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Lan H, Shu W, Jiang D, Yu L, Xu G. Cas-based bacterial detection: recent advances and perspectives. Analyst 2024; 149:1398-1415. [PMID: 38357966 DOI: 10.1039/d3an02120c] [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: 02/16/2024]
Abstract
Persistent bacterial infections pose a formidable threat to global health, contributing to widespread challenges in areas such as food safety, medical hygiene, and animal husbandry. Addressing this peril demands the urgent implementation of swift and highly sensitive detection methodologies suitable for point-of-care testing and large-scale screening. These methodologies play a pivotal role in the identification of pathogenic bacteria, discerning drug-resistant strains, and managing and treating diseases. Fortunately, new technology, the CRISPR/Cas system, has emerged. The clustered regularly interspaced short joint repeats (CRISPR) system, which is part of bacterial adaptive immunity, has already played a huge role in the field of gene editing. It has been employed as a diagnostic tool for virus detection, featuring high sensitivity, specificity, and single-nucleotide resolution. When applied to bacterial detection, it also surpasses expectations. In this review, we summarise recent advances in the detection of bacteria such as Mycobacterium tuberculosis (MTB), methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli (E. coli), Salmonella and Acinetobacter baumannii (A. baumannii) using the CRISPR/Cas system. We emphasize the significance and benefits of this methodology, showcasing the capability of diverse effector proteins to swiftly and precisely recognize bacterial pathogens. Furthermore, the CRISPR/Cas system exhibits promise in the identification of antibiotic-resistant strains. Nevertheless, this technology is not without challenges that need to be resolved. For example, CRISPR/Cas systems must overcome natural off-target effects and require high-quality nucleic acid samples to improve sensitivity and specificity. In addition, limited applicability due to the protospacer adjacent motif (PAM) needs to be addressed to increase its versatility. Despite the challenges, we are optimistic about the future of bacterial detection using CRISPR/Cas. We have already highlighted its potential in medical microbiology. As research progresses, this technology will revolutionize the detection of bacterial infections.
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Affiliation(s)
- Huatao Lan
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Weitong Shu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Dan Jiang
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Guangxian Xu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
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Yi M, Gong Y, Zhan Q, Dai Y, Yang T, Cheng X, Ding S, Gu B, Cheng W, Zhang D. A one-pot CRISPR-Cas12a-based toolbox enables determination of terminal deoxynucleotidyl transferase activity for acute leukemia screening. Anal Chim Acta 2023; 1254:341115. [PMID: 37005025 DOI: 10.1016/j.aca.2023.341115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
An isothermal, one-pot toolbox (called OPT-Cas) based on CRISPR-Cas12a collateral cleavage capability is proposed for highly sensitive and selective determination of terminal deoxynucleotidyl transferase (TdT) activity. Oligonucleotide primers with 3'-hydroxyl (OH) terminal were randomly introduced for TdT-induced elongation. In the presence of TdT, dTTP nucleotides polymerized at the 3' terminals of the primers to generate abundant polyT-tails, which function as triggers for the synchronous activation of Cas12a proteins. Finally, the activated Cas12a trans-cleaved FAM and BHQ1 dual-labeled single-stranded DNA (ssDNA-FQ) reporters, producing significantly amplified fluorescence signals. This one-pot assay, that is primer, crRNA, Cas12a protein and ssDNA-FQ reporter are all in one tube, allows simple but high-sensitive quantification of TdT activity with a low detection limit of 6.16 × 10-5 U μL-1 in the concentration scope from 1 × 10-4 U μL-1 to 1 × 10-1 U μL-1, and achieves extraordinary selectivity with other interfering proteins. Furthermore, the OPT-Cas was successfully used to detect TdT in complex matrices and accurate determination of TdT activity in acute lymphoblastic leukemia cells, which might be a reliable technique platform for the diagnosis of TdT-related diseases and biomedical research applications.
