1
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Ye C, Lukas H, Wang M, Lee Y, Gao W. Nucleic acid-based wearable and implantable electrochemical sensors. Chem Soc Rev 2024. [PMID: 38985007 DOI: 10.1039/d4cs00001c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The rapid advancements in nucleic acid-based electrochemical sensors for implantable and wearable applications have marked a significant leap forward in the domain of personal healthcare over the last decade. This technology promises to revolutionize personalized healthcare by facilitating the early diagnosis of diseases, monitoring of disease progression, and tailoring of individual treatment plans. This review navigates through the latest developments in this field, focusing on the strategies for nucleic acid sensing that enable real-time and continuous biomarker analysis directly in various biofluids, such as blood, interstitial fluid, sweat, and saliva. The review delves into various nucleic acid sensing strategies, emphasizing the innovative designs of biorecognition elements and signal transduction mechanisms that enable implantable and wearable applications. Special perspective is given to enhance nucleic acid-based sensor selectivity and sensitivity, which are crucial for the accurate detection of low-level biomarkers. The integration of such sensors into implantable and wearable platforms, including microneedle arrays and flexible electronic systems, actualizes their use in on-body devices for health monitoring. We also tackle the technical challenges encountered in the development of these sensors, such as ensuring long-term stability, managing the complexity of biofluid dynamics, and fulfilling the need for real-time, continuous, and reagentless detection. In conclusion, the review highlights the importance of these sensors in the future of medical engineering, offering insights into design considerations and future research directions to overcome existing limitations and fully realize the potential of nucleic acid-based electrochemical sensors for healthcare applications.
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Affiliation(s)
- Cui Ye
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Heather Lukas
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Minqiang Wang
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Yerim Lee
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Wei Gao
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
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2
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Ma H, Tian Y, Kong D, Guo M, Dai C, Wang Q, Li S, Tian Z, Liu Y, Wei D. One-base-mismatch CRISPR-based transistors for single nucleotide resolution assay. Biosens Bioelectron 2024; 262:116548. [PMID: 38986250 DOI: 10.1016/j.bios.2024.116548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/13/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
An effective strategy for accurately detecting single nucleotide variants (SNVs) is of great significance for genetic research and diagnostics. However, strict amplification conditions, complex experimental instruments, and specialized personnel are required to obtain a satisfactory tradeoff between sensitivity and selectivity for SNV discrimination. In this study, we present a CRISPR-based transistor biosensor for the rapid and highly selective detection of SNVs in viral RNA. By introducing a synthetic mismatch in the crRNA, the CRISPR-Cas13a protein can be engineered to capture the target SNV RNA directly on the surface of the graphene channel. This process induces a fast electrical signal response in the transistor, obviating the need for amplification or reporter molecules. The biosensor exhibits a detection limit for target RNA as low as 5 copies in 100 μL, which is comparable to that of real-time quantitative polymerase chain reaction (PCR). Its operational range spans from 10 to 5 × 105 copy mL-1 in artificial saliva solution. This capability enables the biosensor to discriminate between wild-type and SNV RNA within 15 min. By introducing 10 μL of swab samples during clinical testing, the biosensor provides specific detection of respiratory viruses in 19 oropharyngeal specimens, including influenza A, influenza B, and variants of SARS-CoV-2. This study emphasizes the CRISPR-transistor technique as a highly accurate and sensitive approach for field-deployable nucleic acid screening or diagnostics.
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Affiliation(s)
- Hongwenjie Ma
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China
| | - Yicheng Tian
- Shanghai Medical College, Fudan University, Shanghai, 200031, PR China
| | - Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China.
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, PR China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China
| | - Qiang Wang
- Shanghai International Travel Healthcare Center, Shanghai Customs PR China, Shanghai, 200335, PR China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai Customs PR China, Shanghai, 200335, PR China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai Customs PR China, Shanghai, 200335, PR China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, PR China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China.
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3
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Zhou L, Simonian AL. CRISPR/Cas Technology: The Unique Synthetic Biology Genome-Editing Tool Shifting the Paradigm in Viral Diagnostics, Defense, and Therapeutics. Annu Rev Biomed Eng 2024; 26:247-272. [PMID: 38346278 DOI: 10.1146/annurev-bioeng-081723-013033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The emergence of the COVID-19 pandemic has starkly exposed our significantly limited ability to promptly identify and respond to emergent biological threats. Consequently, there is an urgent need to advance biotechnological methods for addressing both known and unforeseen biological hazards. Recently, the CRISPR/Cas system has revolutionized genetic engineering, enabling precise and efficient synthetic biology applications. Therefore, this review aims to provide a comprehensive introduction to the fundamental principles underlying the CRISPR/Cas system and assess the advantages and limitations of various CRISPR/Cas-based techniques applicable to the detection of, defense against, and treatment of viral infections. These techniques include viral diagnostics, the development of antiviral vaccines, B cell engineering for antibody production, viral activation/interference, and epigenetic modifications. Furthermore, this review delves into the challenges and bioethical considerations associated with use of the CRISPR/Cas system. With the continuous evolution of technology, the CRISPR/Cas system holds considerable promise for addressing both existing and unforeseen biological threats.
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Affiliation(s)
- Lang Zhou
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
| | - Aleksandr L Simonian
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
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4
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Wachholz Junior D, Kubota LT. CRISPR-based electrochemical biosensors: an alternative for point-of-care diagnostics? Talanta 2024; 278:126467. [PMID: 38968657 DOI: 10.1016/j.talanta.2024.126467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/07/2024]
Abstract
The combination of CRISPR technology and electrochemical sensors has sparked a paradigm shift in the landscape of point-of-care (POC) diagnostics. This review explores the dynamic convergence between CRISPR and electrochemical sensing, elucidating their roles in rapid and precise biosensing platforms. CRISPR, renowned for its remarkable precision in genome editing and programmability capability, has found a novel application in conjunction with electrochemical sensors, promising highly sensitive and specific detection of nucleic acids and biomarkers associated with diverse diseases. This article navigates through fundamental principles, research developments, and applications of CRISPR-based electrochemical sensors, highlighting their potential to revolutionize healthcare accessibility and patient outcomes. In addition, some key points and challenges regarding applying CRISPR-powered electrochemical sensors in real POC settings are presented. By discussing recent advancements and challenges in this interdisciplinary field, this review evaluates the potential of these innovative sensors as an alternative for decentralized, rapid, and accurate POC testing, offering some insights into their applications across clinical scenarios and their impact on the future of diagnostics.
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Affiliation(s)
- Dagwin Wachholz Junior
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), 13083-970, Brazil; National Institute of Science and Technology in Bioanalytic (INCTBio), Brazil
| | - Lauro Tatsuo Kubota
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), 13083-970, Brazil; National Institute of Science and Technology in Bioanalytic (INCTBio), Brazil.
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5
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Al-Younis ZK, Almajidi YQ, Mansouri S, Ahmad I, Turdialiyev U, O Alsaab H, F Ramadan M, Joshi SK, Alawadi AH, Alsaalamy A. Label-Free Field Effect Transistors (FETs) for Fabrication of Point-of-Care (POC) Biomedical Detection Probes. Crit Rev Anal Chem 2024:1-22. [PMID: 38829552 DOI: 10.1080/10408347.2024.2356842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Field effect transistors (FETs)-based detection probes are powerful platforms for quantification in biological media due to their sensitivity, ease of miniaturization, and ability to function in biological media. Especially, FET-based platforms have been utilized as promising probes for label-free detections with the potential for use in real-time monitoring. The integration of new materials in the FET-based probe enhances the analytical performance of the developed probes by increasing the active surface area, rejecting interfering agents, and providing the possibility for surface modification. Furthermore, the use of new materials eliminates the need for traditional labeling techniques, providing rapid and cost-effective detection of biological analytes. This review discusses the application of materials in the development of FET-based label-free systems for point-of-care (POC) analysis of different biomedical analytes from 2018 to 2024. The mechanism of action of the reported probes is discussed, as well as their pros and cons were also investigated. Also, the possible challenges and potential for the fabrication of commercial devices or methods for use in clinics were discussed.
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Affiliation(s)
| | - Yasir Qasim Almajidi
- Department of Pharmacy (Pharmaceutics), Baghdad College of Medical Sciences, Baghdad, Iraq
| | - Sofiene Mansouri
- Department of Biomedical Technology, College of Applied Medical Sciences, Al-Kharj, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabiain
- Laboratory of Biophysics and Medical Technologies, Higher Institute of Medical Technologies of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia
| | - Umid Turdialiyev
- Department of Technical Sciences, Andijan Machine-Building Institute, Andijan, Uzbekistan
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, Saudi Arabia
| | | | - S K Joshi
- Department of Mechanical Engineering, Uttaranchal Institute of Technology, Uttaranchal University, Dehradun, India
| | - Ahmed Hussien Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq
- College of Technical Engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, the Islamic University of Babylon, Babylon, Iraq
| | - Ali Alsaalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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6
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Raza S, Poria R, Kala D, Sharma N, Sharma AK, Florien N, Tuli HS, Kaushal A, Gupta S. Innovations in dengue virus detection: An overview of conventional and electrochemical biosensor approaches. Biotechnol Appl Biochem 2024; 71:481-500. [PMID: 38225854 DOI: 10.1002/bab.2553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024]
Abstract
Globally, people are in great threat due to the highly spreading of viral infectious diseases. Every year like 100-300 million cases of infections are found, and among them, above 80% are not recognized and irrelevant. Dengue virus (DENV) is an arbovirus infection that currently infects people most frequently. DENV encompasses four viral serotypes, and they each express comparable sign. From a mild febrile sickness to a potentially fatal dengue hemorrhagic fever, dengue can induce a variety of symptoms. Presently, the globe is being challenged by the untimely identification of dengue infection. Therefore, this review summarizes advances in the detection of dengue from conventional methods (nucleic acid-based, polymerase chain reaction-based, and serological approaches) to novel biosensors. This work illustrates an extensive study of the current designs and fabrication approaches involved in the formation of electrochemical biosensors for untimely identifications of dengue. Additionally, in electrochemical sensing of DENV, we skimmed through significances of biorecognition molecules like lectins, nucleic acid, and antibodies. The introduction of emerging techniques such as the CRISPR/Cas' system and their integration with biosensing platforms has also been summarized. Furthermore, the review revealed the importance of electrochemical approach compared with traditional diagnostic methods.
