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Zeng Q, Zhou M, Deng W, Gao Q, Li Z, Wu L, Liang D. Sensitive and visual detection of SARS-CoV-2 using RPA-Cas12a one-step assay with ssDNA-modified crRNA. Anal Chim Acta 2024; 1309:342693. [PMID: 38772660 DOI: 10.1016/j.aca.2024.342693] [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: 01/12/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND CRISPR-Cas12a based one-step assays are widely used for nucleic acid detection, particularly for pathogen detection. However, the detection capability of the one-step assay is reduced because the Cas12a protein competes with the isothermal amplification enzymes for the target DNA and cleaves it. Therefore, the key to improving the sensitivity of the one-step assay is to address the imbalance between isothermal amplification and CRISPR detection. In previous study, we developed a Cas12a one-step assay using single-stranded DNA (ssDNA)-modified crRNA (mD-crRNA) and applied this method for the detection of pathogenic DNA. RESULTS Here, we utilized mD-crRNA to establish a sensitive one-step assay that enables the visual detection of SARS-CoV-2 under ultraviolet light, achieving a detection limit of 5 aM without cross-reactivity. The sensitivity of mD-crRNA in the one-step assay was 100-fold higher than that of wild-type crRNA. Mechanistic studies revealed that the addition of ssDNA at the 3' end of mD-crRNA attenuates the binding affinity between the Cas12a-mD-crRNA complex and the target DNA. Consequently, this reduction in binding affinity decreases the cis-cleavage activity of Cas12a, mitigating its cleavage of the target DNA in the one-step assay. As a result, there is an augmentation in the amplification and accumulation of target DNA, thereby enhancing detection sensitivity. In the clinical testing of 40 SARS-CoV-2 RNA samples, the concordance between the results of the one-step assay and known qPCR results was 97.5 %. SIGNIFICANCE The one-step assay using mD-crRNA proves to be highly sensitive and specificity and visually effective for the detection of SARS-CoV-2. Our study delves into the application of the mD-crRNA-mediated one-step assay in nucleic acid detection and its associated reaction mechanism. This holds great significance in addressing the inherent incompatibility issues between isothermal amplification and CRISPR detection.
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Affiliation(s)
- Qinlong Zeng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Miaojin Zhou
- MOE Key Lab of Rare Pediatric Diseases, Department of Cell Biology and Genetics, School of Basic Medical Sciences, University of South China, Hengyang, 421200, China
| | - Weiheng Deng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Qian Gao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
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2
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Shi K, Tian Y, Liu S, Luo W, Liu K, Zhang L, Zhang Y, Chang J, Zhang J, Wang S. Phosphorothioate-modified G-quadruplex as a signal-on dual-mode reporter for CRISPR/Cas12a-based portable detection of environmental pollutants. Anal Chim Acta 2024; 1308:342649. [PMID: 38740457 DOI: 10.1016/j.aca.2024.342649] [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: 02/16/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-powered biosensor with a G-quadruplex (G4) reporter offer the benefits of simplicity and sensitivity, making them extensively utilized in detection applications. However, these biosensors used for monitoring pollutants in environmental water samples may face the problem of high background signal and easy interference due to the "signal-off" output. It is obvious that a biosensor based on the CRISPR/Cas12a system and G4 with a "signal on" output mode needs to be designed for detecting environmental pollutants. RESULTS By using phosphorothioate-modified G4 as a reporter and catalytic hairpin assembly (CHA) integrated with Cas12a as an amplification strategy, a "signal-on" colorimetric/photothermal biosensor (psG4-CHA/Cas) for portable detection of environmental pollutants was developed. With the help of functional nucleotides, the target pollutant (kanamycin or Pb2+) triggers a CHA reaction to produce numerous double-strand DNA, which can activate Cas12a's trans-cleavage activity. The active Cas12a cleaves locked DNA to release caged psG-rich sequences. Upon binding hemin, the psG-rich sequence forms a psG4/hemin complex, facilitating the oxidation of the colorless 3,3',5,5'-tetramethylbenzidine (TMB) into the blue photothermal agent (oxTMB). The smartphone was employed for portable colorimetric detection of kanamycin and Pb2+. The detection limits were found to be 100 pM for kanamycin and 50 pM for Pb2+. Detection of kanamycin and Pb2+ was also carried out using a portable thermometer with a detection limit of 10 pM for kanamycin and 8 pM for Pb2+. SIGNIFICANCE Sensitive, selective, simple and robust detection of kanamycin and Pb2+ in environmental water samples is achieved with the psG4-CHA/Cas system. This system not only provides a new perspective on the development of efficient CRISPR/Cas12a-based "signal-on" designs, but also has a promising application for safeguarding human health and environmental monitoring.