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3
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Jiang Y, Zheng C, Jin M, Zhou R, Wu Q, Huang F, Lou Y, Zheng L. An Ultrasensitive Colorimetric Foodborne Pathogenic Detection Method Using a CRISPR/Cas12a Mediated Strand Displacement/Hybridization Chain Reaction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4193-4200. [PMID: 36812357 DOI: 10.1021/acs.jafc.2c08888] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Accurate, rapid, and sensitive pathogenic detections play an important role in food safety. Herein, we developed a novel CRISPR/Cas12a mediated strand displacement/hybridization chain reaction (CSDHCR) nucleic acid assay for foodborne pathogenic colorimetric detection. A biotinylated DNA toehold is coupled on avidin magnetic beads and acts as an initiator strand to trigger the SDHCR. The SDHCR amplification allowed the formation of long hemin/G-quadruplex-based DNAzyme products to catalyze the TMB-H2O2 reaction. In the presence of the DNA targets, the trans-cleavage activity of CRISPR/Cas12a was activated to cleave the initiator DNA, resulting in the failure of SDHCR and no color change. Under optimal conditions, the CSDHCR has a satisfactory linear detection of DNA targets with a regression equation Y = 0.0531*X - 0.0091 (R2 = 0.9903) in the range of 10 fM to 1 nM, and the limit of detection was determined as 4.54 fM. In addition, Vibrio vulnificus, one foodborne pathogen, was used to verify the practical application of the method, and it showed satisfactory specificity and sensitivity with a limit of detection at 1.0 × 100 CFU/mL coupling with recombinase polymerase amplification. Our proposed CSDHCR biosensor could be a promising alternative method for ultrasensitive and visual detection of nucleic acids and the practical application of foodborne pathogens.
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Affiliation(s)
- Yayun Jiang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
- Department of Clinical Laboratory, People's Hospital of Deyang City, Deyang, China 618000
| | - Chaochuan Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Ming Jin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Ruolan Zhou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Qiaoli Wu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Fuyuan Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
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4
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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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McCourt KM, Cochran J, Abdelbasir SM, Carraway ER, Tzeng TRJ, Tsyusko OV, Vanegas DC. Potential Environmental and Health Implications from the Scaled-Up Production and Disposal of Nanomaterials Used in Biosensors. BIOSENSORS 2022; 12:1082. [PMID: 36551049 PMCID: PMC9775545 DOI: 10.3390/bios12121082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Biosensors often combine biological recognition elements with nanomaterials of varying compositions and dimensions to facilitate or enhance the operating mechanism of the device. While incorporating nanomaterials is beneficial to developing high-performance biosensors, at the stages of scale-up and disposal, it may lead to the unmanaged release of toxic nanomaterials. Here we attempt to foster connections between the domains of biosensors development and human and environmental toxicology to encourage a holistic approach to the development and scale-up of biosensors. We begin by exploring the toxicity of nanomaterials commonly used in biosensor design. From our analysis, we introduce five factors with a role in nanotoxicity that should be considered at the biosensor development stages to better manage toxicity. Finally, we contextualize the discussion by presenting the relevant stages and routes of exposure in the biosensor life cycle. Our review found little consensus on how the factors presented govern nanomaterial toxicity, especially in composite and alloyed nanomaterials. To bridge the current gap in understanding and mitigate the risks of uncontrolled nanomaterial release, we advocate for greater collaboration through a precautionary One Health approach to future development and a movement towards a circular approach to biosensor use and disposal.
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Affiliation(s)
- Kelli M. McCourt
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
- Global Alliance for Rapid Diagnostics (GARD), Michigan State University, East Lancing, MI 48824, USA
| | - Jarad Cochran
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Sabah M. Abdelbasir
- Central Metallurgical Research and Development Institute, P.O. Box 87, Helwan 11421, Egypt
| | - Elizabeth R. Carraway
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
| | - Tzuen-Rong J. Tzeng
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Olga V. Tsyusko
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Diana C. Vanegas
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
- Global Alliance for Rapid Diagnostics (GARD), Michigan State University, East Lancing, MI 48824, USA
- Interdisciplinary Group for Biotechnology Innovation and Ecosocial Change (BioNovo), Universidad del Valle, Cali 76001, Colombia
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6
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Misiurina MA, Chirinskaite AV, Fotina AS, Zelinsky AA, Sopova JV, Leonova EI. New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111927. [PMID: 36431062 PMCID: PMC9698171 DOI: 10.3390/life12111927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022]
Abstract
The RNA-guided Cas12a nuclease forms a complex with a CRISPR RNA (crRNA) to cleave the double-stranded DNA target. Among others, Cas12a protein from Lachnospiraceae bacterium (LbCas12a) is widely used for biomedical research. For target recognition, LbCas12a requires a specific nucleotide sequence, named a protospacer adjacent motif (PAM). Besides the canonical TTTV PAM, LbCas12a can recognize other suboptimal PAMs. We examined a novel TTAA PAM for the LbCas12a nuclease and found that the specificity of cleavage was increased. We found that single nucleotide substitutions at all positions of the guide RNA except the 20th position blocked the cleavage of the target DNA. The type of nucleotide substitutions (U-A, U-C or U-G) did not affect the efficiency of cleavage in the 20th position. When we used the canonical PAM under the same conditions, we observed the cleavage of target DNA by LbCas12a in many positions, showing less specificity in given conditions. The efficiency and specificity of the LbCas12a nuclease were evaluated both by gel-electrophoresis and using FAM-labeled single-stranded probes. We were able to assess the change in fluorescence intensity only for several variants of guide RNAs. High specificity allows us to type single nucleotide substitutions and small deletions/insertions (1-2 nucleotides) and look for target mutations when knocking out.
