospheres (PDANSs) for signal amplification and result readout. Exemplified by miR-19b, which has been confirmed to be related to several tumors, the quantitative detection through the DUNCAN strategy was achieved in the dynamic range of 10-106 fM, with a calculated detection limit of 1.27 fM. Besides, the DUNCAN strategy presented well selectivity and anti-interference performance for accurate detection of miR-19b in complex miRNA mixtures, different cell lines and clinical samples compared with qRT-PCR. All these performances demonstrated the promising potential of the DUNCAN strategy in clinical miRNA detection and diagnosis.
Collapse
Affiliation(s)
- Di Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Peijie Shen
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Chutian Xu
- Department of Biomedical Engineering, School of Engineering, Tufts University, Medford, MA, 02155, USA
| | - Zhipeng Xu
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310027, China
| | - Dongyuan Cheng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, 410000, China
| | - Mengjun Fang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Ziyi Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| |
Collapse
|
13
|
Qin C, Wang Y, Hu J, Wang T, Liu D, Dong J, Lu Y. Artificial Olfactory Biohybrid System: An Evolving Sense of Smell. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204726. [PMID: 36529960 PMCID: PMC9929144 DOI: 10.1002/advs.202204726] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The olfactory system can detect and recognize tens of thousands of volatile organic compounds (VOCs) at low concentrations in complex environments. Bioelectronic nose (B-EN), which mimics olfactory systems, is becoming an emerging sensing technology for identifying VOCs with sensitivity and specificity. B-ENs integrate electronic sensors with bioreceptors and pattern recognition technologies to enable medical diagnosis, public security, environmental monitoring, and food safety. However, there is currently no commercially available B-EN on the market. Apart from the high selectivity and sensitivity necessary for volatile organic compound analysis, commercial B-ENs must overcome issues impacting sensor operation and other problems associated with odor localization. The emergence of nanotechnology has provided a novel research concept for addressing these problems. In this work, the structure and operational mechanisms of biomimetic olfactory systems are discussed, with an emphasis on the development and immobilization of materials. Various biosensor applications and current developments are reviewed. Challenges and opportunities for fulfilling the potential of artificial olfactory biohybrid systems in fundamental and practical research are investigated in greater depth.
Collapse
Affiliation(s)
- Chuanting Qin
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
- Tianjin Industrial Microbiology Key LaboratoryCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Yi Wang
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
- Tianjin Industrial Microbiology Key LaboratoryCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Jiawang Hu
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
| | - Ting Wang
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
| | - Dong Liu
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
| | - Jian Dong
- Tianjin Industrial Microbiology Key LaboratoryCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Yuan Lu
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
| |
Collapse
|
14
|
Kumaran A, Jude Serpes N, Gupta T, James A, Sharma A, Kumar D, Nagraik R, Kumar V, Pandey S. Advancements in CRISPR-Based Biosensing for Next-Gen Point of Care Diagnostic Application. BIOSENSORS 2023; 13:202. [PMID: 36831968 PMCID: PMC9953454 DOI: 10.3390/bios13020202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 05/25/2023]
Abstract
With the move of molecular tests from diagnostic labs to on-site testing becoming more common, there is a sudden rise in demand for nucleic acid-based diagnostic tools that are selective, sensitive, flexible to terrain changes, and cost-effective to assist in point-of-care systems for large-scale screening and to be used in remote locations in cases of outbreaks and pandemics. CRISPR-based biosensors comprise a promising new approach to nucleic acid detection, which uses Cas effector proteins (Cas9, Cas12, and Cas13) as extremely specialized identification components that may be used in conjunction with a variety of readout approaches (such as fluorescence, colorimetry, potentiometry, lateral flow assay, etc.) for onsite analysis. In this review, we cover some technical aspects of integrating the CRISPR Cas system with traditional biosensing readout methods and amplification technologies such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA) and continue to elaborate on the prospects of the developed biosensor in the detection of some major viral and bacterial diseases. Within the scope of this article, we also discuss the recent COVID pandemic and the numerous CRISPR biosensors that have undergone development since its advent. Finally, we discuss some challenges and future prospects of CRISPR Cas systems in point-of-care testing.