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Affiliation(s)
- Shadan Raza
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala, India
| | - Renu Poria
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala, India
| | - Deepak Kala
- Centera Laboratories, Institute of High Pressure Physics PAS, Warsaw, Poland
| | - Nishant Sharma
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala, India
| | - Anil K Sharma
- Department of Biotechnology, Amity University of Punjab, Mohali, Punjab, India
| | - Nkurunziza Florien
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala, India
| | - Hardeep S Tuli
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala, India
| | - Ankur Kaushal
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala, India
| | - Shagun Gupta
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala, India
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7
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Xia Y, Rao R, Xiong M, He B, Zheng B, Jia Y, Li Y, Yang Y. CRISPR-Powered Strategies for Amplification-Free Diagnostics of Infectious Diseases. Anal Chem 2024; 96:8091-8108. [PMID: 38451204 DOI: 10.1021/acs.analchem.3c04363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Affiliation(s)
- Yupiao Xia
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruotong Rao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengqiu Xiong
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bangshun He
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bingxin Zheng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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8
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Choi W, Shin S, Do J, Son J, Kim K, Lee JS. Influence of Surface Treatments on Urea Detection Using Si Electrolyte-Gated Transistors with Different Gate Electrodes. MICROMACHINES 2024; 15:621. [PMID: 38793194 PMCID: PMC11123436 DOI: 10.3390/mi15050621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
We investigated the impact of surface treatments on Si-based electrolyte-gated transistors (EGTs) for detecting urea. Three types of EGTs were fabricated with distinct gate electrodes (Ag, Au, Pt) using a top-down method. These EGTs exhibited exceptional intrinsic electrical properties, including a low subthreshold swing of 80 mV/dec, a high on/off current ratio of 106, and negligible hysteresis. Three surface treatment methods ((3-amino-propyl) triethoxysilane (APTES) and glutaraldehyde (GA), 11-mercaptoundecanoic acid (11-MUA), 3-mercaptopropionic acid (3-MPA)) were individually applied to the EGTs with different gate electrodes (Ag, Au, Pt). Gold nanoparticle binding tests were performed to validate the surface functionalization. We compared their detection performance of urea and found that APTES and GA exhibited the most superior detection characteristics, followed by 11-MUA and 3-MPA, regardless of the gate metal. APTES and GA, with the highest pKa among the three surface treatment methods, did not compromise the activity of urease, making it the most suitable surface treatment method for urea sensing.
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Affiliation(s)
- Wonyeong Choi
- Department of Electrical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea; (W.C.); (S.S.); (J.D.); (J.S.)
| | - Seonghwan Shin
- Department of Electrical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea; (W.C.); (S.S.); (J.D.); (J.S.)
| | - Jeonghyeon Do
- Department of Electrical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea; (W.C.); (S.S.); (J.D.); (J.S.)
| | - Jongmin Son
- Department of Electrical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea; (W.C.); (S.S.); (J.D.); (J.S.)
| | - Kihyun Kim
- Division of Electronics Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Jeong-Soo Lee
- Department of Electrical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea; (W.C.); (S.S.); (J.D.); (J.S.)
- Innovative General Electronic Sensor Technology (i-GEST) Co., Ltd., Pohang 37673, Republic of Korea
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9
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Foster ZSL, Tupper AS, Press CM, Grünwald NJ. Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data. PLoS Comput Biol 2024; 20:e1012139. [PMID: 38768250 PMCID: PMC11142669 DOI: 10.1371/journal.pcbi.1012139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/31/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Recent pandemics like COVID-19 highlighted the importance of rapidly developing diagnostics to detect evolving pathogens. CRISPR-Cas technology has recently been used to develop diagnostic assays for sequence-specific recognition of DNA or RNA. These assays have similar sensitivity to the gold standard qPCR but can be deployed as easy to use and inexpensive test strips. However, the discovery of diagnostic regions of a genome flanked by conserved regions where primers can be designed requires extensive bioinformatic analyses of genome sequences. We developed the Python package krisp to aid in the discovery of primers and diagnostic sequences that differentiate groups of samples from each other, using either unaligned genome sequences or a variant call format (VCF) file as input. Krisp has been optimized to handle large datasets by using efficient algorithms that run in near linear time, use minimal RAM, and leverage parallel processing when available. The validity of krisp results has been demonstrated in the laboratory with the successful design of a CRISPR diagnostic assay to distinguish the sudden oak death pathogen Phytophthora ramorum from closely related Phytophthora species. Krisp is released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays.
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Affiliation(s)
- Zachary S. L. Foster
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Andrew S. Tupper
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Caroline M. Press
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Niklaus J. Grünwald
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
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10
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Liang G, Cao W, Tang D, Zhang H, Yu Y, Ding J, Karges J, Xiao H. Nanomedomics. ACS NANO 2024; 18:10979-11024. [PMID: 38635910 DOI: 10.1021/acsnano.3c11154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Nanomaterials have attractive physicochemical properties. A variety of nanomaterials such as inorganic, lipid, polymers, and protein nanoparticles have been widely developed for nanomedicine via chemical conjugation or physical encapsulation of bioactive molecules. Superior to traditional drugs, nanomedicines offer high biocompatibility, good water solubility, long blood circulation times, and tumor-targeting properties. Capitalizing on this, several nanoformulations have already been clinically approved and many others are currently being studied in clinical trials. Despite their undoubtful success, the molecular mechanism of action of the vast majority of nanomedicines remains poorly understood. To tackle this limitation, herein, this review critically discusses the strategy of applying multiomics analysis to study the mechanism of action of nanomedicines, named nanomedomics, including advantages, applications, and future directions. A comprehensive understanding of the molecular mechanism could provide valuable insight and therefore foster the development and clinical translation of nanomedicines.
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Affiliation(s)
- Ganghao Liang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wanqing Cao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Dongsheng Tang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hanchen Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yingjie Yu
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Johannes Karges
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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11
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Wang Z, Wang Y, Zhang Y, Qin G, Sun W, Wang A, Wang Y, Zhang G, Zhao J. On-site detection and differentiation of African swine fever virus variants using an orthogonal CRISPR-Cas12b/Cas13a-based assay. iScience 2024; 27:109050. [PMID: 38571763 PMCID: PMC10987800 DOI: 10.1016/j.isci.2024.109050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/14/2023] [Accepted: 01/23/2024] [Indexed: 04/05/2024] Open
Abstract
The African swine fever virus (ASFV) and its variants have induced substantial economic losses in China, prompting a critical need for efficient detection methods. Several PCR-based methods have been developed to discriminate between wild-type ASFV and gene-deleted variants. However, the requirement for sophisticated equipment and skilled operators limits their use in field settings. Here, we developed a CRISPR-Cas12b/Cas13a-based detection assay that can identify ASFV variants with minimal equipment requirements and a short turnaround time. The assay utilizes the distinct DNA/RNA collateral cleavage preferences of Cas12b/Cas13a to detect two amplified targets from multiplex recombinase polymerase amplification (RPA) in a single tube, and the results can be visualized through fluorescent or lateral-flow readouts. When tested with clinical samples in field settings, our assay successfully detected all ASFV-positive samples in less than 60 min. This assay provides a rapid on-site surveillance tool for detecting ASFV and its emerging variants.
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Affiliation(s)
- Zhe Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Longhu Laboratory, Zhengzhou 450046, China
- Henan Key Laboratory of Immunobiology, Zhengzhou 450001, China
| | - Yu Wang
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guosong Qin
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Sun
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Longhu Laboratory, Zhengzhou 450046, China
- Henan Key Laboratory of Immunobiology, Zhengzhou 450001, China
| | - Yanfang Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Gaiping Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Longhu Laboratory, Zhengzhou 450046, China
- Henan Key Laboratory of Immunobiology, Zhengzhou 450001, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jianguo Zhao
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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12
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Diforti JF, Cunningham T, Piccinini E, Marmisollé WA, Piccinini JM, Azzaroni O. Noninvasive and Multiplex Self-Test of Kidney Disease Biomarkers with Graphene-Based Lab-on-a-Chip (G-LOC): Toward Digital Diagnostics in the Hands of Patients. Anal Chem 2024; 96:5832-5842. [PMID: 38573917 DOI: 10.1021/acs.analchem.3c05148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Chronic kidney disease is one of the major health issues worldwide. However, diagnosis is now highly centralized in large laboratories, resulting in low access to patient monitoring and poor personalized treatments. This work reports the development of a graphene-based lab-on-a-chip (G-LOC) for the digital testing of renal function biomarkers in serum and saliva samples. G-LOC integrates multiple bioelectronic sensors with a microfluidic system that enables multiplex self-testing of urea, potassium, sodium, and chloride. The linearity, limit of detection (LOD), accuracy, and coefficient of variability (CV) were studied. Accuracy values higher than 95.5% and CV lower than 9% were obtained for all of the biomarkers. The analytical performance was compared against three reference lab benchtop analyzers by measuring healthy- and renal-failure-level samples of serum. From receiver operating characteristic (ROC) plots, sensitivities (%) of 99.7, 97.6, 99.1, and 89.0 were obtained for urea, potassium, sodium, and chloride, respectively. Then, the test was evaluated in noninvasive saliva samples and compared against reference methods. Correlation and Bland-Altman plots showed good correlation and agreement of the G-LOC with the reference methods. It is noteworthy that the precision of G-LOC was similar to better than benchtop lab analyzers, with the advantage of being highly portable. Finally, a user testing study was conducted. The analytical performance obtained with untrained volunteers was similar to that obtained with trained chemists. Additionally, based on a user experience survey, G-LOC was found to have very simple usability and would be suitable for at-home diagnostics.
