201
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Liu W, Yue F, Lee LP. Integrated Point-of-Care Molecular Diagnostic Devices for Infectious Diseases. Acc Chem Res 2021; 54:4107-4119. [PMID: 34699183 DOI: 10.1021/acs.accounts.1c00385] [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] [Indexed: 12/26/2022]
Abstract
The global outbreaks of deadly infectious diseases caused by pathogenic microorganisms have threatened public health worldwide and significantly motivated scientists to satisfy an urgent need for a rapid and accurate detection of pathogens. Traditionally, the culture-based technique is considered as the gold standard for pathogen detection, yet it has a long turnaround time due to the overnight culturing and pathogen isolation. Alternatively, nucleic acid amplification tests provide a relatively shorter turnaround time to identify whether pathogens exist in individuals with high sensitivity and high specificity. In most cases, nucleic acid amplification tests undergo three steps: sample preparation, nucleic acid amplification, and signal transduction. Despite the explosive advancement in nucleic acid amplification and signal transduction technologies, the complex and labor-intensive sample preparation steps remain a bottleneck to create a transformative integrated point-of-care (POC) molecular diagnostic device. Researchers have attempted to simplify and integrate the sample preparations for nucleic acid-based molecular diagnostic devices with innovative progress in integration strategies, engineered materials, reagent storages, and fluid actuation. Therefore, understanding the know-how and obtaining truthful knowledge of existing integrated POC molecular diagnostic devices comprising sample preparations, nucleic acid amplification, and signal transduction can generate innovative solutions to achieve personalized precision medicine and improve global health.In this Account, we discuss the challenges of automated sample preparation solutions integrated with nucleic acid amplification and signal transduction for rapid and precise home diagnostics. Blood, nasal swab, saliva, urine, and stool are emphasized as the most commonly used clinical samples for integrated POC molecular diagnostics of infectious diseases. Even though these five types of samples possess relatively correlated biomarkers due to the human body's circulatory system, each shows unique properties and exclusive advantages for molecular diagnostics in specific situations, which are included in this Account. We examine different integrated POC devices for sample preparation, which includes pathogen isolation and enrichment from the crude sample and nucleic acid purification from isolated pathogens. We present the promising on-chip integration approaches for nucleic acid amplification. We also investigate the on-chip integration methods for reagent storage, which is crucial to simplify the manual operation for end-users. Finally, we present several integrated POC molecular diagnostic devices for infectious diseases. The integrated sample preparation and nucleic acid amplification approach reviewed here can potentially impact the next generation of POC molecular home diagnostic chips, which will significantly impact public health, emergency medicine, and global biosecurity.
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Affiliation(s)
- Wenpeng Liu
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Fei Yue
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Luke P Lee
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley 94720, California, United States
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
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202
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Halima HB, Errachid A, Jaffrezic‐Renault N. Electrochemical Affinity Sensors Using Field Effect Transducer Devices for Chemical Analysis. ELECTROANAL 2021. [DOI: 10.1002/elan.202100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hamdi Ben Halima
- University of Lyon Institute of Analytical Sciences 69100 Villeurbanne France
| | - Abdelhamid Errachid
- University of Lyon Institute of Analytical Sciences 69100 Villeurbanne France
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203
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Pisarev EK, Kapitanova OO, Vesolova IA, Zvereva MI. Amplification-Free Identification and Determination of Nucleic Acids by Surface Plasmon Resonance and Surface-Enhanced Raman Spectroscopy. MOSCOW UNIVERSITY CHEMISTRY BULLETIN 2021. [PMCID: PMC8647960 DOI: 10.3103/s0027131421060079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
This review discusses contemporary approaches to designing sensory systems for the identification and determination of nucleic acids (NAs) without amplifying target molecules. Here we summarize the data about methods based on surface plasmon resonance and surface-enhanced Raman spectroscopy, as well as their possibilities, limitations, and prospects for further development.
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204
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Hillary VE, Ignacimuthu S, Ceasar SA. Potential of CRISPR/Cas system in the diagnosis of COVID-19 infection. Expert Rev Mol Diagn 2021; 21:1179-1189. [PMID: 34409907 PMCID: PMC8607542 DOI: 10.1080/14737159.2021.1970535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Emerging novel infectious diseases and persistent pandemics with potential to destabilize normal life remain a public health concern for the whole world. The recent outbreak of pneumonia caused by Coronavirus infectious disease-2019 (COVID-19) resulted in high mortality due to a lack of effective drugs or vaccines. With a constantly increasing number of infections with mutated strains and deaths across the globe, rapid, affordable and specific detections with more accurate diagnosis and improved health treatments are needed to combat the spread of this novel pathogen COVID-19. AREAS COVERED Researchers have started to utilize the recently invented clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR/Cas)-based tools for the rapid detection of novel COVID-19. In this review, we summarize the potential of CRISPR/Cas system for the diagnosis and enablement of efficient control of COVID-19. EXPERT OPINION Multiple groups have demonstrated the potential of utilizing CRISPR-based diagnosis tools for the detection of SARS-CoV-2. In coming months, we expect more novel and rapid CRISPR-based kits for mass detection of COVID-19-infected persons within a fraction of a second. Therefore, we believe science will conquer COVID-19 in the near future.
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Affiliation(s)
- V. Edwin Hillary
- Division of Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | | | - S. Antony Ceasar
- Department of Biosciences, Bharath Institute of Higher Education and Research, Chennai, India
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin, India
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205
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Tang Y, Gao L, Feng W, Guo C, Yang Q, Li F, Le XC. The CRISPR-Cas toolbox for analytical and diagnostic assay development. Chem Soc Rev 2021; 50:11844-11869. [PMID: 34611682 DOI: 10.1039/d1cs00098e] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems have revolutionized biological and biomedical sciences in many ways. The last few years have also seen tremendous interest in deploying the CRISPR-Cas toolbox for analytical and diagnostic assay development because CRISPR-Cas is one of the most powerful classes of molecular machineries for the recognition and manipulation of nucleic acids. In the short period of development, many CRISPR-enabled assays have already established critical roles in clinical diagnostics, biosensing, and bioimaging. We describe in this review the recent advances and design principles of CRISPR mediated analytical tools with an emphasis on the functional roles of CRISPR-Cas machineries as highly efficient binders and molecular scissors. We highlight the diverse engineering approaches for molecularly modifying CRISPR-Cas machineries and for devising better readout platforms. We discuss the potential roles of these new approaches and platforms in enhancing assay sensitivity, specificity, multiplexity, and clinical outcomes. By illustrating the biochemical and analytical processes, we hope this review will help guide the best use of the CRISPR-Cas toolbox in detecting, quantifying and imaging biologically and clinically important molecules and inspire new ideas, technological advances and engineering strategies for addressing real-world challenges such as the on-going COVID-19 pandemic.
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Affiliation(s)
- Yanan Tang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Lu Gao
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Wei Feng
- Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Chen Guo
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Qianfan Yang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Feng Li
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China. .,Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, T6G 2G3, Canada
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206
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Fu J, Li J, Chen J, Li Y, Liu J, Su X, Shi S. Ultra-specific nucleic acid testing by target-activated nucleases. Crit Rev Biotechnol 2021; 42:1061-1078. [PMID: 34706599 DOI: 10.1080/07388551.2021.1983757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.
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Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yabei Li
- Department of Neurosurgery, People's Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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207
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Khayamian MA, Parizi MS, Ghaderinia M, Abadijoo H, Vanaei S, Simaee H, Abdolhosseini S, Shalileh S, Faramarzpour M, Naeini VF, Hoseinpour P, Shojaeian F, Abbasvandi F, Abdolahad M. A label-free graphene-based impedimetric biosensor for real-time tracing of the cytokine storm in blood serum; suitable for screening COVID-19 patients. RSC Adv 2021; 11:34503-34515. [PMID: 35494759 PMCID: PMC9042719 DOI: 10.1039/d1ra04298j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/22/2021] [Indexed: 12/27/2022] Open
Abstract
Concurrent with the pandemic announcement of SARS-CoV-2 infection by the WHO, a variety of reports were published confirming the cytokine storm as the most mortal effect of the virus on the infected patients. Hence, cytokine storm as an evidenced consequence in most of the COVID-19 patients could offer a promising opportunity to use blood as a disease progression marker. Here, we have developed a rapid electrochemical impedance spectroscopy (EIS) sensor for quantifying the overall immune activity of the patients. Since during the cytokine storm many types of cytokines are elevated in the blood, there is no need for specific detection of a single type of cytokine and the collective behavior is just measured without any electrode functionalization. The sensor includes a monolayer graphene on a copper substrate as the working electrode (WE) which is able to distinguish between the early and severe stage of the infected patients. The charge transfer resistance (R CT) in the moderate and severe cases varies about 65% and 138% compared to the normal groups, respectively and a specificity of 77% and sensitivity of 100% based on ELISA results were achieved. The outcomes demonstrate a significant correlation between the total mass of the three main hypercytokinemia associated cytokines including IL-6, TNF-α and IFN-γ in patients and the R CT values. As an extra application, the biosensor's capability for diagnosis of COVID-19 patients was tested and a sensitivity of 92% and specificity of 50% were obtained compared to the RT-PCR results.