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Affiliation(s)
- Kai Shi
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China; Leshan West Silicon Materials Photovoltaic and New Energy Industry Technology Research Institute, Leshan, Sichuan, 614000, PR China.
| | - Yi Tian
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China; Leshan West Silicon Materials Photovoltaic and New Energy Industry Technology Research Institute, Leshan, Sichuan, 614000, PR China
| | - Sujun Liu
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China; Leshan West Silicon Materials Photovoltaic and New Energy Industry Technology Research Institute, Leshan, Sichuan, 614000, PR China
| | - Wenjie Luo
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China
| | - Keer Liu
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China
| | - Lin Zhang
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China
| | - Ying Zhang
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China
| | - Jiali Chang
- College of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan, 614000, PR China.
| | - Jiaheng Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Shuo Wang
- National Innovation Center for Advanced Medical Devices, Shenzhen, Guangdong, 518110, PR China.
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Bhattacharya S, Agarwal A, Muniyappa K. Deciphering the Substrate Specificity Reveals that CRISPR-Cas12a Is a Bifunctional Enzyme with Both Endo- and Exonuclease Activities. J Mol Biol 2024; 436:168550. [PMID: 38575054 DOI: 10.1016/j.jmb.2024.168550] [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: 10/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for genome-editing, with applications in biotechnology and medicine. However, significantly less is known about their substrate specificity, but such knowledge may provide instructive insights into their off-target cleavage and previously unrecognized mechanism of action. Here, we document that the Acidaminococcus sp. Cas12a (AsCas12a) binds preferentially, and independently of crRNA, to a suite of branched DNA structures, such as the Holliday junction (HJ), replication fork and D-loops, compared with single- or double-stranded DNA, and promotes their degradation. Further, our study revealed that AsCas12a binds to the HJ, specifically at the crossover region, protects it from DNase I cleavage and renders a pair of thymine residues in the HJ homologous core hypersensitive to KMnO4 oxidation, suggesting DNA melting and/or distortion. Notably, these structural changes enabled AsCas12a to resolve HJ into nonligatable intermediates, and subsequently their complete degradation. We further demonstrate that crRNA impedes HJ cleavage by AsCas12a, and that of Lachnospiraceae bacterium Cas12a, without affecting their DNA-binding ability. We identified a separation-of-function variant, which uncouples DNA-binding and DNA cleavage activities of AsCas12a. Importantly, we found robust evidence that AsCas12a endonuclease also has 3'-to-5' and 5'-to-3' exonuclease activity, and that these two activities synergistically promote degradation of DNA, yielding di- and mononucleotides. Collectively, this study significantly advances knowledge about the substrate specificity of AsCas12a and provides important insights into the degradation of different types of DNA substrates.
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Affiliation(s)
- Supreet Bhattacharya
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India.
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4
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Lei X, Cao S, Liu T, Wu Y, Yu S. Non-canonical CRISPR/Cas12a-based technology: A novel horizon for biosensing in nucleic acid detection. Talanta 2024; 271:125663. [PMID: 38232570 DOI: 10.1016/j.talanta.2024.125663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Nucleic acids are essential biomarkers in molecular diagnostics. The CRISPR/Cas system has been widely used for nucleic acid detection. Moreover, canonical CRISPR/Cas12a based biosensors can specifically recognize and cleave target DNA, as well as single-strand DNA serving as reporter probe, which have become a super star in recent years in the field of nucleic acid detection due to its high specificity, universal programmability and simple operation. However, canonical CRISPR/Cas12a based biosensors are hard to meet the requirements of higher sensitivity, higher specificity, higher efficiency, larger target scope, easier operation, multiplexing, low cost and diversified signal reading. Then, advanced non-canonical CRISPR/Cas12a based biosensors emerge. In this review, applications of non-canonical CRISPR/Cas12a-based biosensors in nucleic acid detection are summarized. And the principles, peculiarities, performances and perspectives of these non-canonical CRISPR/Cas12a based biosensors are also discussed.