Collapse
Affiliation(s)
- Akash Kumaran
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Nathan Jude Serpes
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Tisha Gupta
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Abija James
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Avinash Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Rupak Nagraik
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Vaneet Kumar
- Department of Natural Science, CT University, Ludhiana 142024, Punjab, India
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
| |
Collapse
|
15
|
Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. BIOCHEMISTRY (MOSCOW) 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
Collapse
Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| |
Collapse
|
16
|
Lin C, Huang Q, Tian M, Luo F, Wang J, Qiu B, Yang S, Lin Z. Electrochemiluminescence biosensor for DNA adenine methylation methyltransferase based on CRISPR/Cas12a trans-cleavage-induced dual signal enhancement. Talanta 2023; 251:123748. [PMID: 35921742 DOI: 10.1016/j.talanta.2022.123748] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/30/2022] [Accepted: 07/15/2022] [Indexed: 12/01/2022]
Abstract
In this work, an electrochemiluminescence (ECL) biosensor with dual signal enhancement was constructed and used for DNA adenine methylation methyltransferase (Dam MTase) detection. At present of Dam MTase, restriction endonuclease (DPnI) cleaves hairpin DNA (HP) and releases the HP stem end as a single strand that can activate CRISPR/Cas12a trans-cleavage activity. Assisted by trans-cleavage, the distance between the signal quenching factor ferrocene (Fc) and the ECL signal unit increased, and the repulsion between the signal unit and the Indium Tin Oxides (ITO) electrode decreased. The above results resulted in an enhanced ECL signal. ECL intensity has a good linear relationship with the logarithm of Dam MTase concentration in the range of 5-70 U/mL with a detection limit of 23.4 mU/mL. The proposed biosensor was successfully utilized to detect of Dam MTase in serum samples.
Collapse
Affiliation(s)
- Cuiying Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Qingqing Huang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Mengjian Tian
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Fang Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Jian Wang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Shuofei Yang
- Department of Vascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Pujian Road 160, Shanghai, 200127, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China.
| |
Collapse
|
17
|
Cheng X, Li Y, Kou J, Liao D, Zhang W, Yin L, Man S, Ma L. Novel non-nucleic acid targets detection strategies based on CRISPR/Cas toolboxes: A review. Biosens Bioelectron 2022; 215:114559. [DOI: 10.1016/j.bios.2022.114559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 12/26/2022]
|
18
|
Chen K, Shen Z, Wang G, Gu W, Zhao S, Lin Z, Liu W, Cai Y, Mushtaq G, Jia J, Wan C(C, Yan T. Research progress of CRISPR-based biosensors and bioassays for molecular diagnosis. Front Bioeng Biotechnol 2022; 10:986233. [PMID: 36185462 PMCID: PMC9524266 DOI: 10.3389/fbioe.2022.986233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas technology originated from the immune mechanism of archaea and bacteria and was awarded the Nobel Prize in Chemistry in 2020 for its success in gene editing. Molecular diagnostics is highly valued globally for its development as a new generation of diagnostic technology. An increasing number of studies have shown that CRISPR/Cas technology can be integrated with biosensors and bioassays for molecular diagnostics. CRISPR-based detection has attracted much attention as highly specific and sensitive sensors with easily programmable and device-independent capabilities. The nucleic acid-based detection approach is one of the most sensitive and specific diagnostic methods. With further research, it holds promise for detecting other biomarkers such as small molecules and proteins. Therefore, it is worthwhile to explore the prospects of CRISPR technology in biosensing and summarize its application strategies in molecular diagnostics. This review provides a synopsis of CRISPR biosensing strategies and recent advances from nucleic acids to other non-nucleic small molecules or analytes such as proteins and presents the challenges and perspectives of CRISPR biosensors and bioassays.
Collapse
Affiliation(s)
- Kun Chen
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Ziyi Shen
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Guanzhen Wang
- School of Life Sciences, Shanghai University, Shanghai, China
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining, China
| | - Wei Gu
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Shengchao Zhao
- School of Life Sciences, Shanghai University, Shanghai, China
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining, China
| | - Zihan Lin
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Liu
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining, China
| | - Yi Cai
- Key Laboratory of Molecular Target & Clinical Pharmacology and The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Gohar Mushtaq
- Center for Scientific Research, Faculty of Medicine, Idlib University, Idlib, Syria
| | - Jia Jia
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Jia Jia, ; Chunpeng (Craig) Wan, ; Tingdong Yan,
| | - Chunpeng (Craig) Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Jia Jia, ; Chunpeng (Craig) Wan, ; Tingdong Yan,
| | - Tingdong Yan
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Jia Jia, ; Chunpeng (Craig) Wan, ; Tingdong Yan,
| |
Collapse
|
19
|
Zhu C, Zhang F, Li H, Chen Z, Yan M, Li L, Qu F. CRISPR/Cas Systems Accelerating the Development of Aptasensors. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
20
|
Spangler JR, Leski TA, Schultzhaus Z, Wang Z, Stenger DA. Large scale screening of CRISPR guide RNAs using an optimized high throughput robotics system. Sci Rep 2022; 12:13953. [PMID: 35977955 PMCID: PMC9385653 DOI: 10.1038/s41598-022-17474-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
All CRISPR/CAS systems utilize CRISPR guide RNAs (crRNAs), the design of which depend on the type of CAS protein, genetic target and the environment/matrix. While machine learning approaches have recently been developed to optimize some crRNA designs, candidate crRNAs must still be screened for efficacy under relevant conditions. Here, we demonstrate a high-throughput method to screen hundreds of candidate crRNAs for activation of Cas13a collateral RNA cleavage. Entire regions of a model gene transcript (Y. pestis lcrV gene) were tiled to produce overlapping crRNA sets. We tested for possible effects that included crRNA/target sequence, size and secondary structures, and the commercial source of DNA oligomers used to generate crRNAs. Detection of a 981 nt target RNA was initially successful with 271 out of 296 tested guide RNAs, and that was improved to 287 out of 296 (97%) after protocol optimizations. For this specific example, we determined that crRNA efficacy did not strongly depend on the target region or crRNA physical properties, but was dependent on the source of DNA oligomers used for RNA preparation. Our high-throughput methods for screening crRNAs has general applicability to the optimization of Cas12 and Cas13 guide RNA designs.