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Affiliation(s)
- Mohammad Ali Khayamian
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,School of Mechanical Engineering, College of Engineering, University of Tehran Tehran 11155-4563 Iran
| | - Mohammad Salemizadeh Parizi
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran
| | - Mohammadreza Ghaderinia
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran
| | - Hamed Abadijoo
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran
| | - Shohreh Vanaei
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,School of Biology, College of Science, University of Tehran P. O. Box: 14155-6655 Tehran Iran
| | - Hossein Simaee
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR Tehran Iran
| | - Saeed Abdolhosseini
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran
| | - Shahriar Shalileh
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran
| | - Mahsa Faramarzpour
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran
| | - Vahid Fadaei Naeini
- School of Mechanical Engineering, College of Engineering, University of Tehran Tehran 11155-4563 Iran.,Division of Machine Elements, Luleå University of Technology Luleå SE-97187 Sweden
| | | | - Fatemeh Shojaeian
- Imam Hossein Clinical Research Development Center, Imam Hossein Hospital, Shahid Beheshti University of Medical Science Tehran Iran
| | - Fereshteh Abbasvandi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR P. O. Box 15179/64311 Tehran Iran
| | - Mohammad Abdolahad
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran P. O. Box 14395/515 Tehran Iran .,Cancer Institute, Imam-Khomeini Hospital, Tehran University of Medical Sciences P. O. Box 13145-158 Tehran Iran.,UT&TUMS Cancer electronic Research Center, Tehran University of Medical Sciences Tehran Iran
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208
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Zhang J, Lv H, Li L, Chen M, Gu D, Wang J, Xu Y. Recent Improvements in CRISPR-Based Amplification-Free Pathogen Detection. Front Microbiol 2021; 12:751408. [PMID: 34659186 PMCID: PMC8515055 DOI: 10.3389/fmicb.2021.751408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022] Open
Abstract
Molecular diagnostic (MDx) methods directly detect target nucleic acid sequences and are therefore an important approach for precise diagnosis of pathogen infection. In comparison with traditional MDx techniques such as PCR, the recently developed CRISPR-based diagnostic technologies, which employ the single-stranded nucleic acid trans-cleavage activities of either Cas12 or Cas13, show merits in both sensitivity and specificity and therefore have great potential in both pathogen detection and beyond. With more and more efforts in improving both the CRISPR trans-cleavage efficiencies and the signal detection sensitivities, CRISPR-based direct detection of target nucleic acids without preamplification can be a possibility. Here in this mini-review, we summarize recent research progresses of amplification-free CRISPR-Dx systems and explore the potential changes they will lead to pathogen diagnosis. In addition, discussion of the challenges for both detection sensitivity and cost of the amplification-free systems will also be covered.
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Affiliation(s)
- Jian Zhang
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hailong Lv
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, China
| | - Linxian Li
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Minjie Chen
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Dayong Gu
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jin Wang
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yong Xu
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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209
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Yu H, Zhao Z, Xiao B, Deng M, Wang Z, Li Z, Zhang H, Zhang L, Qian J, Li J. Aptamer-Based Solution-Gated Graphene Transistors for Highly Sensitive and Real-Time Detection of Thrombin Molecules. Anal Chem 2021; 93:13673-13679. [PMID: 34597019 DOI: 10.1021/acs.analchem.1c03129] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombin is an important biomarker for various diseases and biochemical reactions. Rapid and real-time detection of thrombin that quickly neutralizes in early coagulation in the body has gained significant attention for its practical applications. Solution-gated graphene transistors (SGGTs) have been widely studied due to their higher sensitivity and low-cost fabrication for chemical and biological sensing applications. In this paper, the ssDNA aptamer with 29 bases was immobilized on the surface of the gate electrode to specifically recognize thrombin. The SGGT sensor achieved high sensitivity with a limit of detection (LOD) up to fM. The LOD was attributed to the amplification function of SGGTs and the suitable aptamer choice. The ssDNA configuration folding induced by thrombin molecules and the electropositivity of thrombin molecules could arouse the same electrical response of SGGTs, helping the device obtain a high sensitivity. The channel current variation of sensors had a good linear relationship with the logarithm of thrombin concentration in the range of 1 fM to 10 nM. The fabricated device also demonstrated a short response time to thrombin molecules, and the response time to the 1 fM thrombin molecules was about 150 s. In summary, the sensing strategy of aptamer-based SGGTs with high sensitivity and high selectivity has a good prospect in medical diagnosis.
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Affiliation(s)
- Haiyang Yu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China.,Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Zheng Zhao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Bichen Xiao
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Minghua Deng
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Zhaoliang Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Ziqin Li
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Huibin Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Lei Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Jingwen Qian
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Jinhua Li
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
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210
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Diagnostic Techniques for COVID-19: A Mini-review of Early Diagnostic Methods. JOURNAL OF ANALYSIS AND TESTING 2021; 5:314-326. [PMID: 34631199 PMCID: PMC8488931 DOI: 10.1007/s41664-021-00198-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/25/2021] [Indexed: 12/26/2022]
Abstract
The outbreak of severe pneumonia at the end of 2019 was proved to be caused by the SARS-CoV-2 virus spreading out the world. And COVID-19 spread rapidly through a terrible transmission way by human-to-human, which led to many suspected cases waiting to be diagnosed and huge daily samples needed to be tested by an effective and rapid detection method. With an increasing number of COVID-19 infections, medical pressure is severe. Therefore, more efficient and accurate diagnosis methods were keen urgently established. In this review, we summarized several methods that can rapidly and sensitively identify COVID-19; some of them are widely used as the diagnostic techniques for SARS-CoV-2 in various countries, some diagnostic technologies refer to SARS (Severe Acute Respiratory Syndrome) or/and MERS (Middle East Respiratory Syndrome) detection, which may provide potential diagnosis ideas.
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211
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Li Y, Deng F, Hall T, Vesey G, Goldys EM. CRISPR/Cas12a-powered immunosensor suitable for ultra-sensitive whole Cryptosporidium oocyst detection from water samples using a plate reader. WATER RESEARCH 2021; 203:117553. [PMID: 34425437 DOI: 10.1016/j.watres.2021.117553] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Waterborne pathogens, such as Cryptosporidium parvum, pose a major threat to public health globally, and this requires screening of drinking and environmental water for low number of contaminating microbes. However, current detection approaches generally require trained experts with sophisticated instruments, and are not suitable for large-scale screening and rapid outbreak response. Recent advances in ultrasensitive CRISPR/Cas-based biosensing continue to expand the range of detectable molecular targets, however single microbes could not be directly detected so far, especially in environmental samples. Here, we report an ultrasensitive CRISPR/Cas12a-powered immunosensing method suitable for microbial detection which links antibody-based recognition with CRISPR/Cas12a-based fluorescent signal amplification through an antibody-DNA conjugate. This approach is shown here to detect whole 4 µm size Cryptosporidium parvum oocysts with a linear range from 6.25 - 1600 oocysts/mL, at a maximum sensitivity of single oocyst per sample. Its potential to apply to various complex sample matrices has also been demonstrated. After sample dilution by factor of 10, we were able to detect 10 oocysts from a back-wash mud samples from water treatment plate. This method uses the same experimental setup (plate reader) as a conventional ELISA assay thus reducing the need for microscopy-based identification of Cryptosporidium, which represents the gold-standard but requires high level expertise and time-consuming manual counting. This work highlights the potential of CRISPR/Cas-based biosensing for water quality assessment and ultrasensitive whole pathogen detection.
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Affiliation(s)
- Yi Li
- ARC Centre of Excellence in Nanoscale Biophotonics, University of New South Wales, Sydney 2052, Australia; Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia
| | - Fei Deng
- ARC Centre of Excellence in Nanoscale Biophotonics, University of New South Wales, Sydney 2052, Australia; Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.
| | - Tim Hall
- ARC Centre of Excellence in Nanoscale Biophotonics, University of New South Wales, Sydney 2052, Australia
| | - Graham Vesey
- ARC Centre of Excellence in Nanoscale Biophotonics, University of New South Wales, Sydney 2052, Australia
| | - Ewa M Goldys
- ARC Centre of Excellence in Nanoscale Biophotonics, University of New South Wales, Sydney 2052, Australia; Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.
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212
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Piccinini E, Allegretto JA, Scotto J, Cantillo AL, Fenoy GE, Marmisollé WA, Azzaroni O. Surface Engineering of Graphene through Heterobifunctional Supramolecular-Covalent Scaffolds for Rapid COVID-19 Biomarker Detection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:43696-43707. [PMID: 34470205 DOI: 10.1021/acsami.1c12142] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Graphene is a two-dimensional semiconducting material whose application for diagnostics has been a real game-changer in terms of sensitivity and response time, variables of paramount importance to stop the COVID-19 spreading. Nevertheless, strategies for the modification of docking recognition and antifouling elements to obtain covalent-like stability without the disruption of the graphene band structure are still needed. In this work, we conducted surface engineering of graphene through heterofunctional supramolecular-covalent scaffolds based on vinylsulfonated-polyamines (PA-VS). In these scaffolds, one side binds graphene through multivalent π-π interactions with pyrene groups, and the other side presents vinylsulfonated pending groups that can be used for covalent binding. The construction of PA-VS scaffolds was demonstrated by spectroscopic ellipsometry, Raman spectroscopy, and contact angle measurements. The covalent binding of -SH, -NH2, or -OH groups was confirmed, and it evidenced great chemical versatility. After field-effect studies, we found that the PA-VS-based scaffolds do not disrupt the semiconducting properties of graphene. Moreover, the scaffolds were covalently modified with poly(ethylene glycol) (PEG), which improved the resistance to nonspecific proteins by almost 7-fold compared to the widely used PEG-monopyrene approach. The attachment of recognition elements to PA-VS was optimized for concanavalin A (ConA), a model lectin with a high affinity to glycans. Lastly, the platform was implemented for the rapid, sensitive, and regenerable recognition of SARS-CoV-2 spike protein and human ferritin in lab-made samples. Those two are the target molecules of major importance for the rapid detection and monitoring of COVID-19-positive patients. For that purpose, monoclonal antibodies (mAbs) were bound to the scaffolds, resulting in a surface coverage of 436 ± 30 ng/cm2. KD affinity constants of 48.4 and 2.54 nM were obtained by surface plasmon resonance (SPR) spectroscopy for SARS-CoV-2 spike protein and human ferritin binding on these supramolecular scaffolds, respectively.