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Affiliation(s)
- Xueying Lei
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Shengnan Cao
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Tao Liu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Yongjun Wu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Songcheng Yu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China.
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Newsom SN, Wang DS, Rostami S, Schuster I, Parameshwaran HP, Joseph YG, Qin PZ, Liu J, Rajan R. Differential Divalent Metal Binding by SpyCas9's RuvC Active Site Contributes to Nonspecific DNA Cleavage. CRISPR J 2023; 6:527-542. [PMID: 38108519 PMCID: PMC10753984 DOI: 10.1089/crispr.2023.0022] [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: 04/07/2023] [Accepted: 11/10/2023] [Indexed: 12/19/2023] Open
Abstract
To protect against mobile genetic elements (MGEs), some bacteria and archaea have clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) adaptive immune systems. CRISPR RNAs (crRNAs) bound to Cas nucleases hybridize to MGEs based on sequence complementarity to guide the nucleases to cleave the MGEs. This programmable DNA cleavage has been harnessed for gene editing. Safety concerns include off-target and guide RNA (gRNA)-free DNA cleavages, both of which are observed in the Cas nuclease commonly used for gene editing, Streptococcus pyogenes Cas9 (SpyCas9). We developed a SpyCas9 variant (SpyCas9H982A) devoid of gRNA-free DNA cleavage activity that is more selective for on-target cleavage. The H982A substitution in the metal-dependent RuvC active site reduces Mn2+-dependent gRNA-free DNA cleavage by ∼167-fold. Mechanistic molecular dynamics analysis shows that Mn2+, but not Mg2+, produces a gRNA-free DNA cleavage competent state that is disrupted by the H982A substitution. Our study demonstrates the feasibility of modulating cation:protein interactions to engineer safer gene editing tools.
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Affiliation(s)
- Sydney N. Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Isabelle Schuster
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Yadin G. Joseph
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
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6
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Du Y, Ji S, Dong Q, Wang J, Han D, Gao Z. Amplification-free detection of HBV DNA mediated by CRISPR-Cas12a using surface-enhanced Raman spectroscopy. Anal Chim Acta 2023; 1245:340864. [PMID: 36737140 DOI: 10.1016/j.aca.2023.340864] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Nucleic acid markers have been widely used in the detection of various virus-related diseases, including hepatitis B virus (HBV), which is spreading worldwide. The trans-activated CRISPR-Cas system has shown excellent sensitivity and specificity in nucleic acid detection. However, nucleic acid testing usually requires amplification of the target nucleic acid for more accurate and specific detection; furthermore, current nucleic acid assays are time-consuming, costly, and are limited by non-specific cross-reactivity. We developed an amplification-free viral DNA biosensor-based diagnostic method that uses a clustered regularly interspaced short palindromic repeats-associated system (CRISPR/Cas)-based approach with surface enhanced Raman spectroscopy. This method can specifically identify the target site by changing the crRNA sequence. In addition, the incubation period and development of the disease can be determined by quantitative detection of viral DNA. This system could achieve rapid and highly sensitive detection of HBV DNA within 50 min and vast detection range from 0.1 pM to 1 nM. Therefore, a combined CRISPR/Cas12a-SERS-based assay would improve the sensitivity of detection in assays using multiple biomarkers. In conclusion, our CRISPR/Cas12a-based biosensor would enable rapid, simple, and sensitive detection of HBV nucleic acids.
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Affiliation(s)
- Yuwan Du
- Military Medical Sciences Academy Environmental and Operational Medicine Research Department, Tianjin, 300050, PR China
| | - Shuaifeng Ji
- Military Medical Sciences Academy Environmental and Operational Medicine Research Department, Tianjin, 300050, PR China; School of Physical Science and Technology, Xinjiang University, Xinjiang, 71000, PR China
| | - Qingyang Dong
- Military Medical Sciences Academy Environmental and Operational Medicine Research Department, Tianjin, 300050, PR China
| | - Jiang Wang
- Military Medical Sciences Academy Environmental and Operational Medicine Research Department, Tianjin, 300050, PR China.
| | - Dianpeng Han
- Military Medical Sciences Academy Environmental and Operational Medicine Research Department, Tianjin, 300050, PR China.
| | - Zhixian Gao
- Military Medical Sciences Academy Environmental and Operational Medicine Research Department, Tianjin, 300050, PR China.