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Affiliation(s)
- Mariia A. Misiurina
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Aleksandra S. Fotina
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Andrey A. Zelinsky
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Julia V. Sopova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
| | - Elena I. Leonova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia
- Correspondence:
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7
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Khizar S, Al-Dossary AA, Zine N, Jaffrezic-Renault N, Errachid A, Elaissari A. Contribution of magnetic particles in molecular diagnosis of human viruses. Talanta 2022; 241:123243. [PMID: 35121538 PMCID: PMC8779935 DOI: 10.1016/j.talanta.2022.123243] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/16/2022]
Abstract
Viral diseases are the primary source of death, making a worldwide influence on healthcare, social, and economic development. Thus, diagnosis is the vital approach to the main aim of virus control and elimination. On the other hand, the prompt advancement of nanotechnology in the field of medicine possesses the probability of being beneficial to diagnose infections normally in labs as well as specifically. Nanoparticles are efficiently in use to make novel strategies because of permitting analysis at cellular in addition to the molecular scale. Henceforth, they assist towards pronounced progress concerning molecular analysis at the nanoscale. In recent times, magnetic nanoparticles conjugated through covalent bonds to bioanalytes for instance peptides, antibodies, nucleic acids, plus proteins are established like nanoprobes aimed at molecular recognition. These modified magnetic nanoparticles could offer a simple fast approach for extraction, purification, enrichment/concentration, besides viruses' recognition precisely also specifically. In consideration of the above, herein insight and outlook into the limitations of conventional methods and numerous roles played by magnetic nanoparticles to extract, purify, concentrate, and additionally in developing a diagnostic regime for viral outbreaks to combat viruses especially the ongoing novel coronavirus (COVID-19).
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Affiliation(s)
- Sumera Khizar
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France
| | - Amal A. Al-Dossary
- Department of Basic Sciences, Deanship of Preparatory Year and Supporting Studies, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34212, Saudi Arabia
| | - Nadia Zine
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France
| | | | - Abdelhamid Errachid
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France
| | - Abdelhamid Elaissari
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France,Corresponding author. ISA, Université Claude Bernard Lyon-1, 5 rue de La Doua, Villeurbanne, 69100, France
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8
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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9
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Berghuis NF, Mars-Groenendijk R, Busker RW, Paauw A, van Leeuwen HC. Combining CRISPR–Cas12a with terminal deoxynucleotidyl transferase dependent reporter elongation for pathogen detection using lateral flow test strips. Biol Methods Protoc 2022; 7:bpac015. [PMID: 35989704 PMCID: PMC9384837 DOI: 10.1093/biomethods/bpac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/09/2022] [Indexed: 12/03/2022] Open
Abstract
CRISPR–Cas (CC)-based detection technologies have some exceptional features, which hold the promise of developing into the next-generation diagnostic platforms. One of these features is the ability to trigger non-specific single-stranded DNA/RNA cleavage activity after specific target recognition and Cas enzyme activation. This cleavage activity can be visualized either by single-stranded DNA/RNA fluorescence resonance energy transfer quenching reporters or via lateral flow strips, which separate and detect the cleaved reporters. In a previous study, we reported coupling CC-cleavage activity with the enzyme terminal deoxynucleotidyl transferase (TdT) that elongates cleaved ssDNA reporter fragments with dTTP nucleotides. These elongated poly(thymine) tails then act as scaffolds for the formation of copper nanoparticles which generate a bright fluorescent signal upon UV excitation. In the current study, we visualize the poly(thymine) tails on lateral flow strips, using different combinations of biotinylated or fluorescein-labeled nucleotides, various reporters, and capture oligos. One particular approach, using a fluorescein reporter, reached a target sensitivity of <1 pM and was named Cas activity assay on a strip and was tested using Bacillus anthracis genomic DNA.
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Affiliation(s)
- Nicole F Berghuis
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO , 2288 GJ Rijswijk, The Netherlands
| | - Roos Mars-Groenendijk
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO , 2288 GJ Rijswijk, The Netherlands
| | - Ruud W Busker
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO , 2288 GJ Rijswijk, The Netherlands
| | - Armand Paauw
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO , 2288 GJ Rijswijk, The Netherlands
| | - Hans C van Leeuwen
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO , 2288 GJ Rijswijk, The Netherlands
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10
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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...