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Affiliation(s)
- Esteban Piccinini
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Juan A Allegretto
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Juliana Scotto
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Agustín L Cantillo
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
- GISENS BIOTECH, Ciudad Autónoma de Buenos Aires 1195, Argentina
| | - Gonzalo E Fenoy
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Waldemar A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, CC 16 Suc. 4, La Plata B1904DPI, Argentina
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213
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Verosloff MS, Shapiro SJ, Hawkins EM, Alpay E, Verma D, Stanfield EG, Kreindler L, Jain S, McKay B, Hubbell SA, Hendriks CG, Blizard BA, Broughton JP, Chen JS. CRISPR-Cas enzymes: The toolkit revolutionizing diagnostics. Biotechnol J 2021; 17:e2100304. [PMID: 34505742 DOI: 10.1002/biot.202100304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/11/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022]
Abstract
The programmable nature of sequence-specific targeting by CRISPR-Cas nucleases has revolutionized a wide range of genomic applications and is now emerging as a method for nucleic acid detection. We explore how the diversity of CRISPR systems and their fundamental mechanisms have given rise to a wave of new methods for target recognition and readout. These cross-disciplinary advances found at the intersection of CRISPR biology and engineering have led to the ability to rapidly generate solutions for emerging global challenges like the COVID-19 pandemic. We further discuss the advances and potential for CRISPR-based detection to have an impact across a continuum of diagnostic applications.
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Affiliation(s)
| | | | | | - Emel Alpay
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | - Deepika Verma
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | | | | | - Sonal Jain
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | - Bridget McKay
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | | | | | | | | | - Janice S Chen
- Mammoth Biosciences, Inc., Brisbane, California, USA
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214
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Ahmed MZ, Badani P, Reddy R, Mishra G. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas Advancement in Molecular Diagnostics and Signal Readout Approaches. J Mol Diagn 2021; 23:1433-1442. [PMID: 34454111 DOI: 10.1016/j.jmoldx.2021.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/15/2021] [Accepted: 07/28/2021] [Indexed: 12/26/2022] Open
Abstract
Discovery of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system has greatly improved the gene editing technology. Their applications in the area of diagnostic innovation are gaining much attention. The key characteristics of CRISPR/Cas system that allowed its extensive exploitation in the detection platform are their programmable and highly selective target recognition scheme. Herein, this review presents the major three Cas effectors (Cas9, Cas12, and Cas13) and their significance in various detection assays. The CRISPR/Cas detection strategies, based on their target hybridization, cleavage activity, sensor capabilities, and signal readout methods, are discussed. Some of the recent progressions, challenges, and improvement strategies of CRISPR/Cas technology are highlighted and their biosensing detection platforms toward the development of simple, sensitive, and portable point-of-care diagnostic devices are presented.
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Affiliation(s)
- Md Zohaib Ahmed
- Department of Electrochemical and Molecular Biology, Canary Global Inc., Burlington, Ontario, Canada.
| | - Purav Badani
- Department of Electrochemical and Molecular Biology, Canary Global Inc., Burlington, Ontario, Canada
| | - Raj Reddy
- Department of Electrochemical and Molecular Biology, Canary Global Inc., Burlington, Ontario, Canada
| | - Geetesh Mishra
- Department of Electrochemical and Molecular Biology, Canary Global Inc., Burlington, Ontario, Canada
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215
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Bardhan NM, Jansen P, Belcher AM. Graphene, Carbon Nanotube and Plasmonic Nanosensors for Detection of Viral Pathogens: Opportunities for Rapid Testing in Pandemics like COVID-19. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.733126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
With the emergence of global pandemics such as the Black Death (Plague), 1918 influenza, smallpox, tuberculosis, HIV/AIDS, and currently the COVID-19 outbreak caused by the SARS-CoV-2 virus, there is an urgent, pressing medical need to devise methods of rapid testing and diagnostics to screen a large population of the planet. The important considerations for any such diagnostic test include: 1) high sensitivity (to maximize true positive rate of detection); 2) high specificity (to minimize false positives); 3) low cost of testing (to enable widespread adoption, even in resource-constrained settings); 4) rapid turnaround time from sample collection to test result; and 5) test assay without the need for specialized equipment. While existing testing methods for COVID-19 such as RT-PCR (real-time reverse transcriptase polymerase chain reaction) offer high sensitivity and specificity, they are quite expensive – in terms of the reagents and equipment required, the laboratory expertise needed to run and interpret the test data, and the turnaround time. In this review, we summarize the recent advances made using carbon nanotubes for sensors; as a nanotechnology-based approach for diagnostic testing of viral pathogens; to improve the performance of the detection assays with respect to sensitivity, specificity and cost. Carbon nanomaterials are an attractive platform for designing biosensors due to their scalability, tunable functionality, photostability, and unique opto-electronic properties. Two possible approaches for pathogen detection using carbon nanomaterials are discussed here: 1) optical sensing, and 2) electrochemical sensing. We explore the chemical modifications performed to add functionality to the carbon nanotubes, and the physical, optical and/or electronic considerations used for testing devices or sensors fabricated using these carbon nanomaterials. Given this progress, it is reason to be cautiously optimistic that nanosensors based on carbon nanotubes, graphene technology and plasmonic resonance effects can play an important role towards the development of accurate, cost-effective, widespread testing capacity for the world’s population, to help detect, monitor and mitigate the spread of disease outbreaks.
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216
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Choi JH, Shin M, Yang L, Conley B, Yoon J, Lee SN, Lee KB, Choi JW. Clustered Regularly Interspaced Short Palindromic Repeats-Mediated Amplification-Free Detection of Viral DNAs Using Surface-Enhanced Raman Spectroscopy-Active Nanoarray. ACS NANO 2021; 15:13475-13485. [PMID: 34369760 DOI: 10.1021/acsnano.1c03975] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Nucleic acid biomarkers have been widely used to detect various viral-associated diseases, including the recent pandemic COVID-19. The CRISPR-Cas-based trans-activating phenomenon has shown excellent potential for developing sensitive and selective detection of nucleic acids. However, the nucleic acid amplification steps are typically required when sensitive and selective monitoring of the target nucleic acid is needed. To overcome the aforementioned challenges, we developed a CRISPR-Cas12a-based nucleic acid amplification-free biosensor by a surface-enhanced Raman spectroscopy (SERS)-assisted ultrasensitive detection system. We integrated the activated CRISPR-Cas12a by viral DNA with a Raman-sensitive system composed of ssDNA-immobilized Raman probe-functionalized Au nanoparticles (RAuNPs) on the graphene oxide (GO)/triangle Au nanoflower array. Using this CRISPR-based Raman-sensitive system improved the detection sensitivity of the multiviral DNAs such as hepatitis B virus (HBV), human papillomavirus 16 (HPV-16), and HPV-18 with an extremely low detection limit and vast detection range from 1 aM to 100 pM without the amplification steps. We suggest that this ultrasensitive amplification-free detection system for nucleic acids can be widely applied to the precise and early diagnosis of viral infections, cancers, and several genetic diseases.
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Affiliation(s)
- Jin-Ha Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
- School of Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do 54896, Republic of Korea
| | - Minkyu Shin
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Letao Yang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Brian Conley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Jinho Yoon
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Sang-Nam Lee
- Uniance Gene Inc., 1107 Teilhard Hall, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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217
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Kim S, Ji S, Koh HR. CRISPR as a Diagnostic Tool. Biomolecules 2021; 11:1162. [PMID: 34439828 PMCID: PMC8391464 DOI: 10.3390/biom11081162] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.
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Affiliation(s)
| | | | - Hye Ran Koh
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea; (S.K.); (S.J.)
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218
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Molecular tools against the illegal exploitation of the threatened Pacific seahorse Hippocampus ingens Girard, 1858. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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219
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Pham TTT, Tran DP, Nguyen MC, Amen MT, Winter M, Whitehead C, Toh J, Thierry B. A simplified point-of-care testing approach for preeclampsia blood biomarkers based on nanoscale field effect transistors. NANOSCALE 2021; 13:12279-12287. [PMID: 34251003 DOI: 10.1039/d1nr02461b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rapid diagnosis of preeclampsia is necessary to ensure timely administration of appropriate care and prevent the potentially catastrophic complications of the condition affecting both mothers and babies. While the diagnostic superiority of angiogenic blood biomarkers such as placental growth factor has recently been demonstrated, there is an urgent need to develop point-of-care (PoC) technologies that allow rapid, quantitative, and accurate testing for these markers within local communities. Towards addressing this need, here we report on a fully integrated biodiagnostic platform based on nanoscale indium oxide field effect transistor (FET) sensors. The high-performance FET sensors are integrated with blood sample processing cartridges that minimize the need for operator intervention during the assay and eliminate the need for analytical equipment. Within 40 minutes and from 30 μL of blood, the FET platform could reliably measure PlGF with a limit of detection of 0.06 pg mL-1 and a five order of magnitudes dynamic range. Pilot clinical validation in four preeclamptic pregnancies confirmed that the accuracy and reliability of the FET platform, paving the way for further development to a much-needed point-of-care preeclampsia testing.
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Affiliation(s)
- Thuy Thi Thanh Pham
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia 5095, Australia.