Collapse
Affiliation(s)
- J R Spangler
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA.
| | - T A Leski
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - Z Schultzhaus
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Z Wang
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - D A Stenger
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| |
Collapse
|
21
|
Wu L, Wang X, Wu C, Cao X, Tang T, Huang H, Huang X. Ultrasensitive SARS-CoV-2 diagnosis by CRISPR-based screen-printed carbon electrode. Anal Chim Acta 2022; 1221:340120. [PMID: 35934402 PMCID: PMC9249825 DOI: 10.1016/j.aca.2022.340120] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 12/15/2022]
Abstract
Early and accurate diagnosis of SARS-CoV-2 was crucial for COVID-19 control and urgently required ultra-sensitive and rapid detection methods. CRISPR-based detection systems have great potential for rapid SARS-CoV-2 detection, but detecting ultra-low viral loads remains technically challenging. Here, we report an ultrasensitive CRISPR/Cas12a-based electrochemical detection system with an electrochemical biosensor, dubbed CRISPR-SPCE, in which the CRISPR ssDNA reporter was immobilized onto a screen-printed carbon electrode. Electrochemical signals are detected due to CRISPR cleavage, giving enhanced detection sensitivity. CRISPR-SPCE enables ultrasensitive SARS-CoV-2 detection, reaching as few as 0.27 copies μL−1. Moreover, CRISPR-SPCE is also highly specific and inexpensive, providing a fast and simple SARS-CoV-2 assay.
Collapse
|
22
|
Song Y, Chao Y, Guo Y, Zhang F, Mao C, Guan C, Chen G, Feng C. Paper-based netlike rolling circle amplification (NRCA) for ultrasensitive and visual detection of SARS-CoV-2. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 358:131460. [PMID: 35095201 PMCID: PMC8782770 DOI: 10.1016/j.snb.2022.131460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 05/23/2023]
Abstract
COVID-19 is a highly diffuse respiratory infection caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Currently, quantitative real-time polymerase chain reaction (qRT-PCR) technology is commonly used in clinical diagnosis of COVID-19. However, this method is time-consuming and labor-intensive, which is limited in clinical application. Here, we propose a new method for the ultrasensitive and visual detection of SARS-CoV-2 viral nucleic acid. The assay integrates with a paper device and highly efficient isothermal amplification technology - Netlike rolling circle amplification (NRCA), which can reach a limit of detection of 4.12 aM. The paper-based NRCA owns advantages of specificity, portability, visualization and low-cost. Therefore, this method can effectively meet the requirements of point-of-care testing, providing a novel molecular detection technology for clinical diagnosis of COVID-19 and promoting the development of NRCA devices.
Collapse
Affiliation(s)
- Yuchen Song
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yuqing Chao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yi Guo
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Fan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Chaoyang Guan
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| |
Collapse
|
23
|
CRISPR/Cas12a-based electrochemical biosensor for highly sensitive detection of cTnI. Bioelectrochemistry 2022; 146:108167. [DOI: 10.1016/j.bioelechem.2022.108167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/23/2022] [Accepted: 05/16/2022] [Indexed: 12/16/2022]
|
24
|
Shin J, Miller M, Wang YC. Recent advances in CRISPR-based systems for the detection of foodborne pathogens. Compr Rev Food Sci Food Saf 2022; 21:3010-3029. [PMID: 35483732 DOI: 10.1111/1541-4337.12956] [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] [Received: 01/03/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/13/2022]
Abstract
There has long been a need for more advanced forms of pathogen detection in the food industry. Though in its infancy, biosensing based on clustered regularly interspaced short palindromic repeats (CRISPR) has the potential to solve many problems that cannot be addressed using conventional methods. In this review, we briefly introduce and classify the various CRISPR/Cas protein effectors that have thus far been used in biosensors. We then assess the current state of CRISPR technology in food-safety contexts; describe how each Cas effector is utilized in foodborne-pathogen detection; and discuss the limitations of the current technology, as well as how it might usefully be applied in other areas of the food industry. We conclude that, if the limitations of existing CRISPR/Cas-based detection methods are overcome, they can be deployed on a wide scale and produce a range of positive food-safety outcomes.