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11
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Lee S, Nam D, Park JS, Kim S, Lee ES, Cha BS, Park KS. Highly Efficient DNA Reporter for CRISPR/Cas12a-Based Specific and Sensitive Biosensor. BIOCHIP JOURNAL 2022; 16:463-470. [PMID: 36117747 PMCID: PMC9468524 DOI: 10.1007/s13206-022-00081-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/16/2022] [Accepted: 08/26/2022] [Indexed: 12/29/2022]
Abstract
In addition to cis-cleavage activity that recognizes and cleaves nucleic acid sequences, a trans-cleavage activity that indiscriminately and non-specifically cleaves single-stranded DNA or RNA has been discovered in some Cas proteins, including Cas12a and Cas13a. Various detection methods using this activity have been widely reported. Herein, we describe a new highly efficient DNA reporter (5'-TTATT-CCCCC-3'; TTATT-5C) that outperformed the existing AT-rich DNA reporter (5'-TTATT-3') used in most Cas12a-based target nucleic detection assays. By systematically investigating the effect of DNA reporter length and sequence on the trans-cleavage activity of Cas12a, we achieved up to a 100-fold increase in fluorescence signal intensity derived from the trans-cleavage activity of Cas12a compared to that achieved using the existing AT-rich DNA reporter. The new DNA reporter was also applied, along with the existing AT-rich DNA reporter, for the detection of the Salmonella enterotoxin (stn) gene. Importantly, both detection speed and limit were significantly enhanced with the new DNA reporter. In addition, polymerase chain reaction (PCR) was adopted to the CRISR/Cas-Based system of the new DNA reporter, thereby confirming its practical applicability. The high-efficiency DNA reporter described herein can pave the way for further improving the trans-cleavage activity of other Cas proteins, as well as the sensitivity of CRISPR/Cas-Based systems. Supplementary Information The online version contains supplementary material available at 10.1007/s13206-022-00081-0.
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Affiliation(s)
- Seungjin Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Deahan Nam
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jung Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Seokjoon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Eun Sung Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Byung Seok Cha
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
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12
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Wu Y, Battalapalli D, Hakeem MJ, Selamneni V, Zhang P, Draz MS, Ruan Z. Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections. J Nanobiotechnology 2021; 19:401. [PMID: 34863214 PMCID: PMC8642896 DOI: 10.1186/s12951-021-01132-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is spreading rapidly around the world and seriously impeding efforts to control microbial infections. Although nucleic acid testing is widely deployed for the detection of antibiotic resistant bacteria, the current techniques-mainly based on polymerase chain reaction (PCR)-are time-consuming and laborious. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance (AMR). The CRISPR-Cas system is an adaptive immune system found in many prokaryotes that presents attractive opportunities to target and edit nucleic acids with high precision and reliability. Engineered CRISPR-Cas systems are reported to effectively kill bacteria or even revert bacterial resistance to antibiotics (resensitizing bacterial cells to antibiotics). Strategies for combating antimicrobial resistance using CRISPR (i.e., Cas9, Cas12, Cas13, and Cas14) can be of great significance in detecting bacteria and their resistance to antibiotics. This review discusses the structures, mechanisms, and detection methods of CRISPR-Cas systems and how these systems can be engineered for the rapid and reliable detection of bacteria using various approaches, with a particular focus on nanoparticles. In addition, we summarize the most recent advances in applying the CRISPR-Cas system for virulence modulation of bacterial infections and combating antimicrobial resistance.
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Affiliation(s)
- Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Mohammed J Hakeem
- Department of Food Science and Human Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Venkatarao Selamneni
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pengfei Zhang
- Department of Central Laboratory, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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13
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Phan QA, Truong LB, Medina-Cruz D, Dincer C, Mostafavi E. CRISPR/Cas-powered nanobiosensors for diagnostics. Biosens Bioelectron 2021; 197:113732. [PMID: 34741959 DOI: 10.1016/j.bios.2021.113732] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/16/2021] [Accepted: 10/24/2021] [Indexed: 12/26/2022]
Abstract
CRISPR diagnostics (CRISPR-Dx) offer a wide range of enhancements compared to traditional nanobiosensors by taking advantage of the excellent trans-cleavage activity of the CRISPR/Cas systems. However, the single-stranded DNA/RNA reporters of the current CRISPR-Dx suffer from poor stability and limited sensitivity, which make their application in complex biological environments difficult. In comparison, nanomaterials, especially metal nanoparticles, exhibits robust stability and desirable optical and electrocatalytical properties, which make them ideal as reporter molecules. Therefore, biosensing research is moving towards the use of the trans-cleavage activity of CRISPR/Cas effectors on metal nanoparticles and apply the new phenomenon to develop novel nanobiosensors to target various targets such as viral infections, genetic mutations and tumor biomarkers, by using different sensing methods, including, but not limited to fluorescence, luminescence resonance, colorimetric and electrochemical signal readout. In this review, we explore some of the most recent advances in the field of CRISPR-powered nanotechnological biosensors. Demonstrating high accuracy, sensitivity, selectivity and versatility, nanobiosensors along with CRISPR/Cas technology offer tremendous potential for next-generation diagnostics of multiple targets, especially at the point of care and without any target amplification.