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Affiliation(s)
- Joaquin F Diforti
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
- Department of Bioelectronic, GISENS BIOTECH, 2150 Shattuck Ave PH, Berkeley, California 94704, United States
| | - Thomas Cunningham
- Department of Bioelectronic, GISENS BIOTECH, 2150 Shattuck Ave PH, Berkeley, California 94704, United States
| | - Esteban Piccinini
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
| | - Waldemar A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
| | - Jose M Piccinini
- Department of Bioelectronic, GISENS BIOTECH, 2150 Shattuck Ave PH, Berkeley, California 94704, United States
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
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13
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Wang Y, Chen H, Lin K, Han Y, Gu Z, Wei H, Mu K, Wang D, Liu L, Jin R, Song R, Rong Z, Wang S. Ultrasensitive single-step CRISPR detection of monkeypox virus in minutes with a vest-pocket diagnostic device. Nat Commun 2024; 15:3279. [PMID: 38627378 PMCID: PMC11021474 DOI: 10.1038/s41467-024-47518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
The emerging monkeypox virus (MPXV) has raised global health concern, thereby highlighting the need for rapid, sensitive, and easy-to-use diagnostics. Here, we develop a single-step CRISPR-based diagnostic platform, termed SCOPE (Streamlined CRISPR On Pod Evaluation platform), for field-deployable ultrasensitive detection of MPXV in resource-limited settings. The viral nucleic acids are rapidly released from the rash fluid swab, oral swab, saliva, and urine samples in 2 min via a streamlined viral lysis protocol, followed by a 10-min single-step recombinase polymerase amplification (RPA)-CRISPR/Cas13a reaction. A pod-shaped vest-pocket analysis device achieves the whole process for reaction execution, signal acquisition, and result interpretation. SCOPE can detect as low as 0.5 copies/µL (2.5 copies/reaction) of MPXV within 15 min from the sample input to the answer. We validate the developed assay on 102 clinical samples from male patients / volunteers, and the testing results are 100% concordant with the real-time PCR. SCOPE achieves a single-molecular level sensitivity in minutes with a simplified procedure performed on a miniaturized wireless device, which is expected to spur substantial progress to enable the practice application of CRISPR-based diagnostics techniques in a point-of-care setting.
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Affiliation(s)
- Yunxiang Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Hong Chen
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Kai Lin
- Department of Clinical Laboratory, Air Force Medical Center, Air Force Medical University, 100142, Beijing, China
| | - Yongjun Han
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Zhixia Gu
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China
| | - Hongjuan Wei
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Kai Mu
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Dongfeng Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Liyan Liu
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China.
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China.
| | - Zhen Rong
- Bioinformatics Center of AMMS, 100850, Beijing, China.
| | - Shengqi Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China.
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14
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Zhu Y, Zhang J, Cheng T, Tang J, Duan H, Hu Z, Shao J, Wang S, Wei M, Wu H, Li A, Li S, Balci O, Shinde SM, Ramezani H, Wang L, Lin L, Ferrari AC, Yakobson BI, Peng H, Jia K, Liu Z. Controlled Growth of Single-Crystal Graphene Wafers on Twin-Boundary-Free Cu(111) Substrates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308802. [PMID: 37878366 DOI: 10.1002/adma.202308802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/05/2023] [Indexed: 10/26/2023]
Abstract
Single-crystal graphene (SCG) wafers are needed to enable mass-electronics and optoelectronics owing to their excellent properties and compatibility with silicon-based technology. Controlled synthesis of high-quality SCG wafers can be done exploiting single-crystal Cu(111) substrates as epitaxial growth substrates recently. However, current Cu(111) films prepared by magnetron sputtering on single-crystal sapphire wafers still suffer from in-plane twin boundaries, which degrade the SCG chemical vapor deposition. Here, it is shown how to eliminate twin boundaries on Cu and achieve 4 in. Cu(111) wafers with ≈95% crystallinity. The introduction of a temperature gradient on Cu films with designed texture during annealing drives abnormal grain growth across the whole Cu wafer. In-plane twin boundaries are eliminated via migration of out-of-plane grain boundaries. SCG wafers grown on the resulting single-crystal Cu(111) substrates exhibit improved crystallinity with >97% aligned graphene domains. As-synthesized SCG wafers exhibit an average carrier mobility up to 7284 cm2 V-1 s-1 at room temperature from 103 devices and a uniform sheet resistance with only 5% deviation in 4 in. region.
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Affiliation(s)
- Yeshu Zhu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Jincan Zhang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Ting Cheng
- Department of Materials Science & NanoEngineering, Rice University, Houston, TX, 77005, USA
| | - Jilin Tang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Hongwei Duan
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, School of Integrated Circuits, Peking University, Beijing, 100871, P. R. China
| | - Zhaoning Hu
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jiaxin Shao
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Shiwei Wang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Mingyue Wei
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Haotian Wu
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Ang Li
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- College of Science, China University of Petroleum, Beijing, 102249, P. R. China
| | - Sheng Li
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Osman Balci
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Sachin M Shinde
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Hamideh Ramezani
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Luda Wang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, School of Integrated Circuits, Peking University, Beijing, 100871, P. R. China
| | - Li Lin
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Andrea C Ferrari
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Boris I Yakobson
- Department of Materials Science & NanoEngineering, Rice University, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Hailin Peng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Kaicheng Jia
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Zhongfan Liu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
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15
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Wu M, Wu H, Chen X, Wu F, Ma G, Du A, Yang Y. RPA-CRISPR/Cas9-based method for the detection of Toxoplasma gondii: A proof of concept. Vet Parasitol 2024; 327:110115. [PMID: 38232511 DOI: 10.1016/j.vetpar.2024.110115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Toxoplasma gondii is a widespread and specialized intracellular protozoan pathogen that affects one third of the world' s population, posing a great threat to public health. As the definitive host, cats excrete oocysts and play a crucial role in the transmission of toxoplasmosis. The current diagnostic tools usually require bulky equipment and expertize, which hinders the efficient diagnosis and intervention of Toxoplasma infection in cats. In this study, we combined (RPA) with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technique to establish an easier method for the detection of T. gondii oocysts in cat fecal samples. The sensitivity, specificity, and practicability of the established RPA-CRISPR/Cas9 method were evaluated using a lateral flow strip, with the limitation of detection determined at 10 plasmid copies/μL (corresponding to about one oocyst), cross reactivity to none of Giardia lamblia, Cryptosporidium sp., Microsporidium biberi and Blastocystis hominis that also commonly found in cats, and comparable performance in detecting T. gondii in clinical samples to conventional PCR amplification. This RPA-CRISPR/Cas9 method provides an alternative to conventional molecular tools used in the clinical diagnosis of Toxoplasma infection in cats and other animals.
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Affiliation(s)
- Mengchen Wu
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Haiyan Wu
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Xueqiu Chen
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Fei Wu
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Guangxu Ma
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Aifang Du
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Yi Yang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China; South Taihu Modern Agricultural Technology Promotion Center of Huzhou & Zhejiang University, Huzhou, China.
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16
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Tian Z, Yan H, Zeng Y. Solid-Phase Extraction and Enhanced Amplification-Free Detection of Pathogens Integrated by Multifunctional CRISPR-Cas12a. ACS APPLIED MATERIALS & INTERFACES 2024; 16:14445-14456. [PMID: 38472096 DOI: 10.1021/acsami.3c17039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Public healthcare demands effective and pragmatic diagnostic tools to address the escalating challenges in infection management in resource-limited areas. Recent advances in clustered regularly interspaced short palindromic repeat (CRISPR)-based biosensing promise the development of next-generation tools for disease diagnostics, including point-of-care (POC) testing for infectious diseases. The currently prevailing strategy of developing CRISPR/Cas-based diagnostics exploits only the target identification and trans-cleavage activity of a CRISPR-Cas12a/Cas13a system to provide diagnostic results, and they need to be combined with an additional preamplification reaction to enhance sensitivity. In contrast to this dual-function strategy, here, we present a new approach that collaboratively integrates the triple functions of CRISPR-Cas12a: target identification, sequence-specific enrichment, and signal generation. With this approach, we develop a nucleic acid assay termed Solid-Phase Extraction and Enhanced Detection Assay integrated by CRISPR-Cas12a (SPEEDi-CRISPR) that negates the need for preamplification but significantly improves the detection of limit (LOD) from the pM to fM level. Specifically, using Cas12a-coated magnetic beads, this assay combines efficient solid-phase extraction and enrichment of DNA targets enabled by the sequence-specific affinity of CRISPR-Cas12a with fluorogenic detection by activated Cas12a on beads. SPEEDi-CRISPR, for the first time, leverages the possibility of employing CRISPR/Cas12a in nucleic acid extraction and integrates the ability of both enrichment and detection of CRISPR/Cas into a single platform. Our proof-of-concept studies revealed that the SPEEDi-CRISPR assay has great specificity to distinguish HPV-18 from HPV-16, and Parvovirus B19, in addition to being able to detect HPV-18 at a concentration as low as 2.3 fM in 100 min and 4.7 fM in 60 min. Furthermore, we proved that this assay can be coupled with two point-of-care testing strategies: the smartphone-based fluorescence detector and the lateral flow assay. Overall, these results suggested that our assay could pave a new way for developing CRISPR diagnostics.
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Affiliation(s)
- Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Health Cancer Center, Gainesville, Florida 32611, United States
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17
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Deng F, Li Y, Yang B, Sang R, Deng W, Kansara M, Lin F, Thavaneswaran S, Thomas DM, Goldys EM. Topological barrier to Cas12a activation by circular DNA nanostructures facilitates autocatalysis and transforms DNA/RNA sensing. Nat Commun 2024; 15:1818. [PMID: 38443394 PMCID: PMC10914725 DOI: 10.1038/s41467-024-46001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Control of CRISPR/Cas12a trans-cleavage is crucial for biosensor development. Here, we show that small circular DNA nanostructures which partially match guide RNA sequences only minimally activate Cas12a ribonucleoproteins. However, linearizing these structures restores activation. Building on this finding, an Autocatalytic Cas12a Circular DNA Amplification Reaction (AutoCAR) system is established which allows a single nucleic acid target to activate multiple ribonucleoproteins, and greatly increases the achievable reporter cleavage rates per target. A rate-equation-based model explains the observed near-exponential rate trends. Autocatalysis is also sustained with DNA nanostructures modified with fluorophore-quencher pairs achieving 1 aM level (<1 copy/μL) DNA detection (106 times improvement), without additional amplification, within 15 min, at room temperature. The detection range is tuneable, spanning 3 to 11 orders of magnitude. We demonstrate 1 aM level detection of SNP mutations in circulating tumor DNA from blood plasma, genomic DNA (H. Pylori) and RNA (SARS-CoV-2) without reverse transcription as well as colorimetric lateral flow tests of cancer mutations with ~100 aM sensitivity.