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7
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Updated toolkits for nucleic acid-based biosensors. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Abstract
The CRISPR-associated (Cas) Cas12a is the effector protein for type V-A CRISPR systems. Cas12a is a sequence-specific endonuclease that targets and cleaves DNA containing a cognate short signature motif, called the protospacer adjacent motif (PAM), flanked by a 20 nucleotide (nt) segment that is complementary to the "guide" region of its CRISPR RNA (crRNA). The guide sequence of the crRNA can be programmed to target any DNA with a cognate PAM and is the basis for Cas12a's current use for gene editing in numerous organisms and for medical diagnostics. While Cas9 (type II effector protein) is widely used for gene editing, Cas12a possesses favorable features such as its smaller size and creation of staggered double-stranded DNA ends after cleavage that enhances cellular recombination events. Collected here are protocols for the recombinant purification of Cas12a and the transcription of its corresponding programmable crRNA that are used in a variety of Cas12a-specific in vitro activity assays such as the cis, the trans and the guide-RNA independent DNA cleavage activities with multiple substrates. Correspondingly, protocols are included for the quantification of the activity assay data using ImageJ and the use of MATLAB for rate constant calculations. These procedures can be used for further structural and mechanistic studies of Cas12a orthologs and other Cas proteins.
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Affiliation(s)
- Lindsie Martin
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States.
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9
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Biochemical characterization of the two novel mgCas12a proteins from the human gut metagenome. Sci Rep 2022; 12:20857. [PMID: 36460704 PMCID: PMC9718762 DOI: 10.1038/s41598-022-25227-w] [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: 06/02/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
CRISPR/Cas9 and Cas12a belonging to the Class II CRISPR system are characterized by a single-component effector protein. Despite unique features of Cas12a like DNA cleavage with 5' staggered ends and a single crRNA, Cas12a has not been adopted in biotechnological applications to the similar extent as Cas9. To better understand the CRISPR/Cas12 systems, we selected two candidates, designated mgCas12a-1 and mgCas12a-2, from an analysis of the human microbiome metagenome (mg) and provided biochemical characterization. These new Cas12a proteins shared about 37% identity in amino acid sequences and shared the same direct repeat sequences in the crRNA with FnCas12a from Francisella novicida. The purification yield of the recombinant proteins was up to 3.6-fold greater than that of FnCas12a. In cell-free DNA cleavage assays, both mgCas12a proteins showed the higher cleavage efficiencies when Mn2+ was provided with KCl (< 100 mM) than tested other divalent ions. They were able to tolerate ranges of pH points and temperature, and showed the highest cleavage efficiencies at pH 8.0 and 50 °C. In addition, mgCas12a proteins showed 51% less crRNA-independent and 56% less crRNA-dependent non-specific nuclease activity upon prolonged incubation than did FnCas12a. Considering their greater yield in protein preparation and reduced non-specific nuclease activity, our findings may expedite the use of Cas12a especially when genome editing needs to be practiced with the form of ribonucleoproteins.
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Vasilev R, Gunitseva N, Shebanova R, Korzhenkov A, Vlaskina A, Evteeva M, Polushkina I, Nikitchina N, Toshchakov S, Kamenski P, Patrushev M, Mazunin I. Targeted Modification of Mammalian DNA by a Novel Type V Cas12a Endonuclease from Ruminococcus bromii. Int J Mol Sci 2022; 23:ijms23169289. [PMID: 36012553 PMCID: PMC9409102 DOI: 10.3390/ijms23169289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
Abstract
Type V Cas12a nucleases are DNA editors working in a wide temperature range and using expanded protospacer-adjacent motifs (PAMs). Though they are widely used, there is still a demand for discovering new ones. Here, we demonstrate a novel ortholog from Ruminococcus bromii sp. entitled RbCas12a, which is able to efficiently cleave target DNA templates, using the particularly high accessibility of PAM 5′-YYN and a relatively wide temperature range from 20 °C to 42 °C. In comparison to Acidaminococcus sp. (AsCas12a) nuclease, RbCas12a is capable of processing DNA more efficiently, and can be active upon being charged by spacer-only RNA at lower concentrations in vitro. We show that the human-optimized RbCas12a nuclease is also active in mammalian cells, and can be applied for efficient deletion incorporation into the human genome. Given the advantageous properties of RbCas12a, this enzyme shows potential for clinical and biotechnological applications within the field of genome editing.