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Affiliation(s)
- Quynh Anh Phan
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA; Department of Biology, Tufts University, Medford, MA, 02155, USA
| | - Linh B Truong
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
| | - David Medina-Cruz
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Can Dincer
- Department of Microsystems Engineering - IMTEK, University of Freiburg, Freiburg, 79110, Germany; FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, 79110, Germany
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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14
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Yue H, Huang M, Tian T, Xiong E, Zhou X. Advances in Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)-Based Diagnostic Assays Assisted by Micro/Nanotechnologies. ACS NANO 2021; 15:7848-7859. [PMID: 33961413 DOI: 10.1021/acsnano.1c02372] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Clustered, regularly interspaced short palindromic repeats (CRISPR)-based diagnoses, derived from gene-editing technology, have been exploited for less than 5 years and are now reaching the stage of precommercial use. CRISPR tools have some notable features, such as recognition at physiological temperature, excellent specificity, and high-efficiency signal amplification capabilities. These characteristics are promising for the development of next-generation diagnostic technologies. In this Perspective, we present a detailed summary of which micro/nanotechnologies play roles in the advancement of CRISPR diagnosis and how they are involved. The use of nanoprobes, nanochips, and nanodevices, microfluidic technology, lateral flow strips, etc. in CRISPR detection systems has led to new opportunities for CRISPR-based diagnosis assay development, such as achieving equipment-free detection, providing more compact detection systems, and improving sensitivity and quantitative capabilities. Although tremendous progress has been made, CRISPR diagnosis has not yet reached its full potential. We discuss upcoming opportunities and improvements and how micro/nanotechnologies will continue to play key roles.
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Affiliation(s)
- Huahua Yue
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mengqi Huang
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Tian Tian
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Erhu Xiong
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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15
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Spoelstra WK, Jacques JM, Gonzalez-Linares R, Nobrega FL, Haagsma AC, Dogterom M, Meijer DH, Idema T, Brouns SJJ, Reese L. CRISPR-based DNA and RNA detection with liquid-liquid phase separation. Biophys J 2021; 120:1198-1209. [PMID: 33617832 PMCID: PMC8059199 DOI: 10.1016/j.bpj.2021.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/01/2021] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
The ability to detect specific nucleic acid sequences allows for a wide range of applications such as the identification of pathogens, clinical diagnostics, and genotyping. CRISPR-Cas proteins Cas12a and Cas13a are RNA-guided endonucleases that bind and cleave specific DNA and RNA sequences, respectively. After recognition of a target sequence, both enzymes activate indiscriminate nucleic acid cleavage, which has been exploited for sequence-specific molecular diagnostics of nucleic acids. Here, we present a label-free detection approach that uses a readout based on solution turbidity caused by liquid-liquid phase separation (LLPS). Our approach relies on the fact that the LLPS of oppositely charged polymers requires polymers to be longer than a critical length. This length dependence is predicted by the Voorn-Overbeek model, which we describe in detail and validate experimentally in mixtures of polynucleotides and polycations. We show that the turbidity resulting from LLPS can be used to detect the presence of specific nucleic acid sequences by employing the programmable CRISPR-nucleases Cas12a and Cas13a. Because LLPS of polynucleotides and polycations causes solutions to become turbid, the detection of specific nucleic acid sequences can be observed with the naked eye. We furthermore demonstrate that there is an optimal polynucleotide concentration for detection. Finally, we provide a theoretical prediction that hints towards possible improvements of an LLPS-based detection assay. The deployment of LLPS complements CRISPR-based molecular diagnostic applications and facilitates easy and low-cost nucleotide sequence detection.
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Affiliation(s)
- Willem Kasper Spoelstra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Jeroen M Jacques
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Rodrigo Gonzalez-Linares
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Franklin L Nobrega
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Anna C Haagsma
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Dimphna H Meijer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Timon Idema
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Louis Reese
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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