Collapse
Affiliation(s)
- Jiyong Shin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Michael Miller
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yi-Cheng Wang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
25
|
Wasilewski T, Brito NF, Szulczyński B, Wojciechowski M, Buda N, Melo ACA, Kamysz W, Gębicki J. Olfactory Receptor-based Biosensors as Potential Future Tools in Medical Diagnosis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
26
|
Advances in improvement strategies of digital nucleic acid amplification for pathogen detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
27
|
Cova CM, Rincón E, Espinosa E, Serrano L, Zuliani A. Paving the Way for a Green Transition in the Design of Sensors and Biosensors for the Detection of Volatile Organic Compounds (VOCs). BIOSENSORS 2022; 12:51. [PMID: 35200311 PMCID: PMC8869180 DOI: 10.3390/bios12020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 05/06/2023]
Abstract
The efficient and selective detection of volatile organic compounds (VOCs) provides key information for various purposes ranging from the toxicological analysis of indoor/outdoor environments to the diagnosis of diseases or to the investigation of biological processes. In the last decade, different sensors and biosensors providing reliable, rapid, and economic responses in the detection of VOCs have been successfully conceived and applied in numerous practical cases; however, the global necessity of a sustainable development, has driven the design of devices for the detection of VOCs to greener methods. In this review, the most recent and innovative VOC sensors and biosensors with sustainable features are presented. The sensors are grouped into three of the main industrial sectors of daily life, including environmental analysis, highly important for toxicity issues, food packaging tools, especially aimed at avoiding the spoilage of meat and fish, and the diagnosis of diseases, crucial for the early detection of relevant pathological conditions such as cancer and diabetes. The research outcomes presented in the review underly the necessity of preparing sensors with higher efficiency, lower detection limits, improved selectivity, and enhanced sustainable characteristics to fully address the sustainable manufacturing of VOC sensors and biosensors.
Collapse
Affiliation(s)
- Camilla Maria Cova
- Department of Chemistry, University of Florence and CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy;
| | - Esther Rincón
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Eduardo Espinosa
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Luis Serrano
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Alessio Zuliani
- Department of Chemistry, University of Florence and CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy;
| |
Collapse
|
28
|
Zhao F, Xie S, Li B, Zhang X. Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates. Int J Biol Macromol 2022; 201:592-606. [PMID: 35031315 DOI: 10.1016/j.ijbiomac.2022.01.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.
Collapse
Affiliation(s)
- Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Siying Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| |
Collapse
|
29
|
Sohail M, Qin L, Li S, Chen Y, Zaman MH, Zhang X, Li B, Huang H. Molecular reporters for CRISPR/Cas: from design principles to engineering for bioanalytical and diagnostic applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
30
|
Xie S, Qin C, Zhao F, Shang Z, Wang P, Sohail M, Zhang X, Li B. The DNA-Cu nanocluster and exonuclease I integrated label-free reporting system for CRISPR/Cas12a-based SARS-CoV-2 detection with minimized background signal. J Mater Chem B 2022; 10:6107-6117. [DOI: 10.1039/d2tb00857b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CRISPR-driven biosensing is developing rapidly, but current works mostly adopt dye-labeled ssDNA as the signal reporter, which is costly and unstable. Herein, we developed a label-free and low-background reporter for...
Collapse
|
31
|
Sohail M, Xie S, Zhang X, Li B. Methodologies in visualizing the activation of CRISPR/Cas: The last mile in developing CRISPR-Based diagnostics and biosensing – A review. Anal Chim Acta 2022; 1205:339541. [DOI: 10.1016/j.aca.2022.339541] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
|
32
|
Ding R, Chen Y, Wang Q, Wu Z, Zhang X, Li B, Lin L. Recent advances in quantum dots-based biosensors for antibiotic detection. J Pharm Anal 2021; 12:355-364. [PMID: 35811614 PMCID: PMC9257440 DOI: 10.1016/j.jpha.2021.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Affiliation(s)
- Rui Ding
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yue Chen
- School of Nursing, Nanjing Medical University, Nanjing, 211166, China
| | - Qiusu Wang
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
| | - Zhengzhang Wu
- Jiangsu Conat Biological Products Co., Ltd., Taixing, Jiangsu, 225400, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
- Corresponding author.
| | - Lei Lin
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
- Corresponding author. .
| |
Collapse
|