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Affiliation(s)
- Fei Deng
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yi Li
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Biyao Yang
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rui Sang
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Wei Deng
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Maya Kansara
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2011, Australia
- Omico, Australian Genomic Cancer Medicine Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Frank Lin
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Subotheni Thavaneswaran
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2011, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2011, Australia
- Omico, Australian Genomic Cancer Medicine Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ewa M Goldys
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
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18
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Yang B, Wang H, Kong J, Fang X. Long-term monitoring of ultratrace nucleic acids using tetrahedral nanostructure-based NgAgo on wearable microneedles. Nat Commun 2024; 15:1936. [PMID: 38431675 PMCID: PMC10908814 DOI: 10.1038/s41467-024-46215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Real-time and continuous monitoring of nucleic acid biomarkers with wearable devices holds potential for personal health management, especially in the context of pandemic surveillance or intensive care unit disease. However, achieving high sensitivity and long-term stability remains challenging. Here, we report a tetrahedral nanostructure-based Natronobacterium gregoryi Argonaute (NgAgo) for long-term stable monitoring of ultratrace unamplified nucleic acids (cell-free DNAs and RNAs) in vivo for sepsis on wearable device. This integrated wireless wearable consists of a flexible circuit board, a microneedle biosensor, and a stretchable epidermis patch with enrichment capability. We comprehensively investigate the recognition mechanism of nucleic acids by NgAgo/guide DNA and signal transformation within the Debye distance. In vivo experiments demonstrate the suitability for real-time monitoring of cell-free DNA and RNA with a sensitivity of 0.3 fM up to 14 days. These results provide a strategy for highly sensitive molecular recognition in vivo and for on-body detection of nucleic acid.
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Affiliation(s)
- Bin Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Haonan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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19
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Sandler SE, Weckman NE, Yorke S, Das A, Chen K, Gutierrez R, Keyser UF. Sensing the DNA-mismatch tolerance of catalytically inactive Cas9 via barcoded DNA nanostructures in solid-state nanopores. Nat Biomed Eng 2024; 8:325-334. [PMID: 37550424 DOI: 10.1038/s41551-023-01078-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/30/2023] [Indexed: 08/09/2023]
Abstract
Single-molecule quantification of the strength and sequence specificity of interactions between proteins and nucleic acids would facilitate the probing of protein-DNA binding. Here we show that binding events between the catalytically inactive Cas9 ribonucleoprotein and any pre-defined short sequence of double-stranded DNA can be identified by sensing changes in ionic current as suitably designed barcoded linear DNA nanostructures with Cas9-binding double-stranded DNA overhangs translocate through solid-state nanopores. We designed barcoded DNA nanostructures to study the relationships between DNA sequence and the DNA-binding specificity, DNA-binding efficiency and DNA-mismatch tolerance of Cas9 at the single-nucleotide level. Nanopore-based sensing of DNA-barcoded nanostructures may help to improve the design of efficient and specific ribonucleoproteins for biomedical applications, and could be developed into sensitive protein-sensing assays.
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Affiliation(s)
- Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Nicole E Weckman
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Institute for Studies in Transdisciplinary Engineering Education & Practice, Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
| | - Sarah Yorke
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, Cambridge, UK
| | - Akashaditya Das
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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20
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Macchia E, Torricelli F, Caputo M, Sarcina L, Scandurra C, Bollella P, Catacchio M, Piscitelli M, Di Franco C, Scamarcio G, Torsi L. Point-Of-Care Ultra-Portable Single-Molecule Bioassays for One-Health. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309705. [PMID: 38108547 DOI: 10.1002/adma.202309705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Screening asymptomatic organisms (humans, animals, plants) with a high-diagnostic accuracy using point-of-care-testing (POCT) technologies, though still visionary holds great potential. Convenient surveillance requires easy-to-use, cost-effective, ultra-portable but highly reliable, in-vitro-diagnostic devices that are ready for use wherever they are needed. Currently, there are not yet such devices available on the market, but there are a couple more promising technologies developed at readiness-level 5: the Clustered-Regularly-Interspaced-Short-Palindromic-Repeats (CRISPR) lateral-flow-strip tests and the Single-Molecule-with-a-large-Transistor (SiMoT) bioelectronic palmar devices. They both hold key features delineated by the World-Health-Organization for POCT systems and an occurrence of false-positive and false-negative errors <1-5% resulting in diagnostic-selectivity and sensitivity >95-99%, while limit-of-detections are of few markers. CRISPR-strip is a molecular assay that, can detect down to few copies of DNA/RNA markers in blood while SiMoT immunometric and molecular test can detect down to a single oligonucleotide, protein marker, or pathogens in 0.1mL of blood, saliva, and olive-sap. These technologies can prospectively enable the systematic and reliable surveillance of asymptomatic ones prior to worsening/proliferation of illnesses allowing for timely diagnosis and swift prognosis. This could establish a proactive healthcare ecosystem that results in effective treatments for all living organisms generating diffuse and well-being at efficient costs.
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Affiliation(s)
- Eleonora Macchia
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Paolo Bollella
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Michele Catacchio
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Matteo Piscitelli
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | | | - Gaetano Scamarcio
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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21
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Zhou J, Li Z, Seun Olajide J, Wang G. CRISPR/Cas-based nucleic acid detection strategies: Trends and challenges. Heliyon 2024; 10:e26179. [PMID: 38390187 PMCID: PMC10882038 DOI: 10.1016/j.heliyon.2024.e26179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
CRISPR/Cas systems have become integral parts of nucleic acid detection apparatus and biosensors. Various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/Cas12, CRISPR/Cas13, CRISPR/Cas14 and CRISPR/Cas3 utilize different mechanisms to detect or differentiate biological activities and nucleotide sequences. Usually, CRISPR/Cas-based nucleic acid detection systems are combined with polymerase chain reaction, loop-mediated isothermal amplification, recombinase polymerase amplification and transcriptional technologies for effective diagnostics. Premised on these, many CRISPR/Cas-based nucleic acid biosensors have been developed to detect nucleic acids of viral and bacterial pathogens in clinical samples, as well as other applications in life sciences including biosecurity, food safety and environmental assessment. Additionally, CRISPR/Cas-based nucleic acid detection systems have showed better specificity compared with other molecular diagnostic methods. In this review, we give an overview of various CRISPR/Cas-based nucleic acid detection methods and highlight some advances in their development and components. We also discourse some operational challenges as well as advantages and disadvantages of various systems. Finally, important considerations are offered for the improvement of CRISPR/Cas-based nucleic acid testing.
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Affiliation(s)
- Jian Zhou
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510000, People's Republic of China
- Department of Laboratory Medicines, the First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, People's Republic of China
| | - Zhuo Li
- Department of Laboratory Medicines, the First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, People's Republic of China
| | - Joshua Seun Olajide
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510000, People's Republic of China
| | - Gang Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510000, People's Republic of China
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22
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Yin Y, Wen J, Wen M, Fu X, Ke G, Zhang XB. The design strategies for CRISPR-based biosensing: Target recognition, signal conversion, and signal amplification. Biosens Bioelectron 2024; 246:115839. [PMID: 38042054 DOI: 10.1016/j.bios.2023.115839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/27/2023] [Accepted: 11/11/2023] [Indexed: 12/04/2023]
Abstract
Rapid, sensitive and selective biosensing is highly important for analyzing biological targets and dynamic physiological processes in cells and living organisms. As an emerging tool, clustered regularly interspaced short palindromic repeats (CRISPR) system is featured with excellent complementary-dependent cleavage and efficient trans-cleavage ability. These merits enable CRISPR system to improve the specificity, sensitivity, and speed for molecular detection. Herein, the structures and functions of several CRISPR proteins for biosensing are summarized in depth. Moreover, the strategies of target recognition, signal conversion, and signal amplification for CRISPR-based biosensing were highlighted from the perspective of biosensor design principles. The state-of-art applications and recent advances of CRISPR system are then outlined, with emphasis on their fluorescent, electrochemical, colorimetric, and applications in POCT technology. Finally, the current challenges and future prospects of this frontier research area are discussed.
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Affiliation(s)
- Yao Yin
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jialin Wen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Mei Wen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiaoyi Fu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Guoliang Ke
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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23
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Zhang X, Chen S, Ma H, Sun T, Cui X, Huo P, Man B, Yang C. Asymmetric Schottky Barrier-Generated MoS 2/WTe 2 FET Biosensor Based on a Rectified Signal. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:226. [PMID: 38276744 PMCID: PMC10820193 DOI: 10.3390/nano14020226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
Field-effect transistor (FET) biosensors can be used to measure the charge information carried by biomolecules. However, insurmountable hysteresis in the long-term and large-range transfer characteristic curve exists and affects the measurements. Noise signal, caused by the interference coefficient of external factors, may destroy the quantitative analysis of trace targets in complex biological systems. In this report, a "rectified signal" in the output characteristic curve, instead of the "absolute value signal" in the transfer characteristic curve, is obtained and analyzed to solve these problems. The proposed asymmetric Schottky barrier-generated MoS2/WTe2 FET biosensor achieved a 105 rectified signal, sufficient reliability and stability (maintained for 60 days), ultra-sensitive detection (10 aM) of the Down syndrome-related DYRK1A gene, and excellent specificity in base recognition. This biosensor with a response range of 10 aM-100 pM has significant application potential in the screening and rapid diagnosis of Down syndrome.
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Affiliation(s)
- Xinhao Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
| | - Shuo Chen
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
| | - Heqi Ma
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
| | - Tianyu Sun
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
| | - Xiangyong Cui
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
| | - Panpan Huo
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
| | - Baoyuan Man
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
| | - Cheng Yang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China; (X.Z.); (S.C.); (H.M.); (T.S.); (X.C.); (P.H.)
- Shandong Provincial Engineering and Technical Center of Light Manipulations, Shandong Normal University, Jinan 250014, China
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24
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Li J, Zhang K, Lin G, Li J. CRISPR-Cas system: A promising tool for rapid detection of SARS-CoV-2 variants. J Med Virol 2024; 96:e29356. [PMID: 38180237 DOI: 10.1002/jmv.29356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
COVID-19, caused by SARS-CoV-2, remains a global health crisis. The emergence of multiple variants with enhanced characteristics necessitates their detection and monitoring. Genome sequencing, the gold standard, faces implementation challenges due to complexity, cost, and limited throughput. The CRISPR-Cas system offers promising potential for rapid variant detection, with advantages such as speed, sensitivity, specificity, and programmability. This review provides an in-depth examination of the applications of CRISPR-Cas in mutation detection specifically for SARS-CoV-2. It begins by introducing SARS-CoV-2 and existing variant detection platforms. The principles of the CRISPR-Cas system are then clarified, followed by an exploration of three CRISPR-Cas-based mutation detection platforms, which are evaluated from different perspectives. The review discusses strategies for mutation site selection and the utilization of CRISPR-Cas, offering valuable insights for the development of mutation detection methods. Furthermore, a critical analysis of the clinical applications, advantages, disadvantages, challenges, and prospects of the CRISPR-Cas system is provided.