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220
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Bao M, Chen Q, Xu Z, Jensen EC, Liu C, Waitkus JT, Yuan X, He Q, Qin P, Du K. Challenges and Opportunities for Clustered Regularly Interspaced Short Palindromic Repeats Based Molecular Biosensing. ACS Sens 2021; 6:2497-2522. [PMID: 34143608 DOI: 10.1021/acssensors.1c00530] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeats, CRISPR, has recently emerged as a powerful molecular biosensing tool for nucleic acids and other biomarkers due to its unique properties such as collateral cleavage nature, room temperature reaction conditions, and high target-recognition specificity. Numerous platforms have been developed to leverage the CRISPR assay for ultrasensitive biosensing applications. However, to be considered as a new gold standard, several key challenges for CRISPR molecular biosensing must be addressed. In this paper, we briefly review the history of biosensors, followed by the current status of nucleic acid-based detection methods. We then discuss the current challenges pertaining to CRISPR-based nucleic acid detection, followed by the recent breakthroughs addressing these challenges. We focus upon future advancements required to enable rapid, simple, sensitive, specific, multiplexed, amplification-free, and shelf-stable CRISPR-based molecular biosensors.
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Affiliation(s)
- Mengdi Bao
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Qun Chen
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Zhiheng Xu
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Erik C. Jensen
- HJ Science & Technology Inc., San Leandro, California 94710, United States
| | - Changyue Liu
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Jacob T. Waitkus
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Xi Yuan
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Qian He
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Ke Du
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
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221
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Liu J, Chen J, Wu D, Huang M, Chen J, Pan R, Wu Y, Li G. CRISPR-/Cas12a-Mediated Liposome-Amplified Strategy for the Surface-Enhanced Raman Scattering and Naked-Eye Detection of Nucleic Acid and Application to Food Authenticity Screening. Anal Chem 2021; 93:10167-10174. [PMID: 34278781 DOI: 10.1021/acs.analchem.1c01163] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Surface-enhanced Raman scattering (SERS) has been recognized as a powerful tool for biosensors due to the ultrahigh sensitivity and unique fingerprint information. However, there are some limitations in trace target nucleic acid detection for the restricted signal-transducing and amplification strategies. Inspired by CRISPR/Cas12a with specific target DNA-activated collateral single-strand DNA (ssDNA) cleavage activity and liposome with signal molecule-loading properties, we first proposed a sensitive SERS-based on-site nucleic acid detection strategy mediated by CRISPR/Cas12a with trans-cleavage activity on ssDNA linkers utilized to capture liposomes. Liposomes loading two kinds of signal molecules, 4-nitrothiophenol (4-NTP) and cysteine, could achieve the dual-mode detection of target DNA with SERS and naked eye, respectively. The promptly amplified signals were initiated by the triggered breakdown of signal molecule-loaded liposomes. Emancipated 4-NTP, a biological-silent Raman reporter, would achieve highly selective and sensitive SERS measurement. Released cysteine induced the aggregation of plasmonic gold nanoparticles, leading to an obvious red to blue colorimetric shift to realize portable naked-eye detection. With this strategy, target nucleic acid concentration was dexterously converted into SERS and visualization signals and could be detected as low as 100 aM and 10 pM, respectively. The approach was also successfully applied to determine meat adulteration, achieving the detection of a low adulteration ratio in the complicated food matrix. We anticipate that this strategy will not only be regarded as a universal platform for the on-site detection of food authenticity but also broaden SERS application for the accurate determination of diverse biomarkers.
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Affiliation(s)
- Jianghua Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jiahui Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
| | - Mingquan Huang
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, China
| | - Jian Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Ruiyuan Pan
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.,NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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222
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Bonini A, Poma N, Vivaldi F, Biagini D, Bottai D, Tavanti A, Di Francesco F. A label-free impedance biosensing assay based on CRISPR/Cas12a collateral activity for bacterial DNA detection. J Pharm Biomed Anal 2021; 204:114268. [PMID: 34298471 DOI: 10.1016/j.jpba.2021.114268] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022]
Abstract
The rapid and selective identification in the clinical setting of pathogenic bacteria causing healthcare associated infections (HAIs) and in particular blood stream infections (BSIs) is a major challenge, as the number of people affected worldwide and the associated mortality are on the rise. In fact, traditional laboratory techniques such culture and polymerase chain reaction (PCR)-based methodologies are often associated to long turnaround times, which justify the pressing need for the development of rapid, specific and portable point of care devices. The recently discovered clustered regularly interspaced short palindromic repeat loci (CRISPR) and the new class of programmable endonuclease enzymes called CRISPR associated proteins (Cas) have revolutionised molecular diagnostics. The use of Cas proteins in optical and electrochemical biosensing devices has significantly improved the detection of nucleic acids in clinical samples. In this study, a CRISPR/Cas12a system was coupled with electrochemical impedance spectroscopy (EIS) measurements to develop a label-free biosensing assay for the detection of Escherichia coli and Staphylococcus aureus, two bacterial species commonly associated to BSI infections. The programmable Cas12a endonuclease activity, induced by a specific guide RNA (gRNA), and the triggered collateral activity were assessed in in vitro restriction analyses, and evaluated thanks to impedance measurements using a modified gold electrode. The Cas12a/gRNA system was able to specifically recognize amplicons from different clinical isolates of E. coli and S. aureus with a limit of detection of 3 nM and a short turnaround time approximately of 1.5 h. To the best of our knowledge, this is the first biosensing device based on CRISPR/Cas12a label free impedance assay.
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Affiliation(s)
- Andrea Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy.
| | - Noemi Poma
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy.
| | - Federico Vivaldi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy; Institute of Clinical Physiology, National Research Council, Via G. Moruzzi 1, Pisa, Italy.
| | - Denise Biagini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy.
| | - Daria Bottai
- Department of Biology, University of Pisa, Via San Zeno 35-39, Pisa, Italy.
| | - Arianna Tavanti
- Department of Biology, University of Pisa, Via San Zeno 35-39, Pisa, Italy.
| | - Fabio Di Francesco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy; INSTM, Via G. Giusti 9, Florence, Italy.
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223
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Balderston S, Taulbee JJ, Celaya E, Fung K, Jiao A, Smith K, Hajian R, Gasiunas G, Kutanovas S, Kim D, Parkinson J, Dickerson K, Ripoll JJ, Peytavi R, Lu HW, Barron F, Goldsmith BR, Collins PG, Conboy IM, Siksnys V, Aran K. Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng 2021; 5:713-725. [PMID: 33820980 DOI: 10.1038/s41551-021-00706-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 02/23/2021] [Indexed: 02/02/2023]
Abstract
Simple and fast methods for the detection of target genes with single-nucleotide specificity could open up genetic research and diagnostics beyond laboratory settings. We recently reported a biosensor for the electronic detection of unamplified target genes using liquid-gated graphene field-effect transistors employing an RNA-guided catalytically deactivated CRISPR-associated protein 9 (Cas9) anchored to a graphene monolayer. Here, using unamplified genomic samples from patients and by measuring multiple types of electrical response, we show that the biosensors can discriminate within one hour between wild-type and homozygous mutant alleles differing by a single nucleotide. We also show that biosensors using a guide RNA-Cas9 orthologue complex targeting genes within the protospacer-adjacent motif discriminated between homozygous and heterozygous DNA samples from patients with sickle cell disease, and that the biosensors can also be used to rapidly screen for guide RNA-Cas9 complexes that maximize gene-targeting efficiency.
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Affiliation(s)
- Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | | | | | - Kandace Fung
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | | | - Kasey Smith
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Reza Hajian
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | - Giedrius Gasiunas
- CasZyme, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Daehwan Kim
- University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | | | - Hsiang-Wei Lu
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | | | | | | | | | - Virginijus Siksnys
- CasZyme, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA.
- Cardea, San Diego, CA, USA.
- University of California, Berkeley, Berkeley, CA, USA.
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224
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Kaminski MM, Abudayyeh OO, Gootenberg JS, Zhang F, Collins JJ. CRISPR-based diagnostics. Nat Biomed Eng 2021; 5:643-656. [PMID: 34272525 DOI: 10.1038/s41551-021-00760-7] [Citation(s) in RCA: 433] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 06/02/2021] [Indexed: 02/02/2023]
Abstract
The accurate and timely diagnosis of disease is a prerequisite for efficient therapeutic intervention and epidemiological surveillance. Diagnostics based on the detection of nucleic acids are among the most sensitive and specific, yet most such assays require costly equipment and trained personnel. Recent developments in diagnostic technologies, in particular those leveraging clustered regularly interspaced short palindromic repeats (CRISPR), aim to enable accurate testing at home, at the point of care and in the field. In this Review, we provide a rundown of the rapidly expanding toolbox for CRISPR-based diagnostics, in particular the various assays, preamplification strategies and readouts, and highlight their main applications in the sensing of a wide range of molecular targets relevant to human health.
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Affiliation(s)
- Michael M Kaminski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Feng Zhang
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - James J Collins
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, MIT, Cambridge, MA, USA. .,Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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225
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Balderston S, Clouse G, Ripoll JJ, Pratt GK, Gasiunas G, Bock JO, Bennett EP, Aran K. Diversification of the CRISPR Toolbox: Applications of CRISPR-Cas Systems Beyond Genome Editing. CRISPR J 2021; 4:400-415. [PMID: 34152221 PMCID: PMC8418451 DOI: 10.1089/crispr.2020.0137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The discovery of CRISPR has revolutionized the field of genome engineering, but the potential of this technology is far from reaching its limits. In this review, we explore the broad range of applications of CRISPR technology to highlight the rapid expansion of the field beyond gene editing alone. It has been demonstrated that CRISPR technology can control gene expression, spatiotemporally image the genome in vivo, and detect specific nucleic acid sequences for diagnostics. In addition, new technologies are under development to improve CRISPR quality controls for gene editing, thereby improving the reliability of these technologies for therapeutics and beyond. These are just some of the many CRISPR tools that have been developed in recent years, and the toolbox continues to diversify.