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Affiliation(s)
- Ruslan Vasilev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
| | - Natalia Gunitseva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Regina Shebanova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Aleksei Korzhenkov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Anna Vlaskina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Marta Evteeva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Irina Polushkina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Natalia Nikitchina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- UMR7156–Molecular Genetics, Genomics, Microbiology, University of Strasbourg and Centre National de la Recherche Scientifique (CNRS), 67000 Strasbourg, France
| | - Stepan Toshchakov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maxim Patrushev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Ilya Mazunin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Medical Genomics LLC, 119192 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
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11
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Son H, Park J, Choi YH, Jung Y, Lee JW, Bae S, Lee S. Exploring the dynamic nature of divalent metal ions involved in DNA cleavage by CRISPR-Cas12a. Chem Commun (Camb) 2022; 58:1978-1981. [PMID: 35045150 DOI: 10.1039/d1cc04446j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12a has been widely used in genome editing and nucleic acid detection. In both of these applications, Cas12a cleaves target DNA in a divalent metal ion-dependent manner. However, when and how metal ions contribute to the cleavage reaction is unclear. Here, using a single-molecule FRET assay, we reveal that these metal ions are necessary for stabilising cleavage-competent conformations and that they are easily exchangeable, suggesting that they are dynamically coordinated.
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Affiliation(s)
- Heyjin Son
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
| | - Jaeil Park
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea. .,Department of Physics and Optoelectronics Convergence Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - You Hee Choi
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea. .,Ministry of Food and Drug Safety (MFDS), Cheongju 28159, Republic of Korea
| | - Youngri Jung
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Joong-Wook Lee
- Department of Physics and Optoelectronics Convergence Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
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12
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Ittiprasert W, Chatupheeraphat C, Mann VH, Li W, Miller A, Ogunbayo T, Tran K, Alrefaei YN, Mentink-Kane M, Brindley PJ. RNA-Guided AsCas12a- and SpCas9-Catalyzed Knockout and Homology Directed Repair of the Omega-1 Locus of the Human Blood Fluke, Schistosoma mansoni. Int J Mol Sci 2022; 23:631. [PMID: 35054816 PMCID: PMC8775552 DOI: 10.3390/ijms23020631] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 12/17/2022] Open
Abstract
The efficiency of the RNA-guided AsCas12a nuclease of Acidaminococcus sp. was compared with SpCas9 from Streptococcus pyogenes, for functional genomics in Schistosoma mansoni. We deployed optimized conditions for the ratio of guide RNAs to the nuclease, donor templates, and electroporation parameters, to target a key schistosome enzyme termed omega-1. Programmed cleavages catalyzed by Cas12a and Cas9 resulted in staggered- and blunt-ended strand breaks, respectively. AsCas12a was more efficient than SpCas9 for gene knockout, as determined by TIDE analysis. CRISPResso2 analysis confirmed that most mutations were deletions. Knockout efficiency of both nucleases markedly increased in the presence of single-stranded oligodeoxynucleotide (ssODN) template. With AsCas12a, ssODNs representative of both the non-CRISPR target (NT) and target (T) strands were tested, resulting in KO efficiencies of 15.67, 28.71, and 21.43% in the SpCas9 plus ssODN, AsCas12a plus NT-ssODN, and AsCas12a plus T-ssODN groups, respectively. Trans-cleavage against the ssODNs by activated AsCas12a was not apparent in vitro. SpCas9 catalyzed more precise transgene insertion, with knock-in efficiencies of 17.07% for the KI_Cas9 group, 14.58% for KI_Cas12a-NT-ssODN, and 12.37% for KI_Cas12a-T-ssODN. Although AsCas12a induced fewer mutations per genome than SpCas9, the phenotypic impact on transcription and expression of omega-1 was similar for both nucleases.