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Affiliation(s)
- Jing Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
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25
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Aran K, Goldsmith B, Moarefian M. Applications of Graphene Field Effect Biosensors for Biological Sensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:37-70. [PMID: 38418581 DOI: 10.1007/10_2024_252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
This chapter provides a comprehensive overview of the principles, applications, and advancements in graphene field-effect transistor (gFET) biosensors for biological sensing. The unique properties of graphene that make it ideal for biosensing, including its high conductivity, chemical stability, and ability to facilitate label-free detection, will be discussed. The chapter also explores various applications of gFET biosensors, from detecting pH and salinity changes to complex protein-protein interactions and DNA/RNA sensing. It also addresses the challenges and future directions in gFET biosensor technology, emphasizing the need for scalable manufacturing, sophisticated surface chemistry, and the integration of multiomics approaches to enhance biosensing capabilities.
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Affiliation(s)
- Kiana Aran
- Shu Chien-Gene Lay Department of Bioengineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA.
- Division of Geriatrics, Gerontology and Palliative Care, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Center for Technologies for Healthy Aging, Institute of Engineering and Medicine, University of California, San Diego, La Jolla, CA, USA.
- Paragraf, Somersham, UK.
- CRISPR QC, San Diego, CA, USA.
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26
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Li Y, Liu Y, Tang X, Qiao J, Kou J, Man S, Zhu L, Ma L. CRISPR/Cas-Powered Amplification-Free Detection of Nucleic Acids: Current State of the Art, Challenges, and Futuristic Perspectives. ACS Sens 2023; 8:4420-4441. [PMID: 37978935 DOI: 10.1021/acssensors.3c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
CRISPR/Cas system is becoming an increasingly influential technology that has been repositioned in nucleic acid detection. A preamplification step is usually required to improve the sensitivity of CRISPR/Cas-based detection. The striking biological features of CRISPR/Cas, including programmability, high sensitivity and sequence specificity, and single-base resolution. More strikingly, the target-activated trans-cleavage could act as a biocatalytic signal transductor and amplifier, thereby empowering it to potentially perform nucleic acid detection without a preamplification step. The reports of such work are on the rise, which is not only scientifically significant but also promising for futuristic end-user applications. This review started with the introduction of the detection methods of nucleic acids and the CRISPR/Cas-based diagnostics (CRISPR-Dx). Next, we objectively discussed the pros and cons of preamplification steps for CRISPR-Dx. We then illustrated and highlighted the recently developed strategies for CRISPR/Cas-powered amplification-free detection that can be realized through the uses of ultralocalized reactors, cascade reactions, ultrasensitive detection systems, or others. Lastly, the challenges and futuristic perspectives were proposed. It can be expected that this work not only makes the researchers better understand the current strategies for this emerging field, but also provides insight for designing novel CRISPR-Dx without a preamplification step to win practicable use in the near future.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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27
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Patange S, Maragh S. Fire Burn and Cauldron Bubble: What Is in Your Genome Editing Brew? Biochemistry 2023; 62:3500-3511. [PMID: 36306429 PMCID: PMC10734218 DOI: 10.1021/acs.biochem.2c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 11/28/2022]
Abstract
Genome editing is a rapidly evolving biotechnology with the potential to transform many sectors of industry such as agriculture, biomanufacturing, and medicine. This technology is enabled by an ever-growing portfolio of biomolecular reagents that span the central dogma, from DNA to RNA to protein. In this paper, we draw from our unique perspective as the National Metrology Institute of the United States to bring attention to the importance of understanding and reporting genome editing formulations accurately and promoting concepts to verify successful delivery into cells. Achieving the correct understanding may be hindered by the way units, quantities, and stoichiometries are reported in the field. We highlight the variability in how editing formulations are reported in the literature and examine how a reference molecule could be used to verify the delivery of a reagent into cells. We provide recommendations on how more accurate reporting of editing formulations and more careful verification of the steps in an editing experiment can help set baseline expectations of reagent performance, toward the aim of enabling genome editing studies to be more reproducible. We conclude with a future outlook on technologies that can further our control and enable our understanding of genome editing outcomes at the single-cell level.
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Affiliation(s)
- Simona Patange
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Samantha Maragh
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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28
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Jing Q, Liu J, Wang H, Wang Y, Xue H, Ren S, Wang W, Zhang X, Xu Z, Fu W. Ultrasensitive Biochemical Sensing Platform Enabled by Directly Grown Graphene on Insulator. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2305363. [PMID: 38105346 DOI: 10.1002/smll.202305363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/06/2023] [Indexed: 12/19/2023]
Abstract
To fabricate label-free and rapid-resulting semiconducting biosensor devices incorporating graphene, it is pertinent to directly grow uniform graphene films on technologically important dielectric and semiconducting substrates. However, it has long been intuitively believed that the nonideal disordered structures formed during direct growth, and the resulted inferior electrical properties will inevitably lead to deteriorated sensing performance. Here, graphene biosensor chips are constructed based on direct plasma-enhanced chemical vapor deposition (PECVD) grown graphene on a 4-inch silicon wafer with excellent film uniformity and high yield. To surprise, optimal operations of graphene biosensors permit ultrasensitive detection of SARS-CoV-2 virus nucleocapsid protein with dilutions down to sub-femtomolar concentrations. Such impressive limit of detection (LOD) is comparable to or even outperforms that of the state-of-the-art biosensor devices based on high-quality graphene. Further noise spectral characterizations and analysis confirms that the LOD is limited by molecular diffusion and/or known interference signals such as drift and instability of the sensors, rather than the electrical merits of the graphene devices along. Hence, result sheds light on processing directly grown PECVD graphene into high-performance sensor devices with important economic benefits and social significance.
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Affiliation(s)
- Qiushi Jing
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, China
| | - Junjiang Liu
- Songshan Lake Materials Laboratory, Dongguan, 523808, China
| | - Huanming Wang
- Songshan Lake Materials Laboratory, Dongguan, 523808, China
| | - Yanli Wang
- Songshan Lake Materials Laboratory, Dongguan, 523808, China
| | - Honglei Xue
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, China
| | - Shan Ren
- Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Wenjing Wang
- Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xiaoyan Zhang
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, China
| | - Zhi Xu
- Songshan Lake Materials Laboratory, Dongguan, 523808, China
| | - Wangyang Fu
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, China
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29
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Fu Y, Liu Y, Song W, Yang D, Wu W, Lin J, Yang X, Zeng J, Rong L, Xia J, Lei H, Yang R, Zhang M, Liao Y. Early monitoring-to-warning Internet of Things system for emerging infectious diseases via networking of light-triggered point-of-care testing devices. EXPLORATION (BEIJING, CHINA) 2023; 3:20230028. [PMID: 38264687 PMCID: PMC10742204 DOI: 10.1002/exp.20230028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/31/2023] [Indexed: 01/25/2024]
Abstract
Early monitoring and warning arrangements are effective ways to distinguish infectious agents and control the spread of epidemic diseases. Current testing technologies, which cannot achieve rapid detection in the field, have a risk of slowing down the response time to the disease. In addition, there is still no epidemic surveillance system, implementing prevention and control measures is slow and inefficient. Motivated by these clinical needs, a sample-to-answer genetic diagnosis platform based on light-controlled capillary modified with a photocleavable linker is first developed, which could perform nucleic acid separation and release by light irradiation in less than 30 seconds. Then, on site polymerase chain reaction was performed in a handheld closed-loop convective system. Test reports are available within 20 min. Because this method is portable, rapid, and easy to operate, it has great potential for point-of-care testing. Additionally, through multiple device networking, a real-time artificial intelligence monitoring system for pathogens was developed on a cloud server. Through data reception, analysis, and visualization, the system can send early warning signals for disease control and prevention. Thus, anti-epidemic measures can be implemented effectively, and deploying and running this system can improve the capabilities for the prevention and control of infectious diseases.
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Affiliation(s)
- Yu Fu
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
- Longgang District Central Hospital of ShenzhenShenzhenChina
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Yan Liu
- Institute for Health Innovation and TechnologyNational University of SingaporeSingaporeSingapore
| | - Wenlu Song
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
| | - Delong Yang
- Department of Burn Surgerythe First People's Hospital of FoshanFoshanChina
| | - Wenjie Wu
- Department of Burn and Plastic SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Jingyan Lin
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Xiongtiao Yang
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Jian Zeng
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Lingzhi Rong
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Jiaojiao Xia
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Hongyi Lei
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Ronghua Yang
- Department of Burn and Plastic SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Mingxia Zhang
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Yuhui Liao
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
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30
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Yan H, Wen Y, Tian Z, Hart N, Han S, Hughes SJ, Zeng Y. A one-pot isothermal Cas12-based assay for the sensitive detection of microRNAs. Nat Biomed Eng 2023; 7:1583-1601. [PMID: 37106152 PMCID: PMC11108682 DOI: 10.1038/s41551-023-01033-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 03/29/2023] [Indexed: 04/29/2023]
Abstract
The use of microRNAs as clinical cancer biomarkers is hindered by the absence of accurate, fast and inexpensive assays for their detection in biofluids. Here we report a one-step and one-pot isothermal assay that leverages rolling-circle amplification and the endonuclease Cas12a for the accurate detection of specific miRNAs. The assay exploits the cis-cleavage activity of Cas12a to enable exponential rolling-circle amplification of target sequences and its trans-cleavage activity for their detection and for signal amplification. In plasma from patients with pancreatic ductal adenocarcinoma, the assay detected the miRNAs miR-21, miR-196a, miR-451a and miR-1246 in extracellular vesicles at single-digit femtomolar concentrations with single-nucleotide specificity. The assay is rapid (sample-to-answer times ranged from 20 min to 3 h), does not require specialized instrumentation and is compatible with a smartphone-based fluorescence detection and with the lateral-flow format for visual readouts. Simple assays for the detection of miRNAs in blood may aid the development of miRNAs as biomarkers for the diagnosis and prognosis of cancers.
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Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Yunjie Wen
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Nathan Hart
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Song Han
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Steven J Hughes
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA.
- University of Florida Health Cancer Center, Gainesville, FL, USA.
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31
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Chowdhry R, Lu SZ, Lee S, Godhulayyagari S, Ebrahimi SB, Samanta D. Enhancing CRISPR/Cas systems with nanotechnology. Trends Biotechnol 2023; 41:1549-1564. [PMID: 37451945 DOI: 10.1016/j.tibtech.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
CRISPR/Cas systems have revolutionized biology and medicine, and have led to new paradigms in disease diagnostics and therapeutics. However, these complexes suffer from key limitations regarding barriers to cellular entry, stability in biological environments, and off-target effects. Integrating nanotechnology with CRISPR/Cas systems has emerged as a promising strategy to overcome these challenges and has further unlocked structures that accumulate preferentially in tissues of interest, have tunable pharmacological properties, and are activated in response to desired stimuli. Nanomaterials can also enhance CRISPR/Cas-mediated detection platforms by enabling faster, more sensitive, and convenient readouts. We highlight recent advances in this rapidly growing field. We also outline areas that need further development to fully realize the potential of CRISPR technologies.