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Affiliation(s)
- Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabrielle Clouse
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juan-José Ripoll
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Grace K. Pratt
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Giedrius Gasiunas
- Novo Nordisk A/S, Biopharm Research, Gene Therapy Department, Måløv, Denmark; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- CasZyme, Vilnius, Lithuania; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens-Ole Bock
- Cobo Technologies ApS, Maaloev, Denmark; and Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eric Paul Bennett
- Novo Nordisk A/S, Biopharm Research, Gene Therapy Department, Måløv, Denmark; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardea, San Diego, California, USA; Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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226
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Abstract
New CRISPR enzyme activities add to the nucleic acid detection arsenal
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Affiliation(s)
- Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
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227
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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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228
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Li P, Wang L, Yang J, Di LJ, Li J. Applications of the CRISPR-Cas system for infectious disease diagnostics. Expert Rev Mol Diagn 2021; 21:723-732. [PMID: 33899643 DOI: 10.1080/14737159.2021.1922080] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Rapid and accurate diagnostic approaches are essential for impeding the spread of infectious diseases. This review aims to summarize current progress of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) systems in the applications for diagnostics of infectious diseases including the ongoing COVID-19 epidemic. AREAS COVERED In this review, we discuss class 2 CRISPR-Cas biosensing systems-based diagnostics in various emerging and reemerging infectious diseases, CRISPR-Cas systems have created a new era for early diagnostics of infectious diseases, especially with the discovery of the collateral cleavage activity of Cas12 and Cas13. We mainly focus on different CRISPR-Cas effectors for the detection of pathogenic microorganisms as well as provide a detailed explanation of the pros and cons of CRISPR-Cas biosensing systems. In addition, we also introduce future research perspectives. EXPERT COMMENTARY However, further improvement of newly discovered systems and engineering existing ones should be developed to increase the specificity, sensitivity or stability of the diagnostic tools. It may be a long journey to finish the clinical transition from research use. CRISPR-Cas approaches will emerge as more promising and robust tools for infectious disease diagnosis in the future.
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Affiliation(s)
- Peipei Li
- Kobilka Institute of Innovative Drug Discovery, Faculty of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Li Wang
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Junning Yang
- Frontage Laboratories Inc, Exton, Pennsylvania, USA
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Jingjing Li
- Jinming Yu Academician Workstation of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
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229
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Zhang C, Li Z, Chen M, Hu Z, Wu L, Zhou M, Liang D. Cas12a and Lateral Flow Strip-Based Test for Rapid and Ultrasensitive Detection of Spinal Muscular Atrophy. BIOSENSORS-BASEL 2021; 11:bios11050154. [PMID: 34068874 PMCID: PMC8153588 DOI: 10.3390/bios11050154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
Spinal muscular atrophy (SMA) is characterized by severe lethality and irreversible progression. Early diagnosis of SMA is of more practical significance with the emergence of effective therapy. However, existing techniques to identify SMA patients rely on cumbersome instruments, hindering their accessibility and application. An SMA-Cas12a-strip assay was developed with the integration of Cas12a-based nucleic acid detection, isothermal amplification, and lateral flow strip. The analytical performance of the assay was assessed with clinical samples. To explore its extensible utility, various specimens were tested. Validated with 168 clinical samples, the sensitivity and specificity of the SMA-Cas12a-strip assay were both 100%. The minimum detectable concentration of genomic DNA containing the target gene achieved 526 aM. The assay was compatible with specimens from several sources, and the turnaround time could be within 1.5 h. We developed a simple, cost-effective, and highly sensitive and specific assay to detect SMA patients. With little and field-portable equipment, the assay holds great promise in the detection of SMA patients, particularly in low-resource regions.
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Affiliation(s)
| | | | | | | | | | - Miaojin Zhou
- Correspondence: (M.Z.); (D.L.); Tel.: +86-731-84805252 (M.Z. & D.L.); Fax: +86-731-84478152 (M.Z. & D.L.)
| | - Desheng Liang
- Correspondence: (M.Z.); (D.L.); Tel.: +86-731-84805252 (M.Z. & D.L.); Fax: +86-731-84478152 (M.Z. & D.L.)
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230
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Fuentes-Chust C, Parolo C, Rosati G, Rivas L, Perez-Toralla K, Simon S, de Lecuona I, Junot C, Trebicka J, Merkoçi A. The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2006104. [PMID: 33719117 DOI: 10.1002/adma.202006104] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/26/2020] [Indexed: 05/15/2023]
Abstract
Monitoring of the human microbiome is an emerging area of diagnostics for personalized medicine. Here, the potential of different nanomaterials and nanobiosensing technologies is reviewed for the development of novel diagnostic devices for the detection and measurement of microbiome-related biomarkers. Moreover, the current and future landscape of microbiome-based diagnostics is defined by exploring the advantages and disadvantages of current nanotechnology-based approaches, especially in the context of developing point-of-care (PoC) devices that would meet the international guidelines known as REASSURED (Real-time connectivity; Ease of specimen collection; Affordability; Sensitivity; Specificity; User-friendliness; Rapid & robust operation; Equipment-free; and Deliverability). Finally, the strategies of the latest international scientific consortia working in this field are analyzed, the current microbiome diagnostics market are reported and the principal ethical, legal, and societal issues related to microbiome R&D and innovation are discussed.
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Affiliation(s)
- Celia Fuentes-Chust
- Nanobioelectronics and Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), UAB Campus, Bellaterra, Barcelona, 08193, Spain
| | - Claudio Parolo
- Nanobioelectronics and Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), UAB Campus, Bellaterra, Barcelona, 08193, Spain
| | - Giulio Rosati
- Nanobioelectronics and Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), UAB Campus, Bellaterra, Barcelona, 08193, Spain
| | - Lourdes Rivas
- Nanobioelectronics and Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), UAB Campus, Bellaterra, Barcelona, 08193, Spain
| | - Karla Perez-Toralla
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), SPI, Gif-sur-Yvette cedex, 91191, France
| | - Stéphanie Simon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), SPI, Gif-sur-Yvette cedex, 91191, France
| | - Itziar de Lecuona
- Bioethics and Law Observatory -UNESCO Chair in Bioethics-Department of Medicine, University of Barcelona, Barcelona, 08007, Spain
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), SPI, Gif-sur-Yvette cedex, 91191, France
| | - Jonel Trebicka
- Department of Internal Medicine I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
- European Foundation for the Study of Chronic Liver Failure, Travesera de Gracia 11, Barcelona, 08021, Spain
| | - Arben Merkoçi
- Nanobioelectronics and Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), UAB Campus, Bellaterra, Barcelona, 08193, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, Barcelona, 08010, Spain
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231
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Lin W, Tian T, Jiang Y, Xiong E, Zhu D, Zhou X. A CRISPR/Cas9 eraser strategy for contamination-free PCR end-point detection. Biotechnol Bioeng 2021; 118:2053-2066. [PMID: 33615437 PMCID: PMC8013395 DOI: 10.1002/bit.27718] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/02/2021] [Accepted: 02/13/2021] [Indexed: 12/18/2022]
Abstract
Polymerase chain reaction (PCR), a central technology for molecular diagnostics, is highly sensitive but susceptible to the risk of false positives caused by aerosol contamination, especially when an end-point detection mode is applied. Here, we proposed a solution by designing a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 eraser strategy for eliminating potential contamination amplification. The CRISPR/Cas9 engineered eraser is firstly adopted into artpcr reverse-transcription PCR (RT-PCR) system to achieve contamination-free RNA detection. Subsequently, we extended this CRISPR/Cas9 eraser to the PCR system. We engineered conventional PCR primers to enable the amplified products to contain an implanted NGG (protospacer adjacent motif, PAM) site, which is used as a code for specific CRISPR/Cas9 recognition. Pre-incubation of Cas9/sgRNA with PCR mix leads to a selective cleavage of contamination amplicons, thus only the template DNA is amplified. The developed CRISPR/Cas9 eraser, adopted by both RT-PCR and PCR systems, showed high-fidelity detection of SARS-CoV-2 and African swine fever virus with a convenient strip test.
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Affiliation(s)
- Wei Lin
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of BiophotonicsSouth China Normal UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Laser Life Science, College of BiophotonicsSouth China Normal UniversityGuangzhouChina
| | - Tian Tian
- School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Yongzhong Jiang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanChina
- Hubei Provincial Center for Disease Control and PreventionWuhanChina
| | - Erhu Xiong
- School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of ChemistrySouth China Normal UniversityGuangzhouChina
| | - Xiaoming Zhou
- School of Life SciencesSouth China Normal UniversityGuangzhouChina
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232
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Mobed A, Sepehri Shafigh E. Biosensors promising bio-device for pandemic screening "COVID-19". Microchem J 2021; 164:106094. [PMID: 33623173 PMCID: PMC7892310 DOI: 10.1016/j.microc.2021.106094] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 01/12/2023]
Abstract
Undoubtedly, the coronavirus pandemic is one of the most influential events not only in medicine but also in the economic field in the world. Rapid transmission and high mortality rates, as well as prolonged and asymptomatic communal periods, are the most important reasons for the global panic due to coronavirus. Since coronavirus treatment and specific vaccines are not yet available, early detection of the virus is critical. A rapid and accurate diagnosis can play a crucial role in the treatment and control of the COVID 19 disease. Serological, ELISA, and molecular-based tests, including PCR and RT-PCR, are among the most important routine methods for detecting coronaviruses. False-positive/negative results, low sensitivity and specificity, and the need for advanced equipment are among the disadvantages and problems of routine methods. To eliminate the drawbacks of routine methods, new technologies are being developed. Biosensors are one of the most important ones. This paper is a summary of the up-to-date states of innovative bio-sensing tools for the ultrasensitive detection of coronaviruses (COVID 19) with encouraging uses for future challenges in disease diagnosis.