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Affiliation(s)
- Wannaporn Ittiprasert
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
| | - Chawalit Chatupheeraphat
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Victoria H. Mann
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
| | - Wenhui Li
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - André Miller
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Taiwo Ogunbayo
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Kenny Tran
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Yousef N. Alrefaei
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Department of Medical Laboratory Technology, College of Health Sciences, PAEET, Adailiya, Kuwait City 73101, Kuwait
| | - Margaret Mentink-Kane
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
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Mushtaq M, Dar AA, Basu U, Bhat BA, Mir RA, Vats S, Dar MS, Tyagi A, Ali S, Bansal M, Rai GK, Wani SH. Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology. Front Genet 2021; 12:735489. [PMID: 34759957 PMCID: PMC8572880 DOI: 10.3389/fgene.2021.735489] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022] Open
Abstract
Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.
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Affiliation(s)
- Muntazir Mushtaq
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | | | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Sanskriti Vats
- Department of Agricultural Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - M. S. Dar
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Monika Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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Parameshwaran HP, Babu K, Tran C, Guan K, Allen A, Kathiresan V, Qin PZ, Rajan R. The bridge helix of Cas12a imparts selectivity in cis-DNA cleavage and regulates trans-DNA cleavage. FEBS Lett 2021; 595:892-912. [PMID: 33523494 PMCID: PMC8044059 DOI: 10.1002/1873-3468.14051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 12/26/2022]
Abstract
Cas12a is an RNA-guided DNA endonuclease of the type V-A CRISPR-Cas system that has evolved convergently with the type II Cas9 protein. We previously showed that proline substitutions in the bridge helix (BH) impart target DNA cleavage selectivity in Streptococcus pyogenes (Spy) Cas9. Here, we examined a BH variant of Cas12a from Francisella novicida (FnoCas12aKD2P ) to test mechanistic conservation. Our results show that for RNA-guided DNA cleavage (cis-activity), FnoCas12aKD2P accumulates nicked products while cleaving supercoiled DNA substrates with mismatches, with certain mismatch positions being more detrimental for linearization. FnoCas12aKD2P also possess reduced trans-single-stranded DNA cleavage activity. These results implicate the BH in substrate selectivity in both cis- and trans-cleavages and show its conserved role in target discrimination among Cas nucleases.
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Affiliation(s)
- Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Christine Tran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Kevin Guan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Aleique Allen
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | | | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
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15
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DNaseI protects lipopolysaccharide-induced endometritis in mice by inhibiting neutrophil extracellular traps formation. Microb Pathog 2020; 150:104686. [PMID: 33309847 DOI: 10.1016/j.micpath.2020.104686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Endometritis is an inflammatory of the inner lining of the uterus caused by bacterial infections that affect female reproductive health in humans and animals. Neutrophil extracellular traps (NETs) have the ability to resist infections that caused by pathogenic invasions. It has been proved that the formation of NETs is related to certain inflammatory diseases, such as mastitis and chronic obstructive pulmonary disease (COPD). However, there are sparse studies related to NETs and endometritis. In this study, we investigated the role of NETs in lipopolysaccharide (LPS)-induced acute endometritis in mice and evaluated the therapeutic efficiency of DNaseI. We established LPS-induced endometritis model in mice and found that the formation of NETs can be detected in the mice uterine tissues in vivo. In addition, DNaseI treatment can inhibit NETs construction in LPS-induced endometritis in mice. Moreover, myeloperoxidase (MPO) activity assay indicated that DNaseI treatment remarkably alleviated the inflammatory cell infiltrations. ELISA test indicated that the treatment of DNaseI significantly inhibited the expression of the proinflammatory cytokines TNF-α, and IL-1β. Also, DNaseI was found to increase proteins expression of the uterine tissue tight junctions and suppress LPS-induced NF-κB activation. All the results indicated that DNaseI effectively inhibits the formation of NETs by blocking the NF-κB signaling pathway and enhances the expression of tight junction proteins, consequently, alleviates inflammatory reactions in LPS-induced endometritis in mice.
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16
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Ma P, Meng Q, Sun B, Zhao B, Dang L, Zhong M, Liu S, Xu H, Mei H, Liu J, Chi T, Yang G, Liu M, Huang X, Wang X. MeCas12a, a Highly Sensitive and Specific System for COVID-19 Detection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001300. [PMID: 33042732 PMCID: PMC7536916 DOI: 10.1002/advs.202001300] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/30/2020] [Indexed: 05/04/2023]
Abstract
Cas12a-based systems, which detect specific nucleic acids via collateral cleavage of reporter DNA, display huge potentials for rapid diagnosis of infectious diseases. Here, the Manganese-enhanced Cas12a (MeCas12a) system is described, where manganese is used to increase the detection sensitivity up to 13-fold, enabling the detection of target RNAs as low as five copies. MeCas12a is also highly specific, and is able to distinguish between single nucleotide polymorphisms (SNPs) differing by a single nucleotide. MeCas12a can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples and distinguish between SARS-CoV-2 and Middle East respiratory syndrome coronavirus (MERS-CoV) RNA in simulated samples, thus offering an attractive alternative to other methods for the diagnosis of infectious diseases including COVID-19 and MERS.