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Affiliation(s)
- Rupali Chowdhry
- Department of Public Health, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven Z Lu
- Department of Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Seungheon Lee
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Sasha B Ebrahimi
- Drug Product Development - Steriles, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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32
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Liang P, Lv B, Chen K, Qiao W, Li D. An ultrasensitive Cd 2+ detection biosensor based on DNAzyme and CRISPR/Cas12a coupled with hybridization chain reaction. Anal Chim Acta 2023; 1283:341950. [PMID: 37977780 DOI: 10.1016/j.aca.2023.341950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The detection of cadmium is essential because it poses a significant threat to human health and the environment. Recent advancements in biosensors that detect nonnucleic-acid targets using CRISPR/Cas12a in combination with aptamers or DNAzymes show promising performance. Herein, we integrated DNAzyme, hybridization chain reaction (HCR) and CRISPR/Cas12a into a single biosensor for the first time and realized the ultrasensitive detection of Cd2+. A single phosphorothioate ribonucleobase (rA)-containing oligonucleotide (PS substrate) and a Cd2+-specific DNAzyme (Cdzyme) are used for Cd2+ recognition, releasing short single-stranded DNA. Then, the HCR is triggered by the cleavage products for signal transduction and amplification. Next, the trans-cleavage activity of Cas12a is activated due to the presence of crRNA complementary strands and PAM sites in the HCR products. As a result, FQ-reporters are cleaved, and the fluorescence values can be easily read using a fluorometer, allowing Cd2+ quantification by measuring the fluorescent signal. The Cd2+ detection biosensor is ultrasensitive with a detection limit of 1.25 pM. Moreover, the biosensor shows great stability under different pH and various anion conditions. The proposed sensor was utilized for environmental water sample detection, demonstrating the dependability of the detection system. Considering the high sensitivity and reliable performance of the assay, it could be further used in environmental monitoring. In addition, the design strategy reported in this study could extend the application of CRISPR/Cas12a in heavy metal detection.
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Affiliation(s)
- Pengda Liang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Bei Lv
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Ke Chen
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Wenrui Qiao
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
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33
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Barnes B, Wang Z, Alibrahim A, Lin Q, Wu X, Wang Y. Direct Writing of Aligned Carbon Nanotubes across a Trench. ACS NANO 2023; 17:22701-22707. [PMID: 37966901 DOI: 10.1021/acsnano.3c07191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Aligned and suspended carbon nanotubes can outperform randomly oriented networks in electronic biosensing and thin-film electronics. However, carbon nanotubes tend to bundle and form random networks. Here, we show that carbon nanotubes spontaneously align in an ammonium deoxycholate surfactant gel even under low shear forces, allowing direct writing and printing of nanotubes into electrically conducting wires and aligned thin layers across trenches. To demonstrate its application potential, we directly printed arrays of disposable electrical biosensors, which show femtomolar sensitivity in the detection of DNA and SARS-CoV-2 RNA.
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Affiliation(s)
- Benjamin Barnes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Material Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Ziyi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Ayman Alibrahim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Qinglin Lin
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Xiaojian Wu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, United States
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34
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Le PG, Choi SH, Cho S. Alzheimer's Disease Biomarker Detection Using Field Effect Transistor-Based Biosensor. BIOSENSORS 2023; 13:987. [PMID: 37998162 PMCID: PMC10669709 DOI: 10.3390/bios13110987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Alzheimer's disease (AD) is closely related to neurodegeneration, leading to dementia and cognitive impairment, especially in people aged > 65 years old. The detection of biomarkers plays a pivotal role in the diagnosis and treatment of AD, particularly at the onset stage. Field-effect transistor (FET)-based sensors are emerging devices that have drawn considerable attention due to their crucial ability to recognize various biomarkers at ultra-low concentrations. Thus, FET is broadly manipulated for AD biomarker detection. In this review, an overview of typical FET features and their operational mechanisms is described in detail. In addition, a summary of AD biomarker detection and the applicability of FET biosensors in this research field are outlined and discussed. Furthermore, the trends and future prospects of FET devices in AD diagnostic applications are also discussed.
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Affiliation(s)
- Phan Gia Le
- Department of Electronic Engineering, Gachon University, Seongnam-si 13120, Republic of Korea
| | - Seong Hye Choi
- Department of Neurology, College of Medicine, Inha University, Incheon 22332, Republic of Korea
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, Seongnam-si 13120, Republic of Korea
- Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea
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35
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Wang H, Sun Y, Zhou Y, Liu Y, Chen S, Sun W, Zhang Z, Guo J, Yang C, Li Z, Chen L. Unamplified system for sensitive and typing detection of ASFV by the cascade platform that CRISPR-Cas12a combined with graphene field-effect transistor. Biosens Bioelectron 2023; 240:115637. [PMID: 37669587 DOI: 10.1016/j.bios.2023.115637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
At present, the 100% case fatality and the cross-infection of virus strains make the ASFV 's harm to society continue to expand. The absence of an effective commercial vaccine poses early detection remains the most effective means of curbing ASFV infection. Here, we report a cascaded detection platform based on the CRISPR-Cas12a system combined with graphene field-effect transistor sensors. The cascade platform could detect ASFV as low as 0.5 aM within 30 min and achieve typing of wild and vaccine strains of ASFV in a single detection system. The evaluation of 16 clinical samples proved that, compared with the gold standard Real-time PCR method, this platform has outstanding advantages in sensitivity, specificity and typing. Combining CRISPR-Cas12a's high specificity with the bipolar electric field effect of graphene field-effect transistor, the cascade platform is expected to achieve clinical application in the field of DNA disease detection, and provides a new direction for multi-strain disease typing.
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Affiliation(s)
- Hua Wang
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Yang Sun
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
| | - Yuan Zhou
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Yujie Liu
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Shuo Chen
- Department of Physics and Electronics, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Wenbo Sun
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, PR China
| | - Zidong Zhang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Shandong University, No. 17923 Jing Shi Road, Jinan, 250061, PR China
| | - Junqing Guo
- Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116 Huayuan Road, Zhengzhou, 450099, PR China
| | - Cheng Yang
- Department of Physics and Electronics, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China.
| | - Zhengping Li
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
| | - Lei Chen
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China.
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36
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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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37
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Liang T, Qin X, Zhang Y, Yang Y, Chen Y, Yuan L, Liu F, Chen Z, Li X, Yang F. CRISPR/dCas9-Mediated Specific Molecular Assembly Facilitates Genotyping of Mutant Circulating Tumor DNA. Anal Chem 2023; 95:16305-16314. [PMID: 37874695 DOI: 10.1021/acs.analchem.3c03481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Breakthroughs in circulating tumor DNA (ctDNA) analysis are critical in tumor liquid biopsies but remain a technical challenge due to the double-stranded structure, extremely low abundance, and short half-life of ctDNA. Here, we report an electrochemical CRISPR/dCas9 sensor (E-dCas9) for sensitive and specific detection of ctDNA at a single-nucleotide resolution. The E-dCas9 design harnesses the specific capture and unzipping of target ctDNA by dCas9 to introduce a complementary reporter probe for specific molecular assembly and signal amplification. By efficient homogeneous assembly and interfacial click reaction, the assay demonstrates superior sensitivity (up to 2.86 fM) in detecting single-base mutant ctDNA and a broad dynamic range spanning 6 orders of magnitude. The sensor is also capable of measuring 10 fg/μL of a mutated target in excess of wild-type ones (1 ng/μL), equivalent to probing 0.001% of the mutation relative to the wild type. In addition, our sensor can monitor the dynamic expression of cellular genomic DNA and allows accurate analysis of blood samples from patients with nonsmall cell lung cancer, suggesting the potential of E-dCas9 as a promising tool in ctDNA-based cancer diagnosis.
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Affiliation(s)
- Tingting Liang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
- Department of Pharmacy, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, China
| | - Xiaojie Qin
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Yuyuan Zhang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Yu Yang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Yu Chen
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Lin Yuan
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rhumatic Diseases, Hubei Minzu University, Enshi 445000, China
| | - Feng Liu
- Department of Blood Transfusion, the First Affiliated Hospital, Guangxi Medical University, Nanning 530021, China
| | - Zhizhong Chen
- Department of Clinical Laboratory, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China
| | - Xinchun Li
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Fan Yang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rhumatic Diseases, Hubei Minzu University, Enshi 445000, China
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38
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Ren Q, Jiang L, Ma S, Li T, Zhu Y, Qiu R, Xing Y, Yin F, Li Z, Ye X, Zhang Y, Zhang M. Multi-Body Biomarker Entrapment System: An All-Encompassing Tool for Ultrasensitive Disease Diagnosis and Epidemic Screening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304119. [PMID: 37486783 DOI: 10.1002/adma.202304119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/18/2023] [Indexed: 07/26/2023]
Abstract
Ultrasensitive identification of biomarkers in biofluids is essential for the precise diagnosis of diseases. For the gold standard approaches, polymerase chain reaction and enzyme-linked immunosorbent assay, cumbersome operational steps hinder their point-of-care applications. Here, a bionic biomarker entrapment system (BioES) is implemented, which employs a multi-body Y-shaped tetrahedral DNA probe immobilized on carbon nanotube transistors. Clinical identification of endometriosis is successfully realized by detecting an estrogen receptor, ERβ, from the lesion tissue of endometriosis patients and establishing a standard diagnosis procedure. The multi-body Y-shaped BioES achieves a theoretical limit of detection (LoD) of 6.74 aM and a limit of quantification of 141 aM in a complex protein milieu. Furthermore, the BioES is optimized into a multi-site recognition module for enhanced binding efficiency, realizing the first identification of monkeypox virus antigen A35R and unamplified detection of circulating tumor DNA of breast cancer in serum. The rigid and compact probe framework with synergy effect enables the BioES to target A35R and DNA with a LoD down to 991 and 0.21 aM, respectively. Owing to its versatility for proteins and nucleic acids as well as ease of manipulation and ultra-sensitivity, the BioES can be leveraged as an all-encompassing tool for population-wide screening of epidemics and clinical disease diagnosis.