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Affiliation(s)
- Ahmad Mobed
- Aging Research Institute, Faculty of Medicine, Tabriz University of Medical Sciences, Iran,Physical Medicine and Rehabilitation Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Corresponding author at: Aging Research Institute, Faculty of Medicine, Tabriz University of Medical Sciences, Iran
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233
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Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing. Talanta 2021; 226:122146. [PMID: 33676697 DOI: 10.1016/j.talanta.2021.122146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 01/19/2023]
Abstract
Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.
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234
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Hajian R, DeCastro J, Parkinson J, Kane A, Camelo AFR, Chou PP, Yang J, Wong N, Hernandez EDO, Goldsmith B, Conboy I, Aran K. Rapid and Electronic Identification and Quantification of Age-Specific Circulating Exosomes via Biologically Activated Graphene Transistors. Adv Biol (Weinh) 2021; 5:e2000594. [PMID: 33929095 DOI: 10.1002/adbi.202000594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/23/2021] [Indexed: 12/12/2022]
Abstract
Increasing access to modern clinical practices concomitantly extends lifespan, ironically revealing new classes of degenerative and inflammatory diseases of later years. Here, an electronic graphene field-effect transistor (gFET) is reported, termed EV-chip, for label-free, rapid identification and quantification of exosomes (EV) associated with aging through specific surface markers, CD63 and CD151. Studies suggest that blood-derived exosomes carry specific biomolecules that can be used toward diagnostic applications of age and health. However, to observe improvements in patient outcomes, earlier detection at the point-of-care (POC) is required. Unfortunately, conventional techniques and other electronic-based platforms for exosome sensing are burdensome and inept for the POC distinction of aged blood factors. It is shown that EV-chip can quantitatively detect purified exosomes from plasma, with a limit of detection (LOD) of 2 × 104 particles mL-1 and a limit of quantification (LOQ) of 6 × 104 particles mL-1 . The sensitivity and compact electronics of the EV-chip improves upon previously published electronic biosensors, making it ideal for a physician's office or a simple biological laboratory. The sensitivity, selectivity, and portability of the EV-chip demonstrate the potential of the biosensor as a powerful point-of-care diagnostic and prognostic tool for age-related diseases.
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Affiliation(s)
- Reza Hajian
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, 91711, USA.,Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA
| | - Jonalyn DeCastro
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, 91711, USA
| | | | - Alex Kane
- Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA
| | | | - Peichi Peggy Chou
- Keck Science Department, Pitzer College, The Claremont Colleges, Claremont, CA, 91711, USA
| | - Jielin Yang
- Keck Science Department, Claremont McKenna College, The Claremont Colleges, Claremont, CA, 91711, USA
| | - Nathan Wong
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Brett Goldsmith
- Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA
| | - Irina Conboy
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, 91711, USA.,Cardea Bio Inc., 8969 Kenamar Dr. Suite 104, San Diego, CA, 92121, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
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235
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Deepak Singh D, Han I, Choi EH, Yadav DK. CRISPR/Cas9 based genome editing for targeted transcriptional control in triple-negative breast cancer. Comput Struct Biotechnol J 2021; 19:2384-2397. [PMID: 34025931 PMCID: PMC8120801 DOI: 10.1016/j.csbj.2021.04.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) is the most common type of cancer in women at the global level and the highest mortality rate has been observed with triple-negative breast cancer (TNBC). Accumulation of genetic lesions an aberrant gene expression and protein degradation are considered to underlie the onset of tumorigenesis and metastasis. Therefore, the challenge to identify the genes and molecules that could be potentially used as potent biomarkers for personalized medicine against TNBC with minimal or no associated side effects. Discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) arrangement and an increasing repertoire of its new variants has provided a much-needed fillip towards editing TNBC genomes. In this review, we discuss the CRISPR/Cas9 genome editing, CRISPR Technology for diagnosis of (Triple-negative breast cancer) TNBC, Drug Resistance, and potential applications of CRISPR/Cas9 and its variants in deciphering or engineering intricate molecular and epigenetic mechanisms associated with TNBC. Furthermore, we have also explored the TNBC and CRISPR/Cas9 genome editing potential for repairing, genetic modifications in TNBC.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro 191, Yeonsu-gu, Incheon City, Republic of Korea
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236
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Shaffaf T, Ghafar-Zadeh E. COVID-19 Diagnostic Strategies. Part I: Nucleic Acid-Based Technologies. Bioengineering (Basel) 2021; 8:49. [PMID: 33920513 PMCID: PMC8072613 DOI: 10.3390/bioengineering8040049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused respiratory infection, resulting in more than two million deaths globally and hospitalizing thousands of people by March 2021. A considerable percentage of the SARS-CoV-2 positive patients are asymptomatic or pre-symptomatic carriers, facilitating the viral spread in the community by their social activities. Hence, it is critical to have access to commercialized diagnostic tests to detect the infection in the earliest stages, monitor the disease, and follow up the patients. Various technologies have been proposed to develop more promising assays and move toward the mass production of fast, reliable, cost-effective, and portable PoC diagnostic tests for COVID-19 detection. Not only COVID-19 but also many other pathogens will be able to spread and attach to human bodies in the future. These technologies enable the fast identification of high-risk individuals during future hazards to support the public in such outbreaks. This paper provides a comprehensive review of current technologies, the progress in the development of molecular diagnostic tests, and the potential strategies to facilitate innovative developments in unprecedented pandemics.
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Affiliation(s)
- Tina Shaffaf
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Faculty of Science, Department of Biology, York University, Toronto, ON M3J1P3, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Faculty of Science, Department of Biology, York University, Toronto, ON M3J1P3, Canada
- Lassonde School of Engineering, Department of Electrical Engineering and Computer Science, York University, Toronto, ON M3J1P3, Canada
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237
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Nouri R, Tang Z, Dong M, Liu T, Kshirsagar A, Guan W. CRISPR-based detection of SARS-CoV-2: A review from sample to result. Biosens Bioelectron 2021; 178:113012. [PMID: 33497879 PMCID: PMC7826142 DOI: 10.1016/j.bios.2021.113012] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/10/2021] [Accepted: 01/17/2021] [Indexed: 12/23/2022]
Abstract
The current pandemic of the 2019 novel coronavirus (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concern. Rapid, affordable, and accurate diagnostics of SARS-CoV-2 is essential for early treatment and control of the disease spread. In the past few years, CRISPR technology has shown great potential for highly sensitive and specific molecular diagnostics. Amid the ongoing COVID-19 pandemic, there is an increasing interest in implementing CRISPR-based diagnostic principles to develop fast and precise methods for detecting SARS-CoV-2. In this work, we reviewed and summarized these CRISPR-based diagnostic systems as well as their characteristics and challenges. We also provided future perspectives of CRISPR-based sensing towards point-of-care molecular diagnosis applications.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, United States.
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238
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Qiao SP, Liu ZN, Li HC, He X, Pan H, Gao YZ. Construction of a CRISPR-Biolayer Interferometry Platform for Real-Time, Sensitive, and Specific DNA Detection. Chembiochem 2021; 22:1974-1984. [PMID: 33682991 DOI: 10.1002/cbic.202100054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/26/2021] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology has been widely applied for nucleic acid detection because of its high specificity. By using the highly specific and irreversible bond between HaloTag and its alkane chlorine ligand, we modified dCas9 (deactivated CRISPR/Cas9) with biotin as a biosensor to detect nucleic acids. The CRISPR biosensor was facilely prepared to adequately maintain its DNA-recognition capability. Furthermore, by coupling biolayer interferometry (BLI) with the CRISPR biosensor, a real-time, sensitive, and rapid digital system called CRISPR-BLI was established for the detection of double-stranded DNA. The CRISPR biosensor immobilised on the biolayer could recruit the target DNA onto the biosensor surface and change its optical thickness, resulting in a shift in the interference pattern and responding signal of the BLI. The CRISPR-BLI system was further applied to detect the ALP gene of Escherichia coli DH5α combined with a polymerase chain reaction, which demonstrated a linear range from 20 to 20 000 pg and a low detection limit (1.34 pg). The CRISPR-BLI system is a promising approach for rapid and sensitive detection of target DNA analytes.
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Affiliation(s)
- Shan-Peng Qiao
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Zhen-Ni Liu
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Hai-Chao Li
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Xin He
- Department of Jilin City Institute of Biological Products, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 1228 Songjiangnan Road, Jilin, 132013, Jilin, P. R. China
| | - Hong Pan
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Yu-Zhou Gao
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China.,Department of Jinan Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3 Gangxing Road, Jinan, 250000, Shandong, P. R. China
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239
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Speranza G. Carbon Nanomaterials: Synthesis, Functionalization and Sensing Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:967. [PMID: 33918769 PMCID: PMC8069879 DOI: 10.3390/nano11040967] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Recent advances in nanomaterial design and synthesis has resulted in robust sensing systems that display superior analytical performance. The use of nanomaterials within sensors has accelerated new routes and opportunities for the detection of analytes or target molecules. Among others, carbon-based sensors have reported biocompatibility, better sensitivity, better selectivity and lower limits of detection to reveal a wide range of organic and inorganic molecules. Carbon nanomaterials are among the most extensively studied materials because of their unique properties spanning from the high specific surface area, high carrier mobility, high electrical conductivity, flexibility, and optical transparency fostering their use in sensing applications. In this paper, a comprehensive review has been made to cover recent developments in the field of carbon-based nanomaterials for sensing applications. The review describes nanomaterials like fullerenes, carbon onions, carbon quantum dots, nanodiamonds, carbon nanotubes, and graphene. Synthesis of these nanostructures has been discussed along with their functionalization methods. The recent application of all these nanomaterials in sensing applications has been highlighted for the principal applicative field and the future prospects and possibilities have been outlined.