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Affiliation(s)
- Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Qingzhou Meng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University78 Hengzhigang RoadGuangzhou510095China
| | - Baoqing Sun
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated HospitalGuangzhou Medical UniversityGuangzhou510120China
| | - Bing Zhao
- Microbiological Testing LaboratoryShanghai Pudong New Area Center for Disease Control and PreventionShanghai200136China
| | - Lu Dang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University78 Hengzhigang RoadGuangzhou510095China
| | - Mingtian Zhong
- Institute for Brain Research and RehabilitationGuangdong Key Laboratory of Mental Health and Cognitive ScienceCenter for Studies of Psychological ApplicationSouth China Normal UniversityGuangzhou510631China
| | - Siyuan Liu
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Hong Mei
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Tian Chi
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Ming Liu
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated HospitalGuangzhou Medical UniversityGuangzhou510120China
| | - Xingxu Huang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xinjie Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
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Xing S, Lu Z, Huang Q, Li H, Wang Y, Lai Y, He Y, Deng M, Liu W. An ultrasensitive hybridization chain reaction-amplified CRISPR-Cas12a aptasensor for extracellular vesicle surface protein quantification. Theranostics 2020; 10:10262-10273. [PMID: 32929347 PMCID: PMC7481432 DOI: 10.7150/thno.49047] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Tumor-derived extracellular vesicle (TEV) protein biomarkers facilitate cancer diagnosis and prognostic evaluations. However, the lack of reliable and convenient quantitative methods for evaluating TEV proteins prevents their clinical application. Methods: Here, based on dual amplification of hybridization chain reaction (HCR) and CRISPR-Cas12a, we developed the apta-HCR-CRISPR assay for direct high-sensitivity detection of TEV proteins. The TEV protein-targeted aptamer was amplified by HCR to produce a long-repeated sequence comprising multiple CRISPR RNA (crRNA) targetable barcodes, and the signals were further amplified by CRISPR-Cas12a collateral cleavage activities, resulting in a fluorescence signal. Results: The established strategy was verified by detecting the TEV protein markers nucleolin and programmed death ligand 1 (PD-L1). Both achieved limit of detection (LOD) values as low as 102 particles/µL, which is at least 104-fold more sensitive than aptamer-ELISA and 102-fold more sensitive than apta-HCR-ELISA. We directly applied our assay to a clinical analysis of circulating TEVs from 50 µL of serum, revealing potential applications of nucleolin+ TEVs for nasopharyngeal carcinoma cancer (NPC) diagnosis and PD-L1+ TEVs for therapeutic monitoring. Conclusion: The platform was simple and easy to operate, and this approach should be useful for the highly sensitive and versatile quantification of TEV proteins in clinical samples.
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18
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Murugan K, Seetharam AS, Severin AJ, Sashital DG. CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects. J Biol Chem 2020; 295:5538-5553. [PMID: 32161115 PMCID: PMC7186167 DOI: 10.1074/jbc.ra120.012933] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/04/2020] [Indexed: 12/26/2022] Open
Abstract
Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity in vivo, making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a's natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput in vitro cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive sequence-specific nicking of randomized target libraries, with strong nicking of DNA sequences containing up to four mismatches in the Cas12a-targeted DNA-RNA hybrid sequences. We also found that these nicking and cleavage activities depend on mismatch type and position and vary with Cas12a ortholog and CRISPR RNA sequence. Our analysis further revealed robust nonspecific nicking of dsDNA when Cas12a is activated by binding to a target DNA. Together, our findings reveal that Cas12a has multiple nicking activities against dsDNA substrates and that these activities vary among different Cas12a orthologs.
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Affiliation(s)
- Karthik Murugan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011; Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, Iowa 50011
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50011
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50011
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011; Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, Iowa 50011.
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