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Affiliation(s)
- Qinqi Ren
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Leying Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, 518055, China
| | - Shenhui Ma
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Tong Li
- Department of Gynecology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, 518020, China
| | - Yang Zhu
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Rui Qiu
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Yun Xing
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, 518055, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xiyang Ye
- Department of Gynecology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, 518020, China
| | - Yaping Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Min Zhang
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
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Nisar S, Basha B, Dastgeer G, Shahzad ZM, Kim H, Rabani I, Rasheed A, Al‐Buriahi MS, Irfan A, Eom J, Kim D. A Novel Biosensing Approach: Improving SnS 2 FET Sensitivity with a Tailored Supporter Molecule and Custom Substrate. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303654. [PMID: 37863822 PMCID: PMC10667857 DOI: 10.1002/advs.202303654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/28/2023] [Indexed: 10/22/2023]
Abstract
The exclusive features of two-dimensional (2D) semiconductors, such as high surface-to-volume ratios, tunable electronic properties, and biocompatibility, provide promising opportunities for developing highly sensitive biosensors. However, developing practical biosensors that can promptly detect low concentrations of target analytes remains a challenging task. Here, a field-effect-transistor comprising n-type transition metal dichalcogenide tin disulfide (SnS2 ) is developed over the hexagonal boron nitride (h-BN) for the detection of streptavidin protein (Strep.) as a target analyte. A self-designed receptor based on the pyrene-lysine conjugated with biotin (PLCB) is utilized to maintain the sensitivity of the SnS2 /h-BN FET because of the π-π stacking. The detection capabilities of SnS2 /h-BN FET are investigated using both Raman spectroscopy and electrical characterizations. The real-time electrical measurements exhibit that the SnS2 /h-BN FET is capable of detecting streptavidin at a remarkably low concentration of 0.5 pm, within 13.2 s. Additionally, the selectivity of the device is investigated by measuring its response against a Cow-like serum egg white protein (BSA), having a comparative molecular weight to that of the streptavidin. These results indicate a high sensitivity and rapid response of SnS2 /h-BN biosensor against the selective proteins, which can have significant implications in several fields including point-of-care diagnostics, drug discovery, and environmental monitoring.
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Affiliation(s)
- Sobia Nisar
- Department of Electrical EngineeringSejong UniversitySeoul05006Republic of Korea
- Department of Convergence Engineering for Intelligent DroneSejong UniversitySeoul05006Republic of Korea
| | - Beriham Basha
- Department of PhysicsCollege of SciencesPrincess Nourah bint Abdulrahman UniversityP. O Box 84428Riyadh11671Saudi Arabia
| | - Ghulam Dastgeer
- Department of Physics and AstronomySejong UniversitySeoul05006Republic of Korea
| | - Zafar M. Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT) and Department of Chemical and Polymer EngineeringSungkyunkwan UniversitySuwon16419Republic of Korea
- Department of Chemical and Polymer EngineeringUniversity of Engineering & TechnologyFaisalabad CampusLahore38000Pakistan
| | - Honggyun Kim
- Department of Semiconductor Systems EngineeringSejong UniversitySeoul05006Republic of Korea
| | - Iqra Rabani
- Department of Nanotechnology and Advanced Materials EngineeringSejong UniversitySeoul05006Republic of Korea
| | - Aamir Rasheed
- School of Materials Science and EngineeringAnhui UniversityHefeiAnhui230601People's Republic of China
| | | | - Ahmad Irfan
- Department of ChemistryCollege of ScienceKing Khalid UniversityP.O. Box 9004Abha61413Saudi Arabia
| | - Jonghwa Eom
- Department of Physics and AstronomySejong UniversitySeoul05006Republic of Korea
| | - Deok‐kee Kim
- Department of Electrical EngineeringSejong UniversitySeoul05006Republic of Korea
- Department of Semiconductor Systems EngineeringSejong UniversitySeoul05006Republic of Korea
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40
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Zhu Y, Zhang M, Guo S, Xu H, Jie Z, Tao SC. CRISPR-based diagnostics of different biomolecules from nucleic acids, proteins, and small molecules to exosomes. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1539-1550. [PMID: 37528660 PMCID: PMC10577475 DOI: 10.3724/abbs.2023134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/29/2023] [Indexed: 08/03/2023] Open
Abstract
CRISPR-based detection technologies have been widely explored for molecular diagnostics. However, the challenge lies in converting the signal of different biomolecules, such as nucleic acids, proteins, small molecules, exosomes, and ions, into a CRISPR-based nucleic acid detection signal. Understanding the detection of different biomolecules using CRISPR technology can aid in the development of practical and promising detection approaches. Unfortunately, existing reviews rarely provide an overview of CRISPR-based molecular diagnostics from the perspective of different biomolecules. Herein, we first introduce the principles and characteristics of various CRISPR nucleases for molecular diagnostics. Then, we focus on summarizing and evaluating the latest advancements in CRISPR-based detection of different biomolecules. Through a comparison of different methods of amplification and signal readout, we discuss how general detection methods can be integrated with CRISPR. Finally, we conclude by identifying opportunities for the improvement of CRISPR in quantitative, amplification-free, multiplex, all-in-one, and point-of-care testing (POCT) purposes.
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Affiliation(s)
- Yuanshou Zhu
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
| | - Meng Zhang
- Department of Pulmonary and Critical Care MedicineShanghai Fifth People’s HospitalFudan UniversityShanghai200240China
| | - Shujuan Guo
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
| | - Hong Xu
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care MedicineShanghai Fifth People’s HospitalFudan UniversityShanghai200240China
- Center of Community-Based Health ResearchFudan UniversityShanghai200240China
| | - Sheng-ce Tao
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
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41
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Wu G, Zhang ET, Qiang Y, Esmonde C, Chen X, Wei Z, Song Y, Zhang X, Schneider MJ, Li H, Sun H, Weng Z, Santaniello S, He J, Lai RY, Li Y, Bruchas MR, Zhang Y. Long-Term In Vivo Molecular Monitoring Using Aptamer-Graphene Microtransistors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562080. [PMID: 37905115 PMCID: PMC10614860 DOI: 10.1101/2023.10.18.562080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Long-term, real-time molecular monitoring in complex biological environments is critical for our ability to understand, prevent, diagnose, and manage human diseases. Aptamer-based electrochemical biosensors possess the promise due to their generalizability and a high degree of selectivity. Nevertheless, the operation of existing aptamer-based biosensors in vivo is limited to a few hours. Here, we report a first-generation long-term in vivo molecular monitoring platform, named aptamer-graphene microtransistors (AGMs). The AGM incorporates a layer of pyrene-(polyethylene glycol)5-alcohol and DNase inhibitor-doped polyacrylamide hydrogel coating to reduce biofouling and aptamer degradation. As a demonstration of function and generalizability, the AGM achieves the detection of biomolecules such as dopamine and serotonin in undiluted whole blood at 37 °C for 11 days. Furthermore, the AGM successfully captures optically evoked dopamine release in vivo in mice for over one week and demonstrates the capability to monitor behaviorally-induced endogenous dopamine release even after eight days of implantation in freely moving mice. The results reported in this work establish the potential for chronic aptamer-based molecular monitoring platforms, and thus serve as a new benchmark for molecular monitoring using aptamer-based technology.
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Affiliation(s)
- Guangfu Wu
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Eric T. Zhang
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
| | - Yingqi Qiang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Colin Esmonde
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32306, USA
| | - Xingchi Chen
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32306, USA
| | - Zichao Wei
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Yang Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Xincheng Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Michael J. Schneider
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Huijie Li
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - He Sun
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Zhengyan Weng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Sabato Santaniello
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Jie He
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Rebecca Y. Lai
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Yan Li
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32306, USA
| | - Michael R. Bruchas
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Yi Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
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42
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Shigemori H, Fujita S, Tamiya E, Wakida SI, Nagai H. Solid-Phase Collateral Cleavage System Based on CRISPR/Cas12 and Its Application toward Facile One-Pot Multiplex Double-Stranded DNA Detection. Bioconjug Chem 2023; 34:1754-1765. [PMID: 37782626 PMCID: PMC10587867 DOI: 10.1021/acs.bioconjchem.3c00294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/31/2023] [Indexed: 10/04/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 12 (Cas12) system is attracting interest for its potential as a next-generation nucleic acid detection tool. The system can recognize double-stranded DNA (dsDNA) based on Cas12-CRISPR RNA (crRNA) and induce signal transduction by collateral cleavage. This property is expected to simplify comprehensive genotyping. Here, we report a solid-phase collateral cleavage (SPCC) reaction by CRISPR/Cas12 and its application toward one-pot multiplex dsDNA detection with minimal operational steps. In the sensor, Cas12-crRNA and single-stranded DNA (ssDNA) are immobilized on the sensing surface and act as enzyme and reporter substrates, respectively. We also report a dual-target dsDNA sensor prepared by immobilizing Cas12-crRNA and a fluorophore-labeled ssDNA reporter on separate spots. When a spot captures a target dsDNA sequence, it cleaves the ssDNA reporter on the same spot and reduces its fluorescence by 42.1-57.3%. Crucially, spots targeting different sequences do not show a reduction in fluorescence, thus confirming the one-pot multiplex dsDNA detection by SPCC. Furthermore, the sequence specificity has a two-base resolution, and the detectable concentration for the target dsDNA is at least 10-9 M. In the future, the SPCC-based sensor array could achieve one-pot comprehensive genotyping by using an array spotter as a reagent-immobilizing method.
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Affiliation(s)
- Hiroki Shigemori
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Graduate
School of Human Development and Environment, Kobe University, 3-11
Tsurukabuto, Nada-ku, Kobe, Hyogo 657-0011, Japan
| | - Satoshi Fujita
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Eiichi Tamiya
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Institute
of Scientific and Industrial Research (SANKEN), Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shin-ichi Wakida
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Institute
of Scientific and Industrial Research (SANKEN), Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Hidenori Nagai
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Graduate
School of Human Development and Environment, Kobe University, 3-11
Tsurukabuto, Nada-ku, Kobe, Hyogo 657-0011, Japan
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43
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Kulkarni A, Tanga S, Karmakar A, Hota A, Maji B. CRISPR-Based Precision Molecular Diagnostics for Disease Detection and Surveillance. ACS APPLIED BIO MATERIALS 2023; 6:3927-3945. [PMID: 37788375 DOI: 10.1021/acsabm.3c00439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Sensitive, rapid, and portable molecular diagnostics is the future of disease surveillance, containment, and therapy. The recent SARS-CoV-2 pandemic has reminded us of the vulnerability of lives from ever-evolving pathogens. At the same time, it has provided opportunities to bridge the gap by translating basic molecular biology into therapeutic tools. One such molecular biology technique is CRISPR (clustered regularly interspaced short palindromic repeat) which has revolutionized the field of molecular diagnostics at the need of the hour. The use of CRISPR-Cas systems has been widespread in biology research due to the ease of performing genetic manipulations. In 2012, CRISPR-Cas systems were, for the first time, shown to be reprogrammable, i.e., capable of performing sequence-specific gene editing. This discovery catapulted the field of CRISPR-Cas research and opened many unexplored avenues in the field of gene editing, from basic research to therapeutics. One such field that benefitted greatly from this discovery was molecular diagnostics, as using CRISPR-Cas technologies enabled existing diagnostic methods to become more sensitive, accurate, and portable, a necessity in disease control. This Review aims to capture some of the trajectories and advances made in this arena and provides a comprehensive understanding of the methods and their potential use as point-of-care diagnostics.