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Affiliation(s)
- Giorgio Speranza
- CMM—FBK, v. Sommarive 18, 38123 Trento, Italy;
- IFN—CNR, CSMFO Lab., via alla Cascata 56/C Povo, 38123 Trento, Italy
- Department of Industrial Engineering, University of Trento, v. Sommarive 9, 38123 Trento, Italy
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240
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Wang M, Han D, Zhang J, Zhang R, Li J. High-fidelity detection of DNA combining the CRISPR/Cas9 system and hairpin probe. Biosens Bioelectron 2021; 184:113212. [PMID: 33862567 DOI: 10.1016/j.bios.2021.113212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/13/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022]
Abstract
Methods that enable specific and sensitive detection of DNA are greatly required for high-fidelity sequence measurement and single-nucleotide variations (SNVs) genotyping. The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas systems have provided revolutionary tools for detecting nucleic acids. However, most of the current CRISPR/Cas-based DNA biosensing platforms suffer from inherent off-target effects of Cas proteins and require pre-amplification processes, which compromise the analytical fidelity. In this work, a CRISPR/Cas9-triggered hairpin probe-mediated biosensing method (namely CHP) was used to directly read the original DNA sequences, while effectively neutralizing the off-target effect and achieving high sensitivity. This technique can quantify DNA targets with a limit of detection (LOD) at the attomole level and identify SNVs with allelic fractions as low as 0.01%~0.1%. Moreover, we show that the CHP system is applicable in detecting mutations in serum samples without DNA isolation steps. Collectively, the CHP system is a sensitive and high-fidelity platform, which promises a great potential for providing robust tool for DNA sequence analysis and SNVs genotyping.
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Affiliation(s)
- Meng Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jiawei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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241
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Zhang B, Zhou J, Li M, Wei Y, Wang J, Wang Y, Shi P, Li X, Huang Z, Tang H, Song Z. Evaluation of CRISPR/Cas9 site-specific function and validation of sgRNA sequence by a Cas9/sgRNA-assisted reverse PCR technique. Anal Bioanal Chem 2021; 413:2447-2456. [PMID: 33661348 PMCID: PMC7929911 DOI: 10.1007/s00216-021-03173-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/28/2020] [Accepted: 01/13/2021] [Indexed: 12/26/2022]
Abstract
The effective application of the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system in biology, medicine and other fields is hindered by the off-target effects and loci-affinity of Cas9-sgRNA, especially at a genome-wide scale. In order to eliminate the occurrence of off-target effects and evaluate loci-affinity by CRISPR/Cas9 site-specific detection and screening of high-affinity sgRNA sequences, respectively, we develop a CRISPR/Cas9-assisted reverse PCR method for site-specific detection and sgRNA sequence validation. The detection method based on PCR can be used directly in the laboratory with PCR reaction conditions, without the need for an additional detection system, and the whole process of detection can be completed within 2 h. Therefore, it can be easily popularized with a PCR instrument. Finally, this method is fully verified by detecting multiple forms of site mutations and evaluating the affinity of a variety of sgRNA sequences for the CRISPR/Cas9 system. In sum, it provides an effective new analysis tool for CRISPR/Cas9 genome editing-related research. A CRISPR/Cas9-assisted reverse PCR method was developed for Cas9/sgRNA site-specific detection and sgRNA sequence validation. The technique detects target DNA in three steps: (1) target DNA is specifically cut by a pair of Cas9/sgRNA complexes; (2) the cleaved DNA is rapidly linked by T4 DNA ligase; (3) the ligated DNA is efficiently amplified by PCR (PCR or qPCR).
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Affiliation(s)
- Beibei Zhang
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Jiamu Zhou
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Miao Li
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Yuanmeng Wei
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Jiaojiao Wang
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Yange Wang
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Pingling Shi
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Xiaoli Li
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Zixu Huang
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - He Tang
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
| | - Zongming Song
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, 450003 Henan China
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242
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Kim S, Park S, Cho YS, Kim Y, Tae JH, No TI, Shim JS, Jeong Y, Kang SH, Lee KH. Electrical Cartridge Sensor Enables Reliable and Direct Identification of MicroRNAs in Urine of Patients. ACS Sens 2021; 6:833-841. [PMID: 33284011 DOI: 10.1021/acssensors.0c01870] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Urinary miRNAs are biomarkers that demonstrate considerable promise for the noninvasive diagnosis and prognosis of diseases. However, because of background noise resulting from complex physiological features of urine, instability of miRNAs, and their low concentration, accurate monitoring of miRNAs in urine is challenging. To address these limitations, we developed a urine-based disposable and switchable electrical sensor that enables reliable and direct identification of miRNAs in patient urine. The proposed sensing platform combining disposable sensor chips composed of a reduced graphene oxide nanosheet and peptide nucleic acid facilitates the label-free detection of urinary miRNAs with high specificity and sensitivity. Using real-time detection of miRNAs in patient urine without pretreatment or signal amplification, this sensor allows rapid, direct detection of target miRNAs in a broad dynamic range with a detection limit down to 10 fM in human urine specimens within 20 min and enables simultaneous quantification of multiple miRNAs. As confirmed using a blind comparison with the results of pathological examination of patients with prostate cancer, the sensor offers the potential to improve the accuracy of early diagnosis before a biopsy is taken. This study holds the usefulness of the practical sensor for the clinical diagnosis of urological diseases.
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Affiliation(s)
- Seongchan Kim
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sungwook Park
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Young Soo Cho
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Younghoon Kim
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Jong Hyun Tae
- Department of Urology, Korea University, School of Medicine, Seoul 02841, Republic of Korea
| | - Tae Il No
- Department of Urology, Korea University, School of Medicine, Seoul 02841, Republic of Korea
| | - Ji Sung Shim
- Department of Urology, Korea University, School of Medicine, Seoul 02841, Republic of Korea
| | - Youngdo Jeong
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea
| | - Seok Ho Kang
- Department of Urology, Korea University, School of Medicine, Seoul 02841, Republic of Korea
| | - Kwan Hyi Lee
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
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243
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Niu C, Wang C, Li F, Zheng X, Xing X, Zhang C. Aptamer assisted CRISPR-Cas12a strategy for small molecule diagnostics. Biosens Bioelectron 2021; 183:113196. [PMID: 33839534 DOI: 10.1016/j.bios.2021.113196] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/03/2021] [Accepted: 03/20/2021] [Indexed: 12/26/2022]
Abstract
Molecular diagnostics are vital for the identification, prevention, and treatment of numerous diseases and are of particular demand in point-of-care (POC) settings. Nevertheless, most reported biosensors based on the CRISPR-Cas system have focused on nucleic-acid targets. Here, we report a versatile diagnostic strategy for small molecules called Molecular Radar (Random Molecular Aptamer-Dependent CRISPR-Assist Reporter), The workflow is simple, convenient, and rapid (conducted at 37 °C in under 25 min), indicating the substantial potential of the proposed assay could be adapted into a biosensor for POC settings and on-site molecular diagnostics. This strategy is based on the CRISPR Cas12a-assisted fluorescence reporter system that consists of Cas12a, CRISPR RNA (crRNA), a single-stranded DNA (ssDNA) probe labeled with a fluorophore at the 5' end and a quencher at the 3' end (F-Q probe), and a single-stranded DNA aptamer for the target molecule. In the presence of a target molecule, the aptamer binds to this small molecule with high specificity and affinity, resulting in a decrease of aptamer hybridized to the crRNA-Cas12a duplex. This decrease in activated Cas12a leads to a significant reduction in fluorescence signal. In this study, adenosine-5'-triphosphate (ATP) was selected as model target molecule and an ATP detect method was developed with high specificity and sensitivity with a linear range from 25 to 500 μM and a detection limit of 104 nM. Moreover, the particular characteristics of CRISPR-Cas12a that we report here for the first time have enriched our understanding of Cas12a and provided guidance for further research on CRISPR-Cas12a-based biosensors.
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Affiliation(s)
- Chenqi Niu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Chuyi Wang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Fan Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xiang Zheng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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244
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Dhar BC, Steimberg N, Mazzoleni G. Point-of-Care Pathogen Detection with CRISPR-based Programmable Nucleic Acid Binding Proteins. ChemMedChem 2021; 16:1566-1575. [PMID: 33258314 DOI: 10.1002/cmdc.202000782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 12/24/2022]
Abstract
The contemporary discovery of extremely versatile engineered nucleic acid-binding proteins has transformed a brave new world in the genome-editing scientific area. Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated programmable nucleic acid-binding proteins have brought about a revolution in diagnostic platforms. The groundbreaking finding that bacteria and archaea that harbored prokaryotes have transmitted adaptive immunity through CRISPR and CRISPR-associated (Cas) proteins has driven revolutionary advances in molecular biology. Importantly, advances in gene editing focus how expanding visions in CRISPR-Cas biology are revolutionizing the area of molecular diagnostics for identifying DNA and RNA in emerging microbiological pathogens, for single nucleotide polymorphism (SNP) identifications, and for cell-free mutation. Recent advances, such as improvements in multiplexing and quantitative capabilities as well as instrument-free detection of nucleic acids, will potentially leverage the introduction of these novel technologies to detecting bacteria and viruses at the point of care (POC). In this review, we highlight the fundamental features of CRISPR/Cas-based molecular diagnostic technologies and summarize a vision of the next applications for identifying pathogens in POC settings.