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Affiliation(s)
- Akshara Kulkarni
- Ashoka University, Department of Biology, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - Sadiya Tanga
- Ashoka University, Department of Chemistry, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - Arkadeep Karmakar
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
| | - Arpita Hota
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
| | - Basudeb Maji
- Ashoka University, Department of Biology, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
- Ashoka University, Department of Chemistry, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
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44
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Kim G, Li YG, Seo Y, Baek C, Choi JH, Park H, An J, Lee M, Noh S, Min J, Lee T. Fabrication of graphene oxide-based pretreatment filter and Electrochemical-CRISPR biosensor for the field-ready cyanobacteria monitoring system. Biosens Bioelectron 2023; 237:115474. [PMID: 37364302 DOI: 10.1016/j.bios.2023.115474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
Microcystis aeruginosa (M. aeruginosa) cause the eutrophication of lakes and rivers. To effectively control the overgrowth of M. aeruginosa, a suitable measurement method should be required in the aquatic fields. To address this, we developed a field-ready cyanobacterial pretreatment device and an electrochemical clustered regularly interspaced short palindromic repeats (EC-CRISPR) biosensor. The cyanobacterial pretreatment device consists of a syringe, glass bead, and graphene oxide (GO) bead. Then, the M. aeruginosa dissolved in the freshwater sample was added to fabricated filter. After filtration, the purified gene was loaded onto a CRISPR-based electrochemical biosensor chip to detect M. aeruginosa gene fragments. The biosensor was composed of CRISPR/Cpf1 protein conjugated with MXene on an Au microgap electrode (AuMGE) integrated into a printed circuit board (PCB). This AuMGE/PCB system maximizes the signal-to-noise ratio, which controls the working and counter electrode areas requiring only 3 μL samples to obtain high reliability. Using the extracted M. aeruginosa gene with a pre-treatment filter, the CRISPR biosensor showed a limit of detection of 0.089 pg/μl in fresh water. Moreover, selectivity test and matrix condition test carried out using the EC-CRISPR biosensor. These handheld pre-treatment kit and biosensors can enable field-ready detection of CyanoHABs.
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Affiliation(s)
- Gahyeon Kim
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Yun Guang Li
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul 06974, Republic of Korea
| | - Yoseph Seo
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Changyoon Baek
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul 06974, Republic of Korea
| | - Jin-Ha Choi
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Hyunjun Park
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Jeongyun An
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Myoungro Lee
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Seungwoo Noh
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul 06974, Republic of Korea.
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea.
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45
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Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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46
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Wang X, Xia B, Hao Z, Kang H, Liu W, Chen Y, Jiang Q, Liu J, Gou J, Dong B, Wee ATS, Liu Y, Wei D. A closed-loop catalytic nanoreactor system on a transistor. SCIENCE ADVANCES 2023; 9:eadj0839. [PMID: 37729411 PMCID: PMC10511191 DOI: 10.1126/sciadv.adj0839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023]
Abstract
Precision chemistry demands miniaturized catalytic systems for sophisticated reactions with well-defined pathways. An ideal solution is to construct a nanoreactor system functioning as a chemistry laboratory to execute a full chemical process with molecular precision. However, existing nanoscale catalytic systems fail to in situ control reaction kinetics in a closed-loop manner, lacking the precision toward ultimate reaction efficiency. We find an inter-electrochemical gating effect when operating DNA framework-constructed enzyme cascade nanoreactors on a transistor, enabling in situ closed-loop reaction monitoring and modulation electrically. Therefore, a comprehensive system is developed, encapsulating nanoreactors, analyzers, and modulators, where the gate potential modulates enzyme activity and switches cascade reaction "ON" or "OFF." Such electric field-effect property enhances catalytic efficiency of enzyme by 343.4-fold and enables sensitive sarcosine assay for prostate cancer diagnoses, with a limit of detection five orders of magnitude lower than methodologies in clinical laboratory. By coupling with solid-state electronics, this work provides a perspective to construct intelligent nano-systems for precision chemistry.
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Affiliation(s)
- Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Binbin Xia
- Institute of Molecular Medicine, Department of Urology, Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhuang Hao
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Hua Kang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Wentao Liu
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Qunfeng Jiang
- Department of Physics, Fudan University, Shanghai 200433, China
| | - Jingyuan Liu
- Global Clinical Operation, Johnson & Johnson, Shanghai 200233, China
| | - Jian Gou
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Baijun Dong
- Institute of Molecular Medicine, Department of Urology, Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Andrew Thye Shen Wee
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
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47
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Li X, Zhong J, Li H, Qiao Y, Mao X, Fan H, Zhong Y, Imani S, Zheng S, Li J. Advances in the application of CRISPR-Cas technology in rapid detection of pathogen nucleic acid. Front Mol Biosci 2023; 10:1260883. [PMID: 37808520 PMCID: PMC10552857 DOI: 10.3389/fmolb.2023.1260883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are widely used as gene editing tools in biology, microbiology, and other fields. CRISPR is composed of highly conserved repetitive sequences and spacer sequences in tandem. The spacer sequence has homology with foreign nucleic acids such as viruses and plasmids; Cas effector proteins have endonucleases, and become a hotspot in the field of molecular diagnosis because they recognize and cut specific DNA or RNA sequences. Researchers have developed many diagnostic platforms with high sensitivity, high specificity, and low cost by using Cas proteins (Cas9, Cas12, Cas13, Cas14, etc.) in combination with signal amplification and transformation technologies (fluorescence method, lateral flow technology, etc.), providing a new way for rapid detection of pathogen nucleic acid. This paper introduces the biological mechanism and classification of CRISPR-Cas technology, summarizes the existing rapid detection technology for pathogen nucleic acid based on the trans cleavage activity of Cas, describes its characteristics, functions, and application scenarios, and prospects the future application of this technology.
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Affiliation(s)
- Xiaoping Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, China
| | - Jiaye Zhong
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Haoyu Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Yinbiao Qiao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
| | - Xiaolei Mao
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Huayan Fan
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yiwu Zhong
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Saber Imani
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Shusen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Jianhui Li
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- The Organ Repair and Regeneration Medicine Institute of Hangzhou, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Zhejiang Chinese Medical University, Hangzhou, China
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48
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Li Y, Zhao Z, Liu Y, Wang N, Man S, Ma L, Wang S. CRISPR/Cas System: The Accelerator for the Development of Non-nucleic Acid Target Detection in Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13577-13594. [PMID: 37656446 DOI: 10.1021/acs.jafc.3c03619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Non-nucleic acid targets have posed a serious challenge to food safety. The detection of non-nucleic acid targets can enable us to monitor food contamination in a timely manner. In recent years, the CRISPR/Cas system has been extensively explored in biosensing. However, there is a lack of a summary of CRISPR/Cas-powered detection tailored to non-nucleic acid targets involved in food safety. This review comprehensively summarizes the recent advances on the construction of CRISPR/Cas-powered detection and the promising applications in the field of food safety related non-nucleic acid targets. The current challenges and futuristic perspectives are also proposed accordingly. The rapidly evolving CRISPR/Cas system has provided a powerful propellant for non-nucleic acid target detection via integration with aptamer and/or DNAzyme. Compared with traditional analytical methods, CRISPR/Cas-powered detection is conceptually novel, essentially eliminates the dependence on large instruments, and also demonstrates the capability for rapid, accurate, sensitive, and on-site testing.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
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49
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Rananaware SR, Vesco EK, Shoemaker GM, Anekar SS, Sandoval LSW, Meister KS, Macaluso NC, Nguyen LT, Jain PK. Programmable RNA detection with CRISPR-Cas12a. Nat Commun 2023; 14:5409. [PMID: 37669948 PMCID: PMC10480431 DOI: 10.1038/s41467-023-41006-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Cas12a, a CRISPR-associated protein complex, has an inherent ability to cleave DNA substrates and is utilized in diagnostic tools to identify DNA molecules. We demonstrate that multiple orthologs of Cas12a activate trans-cleavage in the presence of split activators. Specifically, the PAM-distal region of the crRNA recognizes RNA targets provided that the PAM-proximal seed region has a DNA target. Our method, Split Activator for Highly Accessible RNA Analysis (SAHARA), detects picomolar concentrations of RNA without sample amplification, reverse-transcription, or strand-displacement by simply supplying a short DNA sequence complementary to the seed region. Beyond RNA detection, SAHARA outperforms wild-type CRISPR-Cas12a in specificity towards point-mutations and can detect multiple RNA and DNA targets in pooled crRNA/Cas12a arrays via distinct PAM-proximal seed DNAs. In conclusion, SAHARA is a simple, yet powerful nucleic acid detection platform based on Cas12a that can be applied in a multiplexed fashion and potentially be expanded to other CRISPR-Cas enzymes.
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Affiliation(s)
| | - Emma K Vesco
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Grace M Shoemaker
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Swapnil S Anekar
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | | | - Katelyn S Meister
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Nicolas C Macaluso
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Long T Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
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Lamb CH, Kang B, Myhrvold C. Multiplexed CRISPR-based Methods for Pathogen Nucleic Acid Detection. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023; 27:100471. [PMID: 37398931 PMCID: PMC10310064 DOI: 10.1016/j.cobme.2023.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Bacterial and viral pathogens are devastating to human health and well-being. In many regions, dozens of pathogen species and variants co-circulate. Thus, it is important to detect many different species and variants of pathogens in a given sample through multiplexed detection methods. CRISPR-based nucleic acid detection has shown to be a promising step towards an easy-to-use sensitive, specific, and high-throughput method to detect nucleic acids from DNA and RNA viruses and bacteria. Here, we review the current state of multiplexed nucleic acid detection methods with a focus on CRISPR-based methods. We also look toward the future of multiplexed point-of-care diagnostics.
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Affiliation(s)
- Caitlin H Lamb
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brian Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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