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Affiliation(s)
- Bidhan C Dhar
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC), 205 S Columbia St., Chapel Hill, NC, 27514, USA
| | - Nathalie Steimberg
- Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.,Interuniversity Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health" (MISTRAL), University of Brescia/ University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Giovanna Mazzoleni
- Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.,Interuniversity Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health" (MISTRAL), University of Brescia/ University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
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245
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Ertas YN, Mahmoodi M, Shahabipour F, Jahed V, Diltemiz SE, Tutar R, Ashammakhi N. Role of biomaterials in the diagnosis, prevention, treatment, and study of corona virus disease 2019 (COVID-19). EMERGENT MATERIALS 2021; 4:35-55. [PMID: 33748672 PMCID: PMC7962632 DOI: 10.1007/s42247-021-00165-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/12/2021] [Indexed: 05/02/2023]
Abstract
Recently emerged novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting corona virus disease 2019 (COVID-19) led to urgent search for methods to prevent and treat COVID-19. Among important disciplines that were mobilized is the biomaterials science and engineering. Biomaterials offer a range of possibilities to develop disease models, protective, diagnostic, therapeutic, monitoring measures, and vaccines. Among the most important contributions made so far from this field are tissue engineering, organoids, and organ-on-a-chip systems, which have been the important frontiers in developing tissue models for viral infection studies. Also, due to low bioavailability and limited circulation time of conventional antiviral drugs, controlled and targeted drug delivery could be applied alternatively. Fortunately, at the time of writing this paper, we have two successful vaccines and new at-home detection platforms. In this paper, we aim to review recent advances of biomaterial-based platforms for protection, diagnosis, vaccination, therapeutics, and monitoring of SARS-CoV-2 and discuss challenges and possible future research directions in this field.
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Affiliation(s)
- Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Mahboobeh Mahmoodi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Fahimeh Shahabipour
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
- Skin Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Vahid Jahed
- Biomedical Engineering Division, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Rumeysa Tutar
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpasa, Avcilar, Istanbul, Turkey
| | - Nureddin Ashammakhi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI USA
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246
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Feng W, Newbigging AM, Tao J, Cao Y, Peng H, Le C, Wu J, Pang B, Li J, Tyrrell DL, Zhang H, Le XC. CRISPR technology incorporating amplification strategies: molecular assays for nucleic acids, proteins, and small molecules. Chem Sci 2021; 12:4683-4698. [PMID: 34163728 PMCID: PMC8179559 DOI: 10.1039/d0sc06973f] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 12/19/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) protein systems have transformed the field of genome editing and transcriptional modulation. Progress in CRISPR-Cas technology has also advanced molecular detection of diverse targets, ranging from nucleic acids to proteins. Incorporating CRISPR-Cas systems with various nucleic acid amplification strategies enables the generation of amplified detection signals, enrichment of low-abundance molecular targets, improvements in analytical specificity and sensitivity, and development of point-of-care (POC) diagnostic techniques. These systems take advantage of various Cas proteins for their particular features, including RNA-guided endonuclease activity, sequence-specific recognition, multiple turnover trans-cleavage activity of Cas12 and Cas13, and unwinding and nicking ability of Cas9. Integrating a CRISPR-Cas system after nucleic acid amplification improves detection specificity due to RNA-guided recognition of specific sequences of amplicons. Incorporating CRISPR-Cas before nucleic acid amplification enables enrichment of rare and low-abundance nucleic acid targets and depletion of unwanted abundant nucleic acids. Unwinding of dsDNA to ssDNA using CRISPR-Cas9 at a moderate temperature facilitates techniques for achieving isothermal exponential amplification of nucleic acids. A combination of CRISPR-Cas systems with functional nucleic acids (FNAs) and molecular translators enables the detection of non-nucleic acid targets, such as proteins, metal ions, and small molecules. Successful integrations of CRISPR technology with nucleic acid amplification techniques result in highly sensitive and rapid detection of SARS-CoV-2, the virus that causes the COVID-19 pandemic.
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Affiliation(s)
- Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Ashley M Newbigging
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Yiren Cao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Connie Le
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Jinjun Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Bo Pang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
- School of Public Health, Jilin University 1163 Xinmin Street Changchun Jilin 130021 China
| | - Juan Li
- School of Public Health, Jilin University 1163 Xinmin Street Changchun Jilin 130021 China
| | - D Lorne Tyrrell
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
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Palaz F, Kalkan AK, Tozluyurt A, Ozsoz M. CRISPR-based tools: Alternative methods for the diagnosis of COVID-19. Clin Biochem 2021; 89:1-13. [PMID: 33428900 PMCID: PMC7796800 DOI: 10.1016/j.clinbiochem.2020.12.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022]
Abstract
The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spread all over the world rapidly and caused a global pandemic. To prevent the virus from spreading to more individuals, it is of great importance to identify and isolate infected individuals through testing. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the gold standard method for the diagnosis of coronavirus disease (COVID-19) worldwide. However, performing RT-qPCR is limited to centralized laboratories because of the need for sophisticated laboratory equipment and skilled personnel. Further, it can sometimes give false negative or uncertain results. Recently, new methods have been developed for nucleic acid detection and pathogen diagnosis using CRISPR-Cas systems. These methods present rapid and cost-effective diagnostic platforms that provide high sensitivity and specificity without the need for complex instrumentation. Using the CRISPR-based SARS-CoV-2 detection methods, it is possible to increase the number of daily tests in existing laboratories, reduce false negative or uncertain result rates obtained with RT-qPCR, and perform testing in resource-limited settings or at points of need where performing RT-qPCR is not feasible. Here, we briefly describe the RT-qPCR method, and discuss its limitations in meeting the current diagnostic needs. We explain how the unique properties of various CRISPR-associated enzymes are utilized for nucleic acid detection and pathogen diagnosis. Then, we highlight the important features of CRISPR-based diagnostic methods developed for SARS-CoV-2 detection. Finally, we examine the advantages and limitations of these methods, and discuss how they can contribute to improving the efficiency of the current testing systems for combating SARS-CoV-2.
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Affiliation(s)
- Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | | | - Abdullah Tozluyurt
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Mehmet Ozsoz
- Department of Biomedical Engineering, Near East University, Nicosia, 10 Mersin, Turkey.
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248
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Li P, Lee GH, Kim SY, Kwon SY, Kim HR, Park S. From Diagnosis to Treatment: Recent Advances in Patient-Friendly Biosensors and Implantable Devices. ACS NANO 2021; 15:1960-2004. [PMID: 33534541 DOI: 10.1021/acsnano.0c06688] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Patient-friendly medical diagnostics and treatments have been receiving a great deal of interest due to their rapid and cost-effective health care applications with minimized risk of infection, which has the potential to replace conventional hospital-based medical procedures. In particular, the integration of recently developed materials into health care devices allows the rapid development of point-of-care (POC) sensing platforms and implantable devices with special functionalities. In this review, the recent advances in biosensors for patient-friendly diagnosis and implantable devices for patient-friendly treatment are discussed. Comprehensive analysis of portable and wearable biosensing platforms for patient-friendly health monitoring and disease diagnosis is provided, including topics such as materials selection, device structure and integration, and biomarker detection strategies. Moreover, specific challenges related to each biological fluid for wearable biosensor-based POC applications are presented. Also, advances in implantable devices, including recent materials development and wireless communication strategies, are discussed. Furthermore, various patient-friendly surgical and treatment approaches are reviewed, such as minimally invasive insertion and mounting, in vivo electrical and optical modulations, and post-operation health monitoring. Finally, the challenges and future perspectives toward the development of the patient-friendly diagnosis and treatment are provided.
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Affiliation(s)
- Pei Li
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gun-Hee Lee
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Su Yeong Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Se Young Kwon
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyung-Ryong Kim
- College of Dentistry and Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 330-714, Republic of Korea
| | - Steve Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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249
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Feng H, Guo J, Wang T, Zhang C, Xing XH. Guide-target mismatch effects on dCas9-sgRNA binding activity in living bacterial cells. Nucleic Acids Res 2021; 49:1263-1277. [PMID: 33503261 PMCID: PMC7897480 DOI: 10.1093/nar/gkaa1295] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
As an effective programmable DNA targeting tool, CRISPR-Cas9 system has been adopted in varieties of biotechnological applications. However, the off-target effects, derived from the tolerance towards guide-target mismatches, are regarded as the major problems in engineering CRISPR systems. To understand this, we constructed two sgRNA libraries carrying saturated single- and double-nucleotide mismatches in living bacteria cells, and profiled the comprehensive landscape of in vivo binding affinity of dCas9 toward DNA target guided by each individual sgRNA with particular mismatches. We observed a synergistic effect in seed, where combinatorial double mutations caused more severe activity loss compared with the two corresponding single mutations. Moreover, we found that a particular mismatch type, dDrG (D = A, T, G), only showed moderate impairment on binding. To quantitatively understand the causal relationship between mismatch and binding behaviour of dCas9, we further established a biophysical model, and found that the thermodynamic properties of base-pairing coupled with strand invasion process, to a large extent, can account for the observed mismatch-activity landscape. Finally, we repurposed this model, together with a convolutional neural network constructed based on the same mechanism, as a predictive tool to guide the rational design of sgRNA in bacterial CRISPR interference.
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Affiliation(s)
- Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jiahui Guo
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Tianmin Wang
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xin-hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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Komisarenko SV, Romaniuk SI. Prospects of genome editing using CRISPR/CAS or how to master genetic scissors. Nobel Prize in Chemistry 2020. UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.01.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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