1
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Zheng W, Tang H, Ye B, Lin J, Wang H, Liu Y, Wang D, Wu Z, Xie W, Dong WF, Zan M. Fast, portable and sensitive detection of group B streptococcus DNA using one-pot MIRA-CRISPR system with suboptimal PAM. Talanta 2024; 279:126574. [PMID: 39029179 DOI: 10.1016/j.talanta.2024.126574] [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: 04/29/2024] [Revised: 06/26/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
The group B Streptococcus (GBS) can generate vertical transmission to infants during delivery, has been seriously threatening the health of infants. Rapid and accurate prenatal GBS diagnosis for pregnant women is a deterministic blueprint to avoid infant viruses. Here, we developed an extraction-free nucleic acid isothermal amplification/CRISPR-Cas12a cutting one-pot system for GBS diagnostic assay by using suboptimal protospacer adjacent motifs, effectively avoiding multiple handling steps and uncapping contamination. The GBS diagnosis assay based on a one-pot system was validated by using fluorescent technique and lateral flow assay strips, exhibited fantastic specificity, accuracy and sensitivity with a limit of detection of 32 copies per reaction (0.64 copies/μL). Moreover, a portable device was constructed and integrated with the one-pot system to realize the GBS detection without professional and scene restrictions, it showed excellent performance in clinical sample detection, which achieved optical and portable GBS detection for point-of-care testing or home-self testing.
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Affiliation(s)
- Weigang Zheng
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou, China; Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China
| | - Huamei Tang
- Medical Laboratory of Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Benchen Ye
- Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China
| | - Jiasheng Lin
- Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China
| | - Huihui Wang
- Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China
| | - Ying Liu
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou, China; Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China
| | - Dong Wang
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou, China; Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China
| | - Zaihui Wu
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou, China; Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China
| | - Wei Xie
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China.
| | - Wen-Fei Dong
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou, China.
| | - Minghui Zan
- CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou, China; Zhengzhou Institute of Biomedical Engineering and Technology, Zhengzhou, China.
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2
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Huang F, Li X, Zhou Y, Tang W, Dang Z, Kui J, Zhang C, Zhang X. Optimization of CRISPR/Cas12a detection assay and its application in the detection of Echinococcus granulosus. Vet Parasitol 2024; 331:110276. [PMID: 39089176 DOI: 10.1016/j.vetpar.2024.110276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/03/2024]
Abstract
Cystic echinococcosis, resulting from infection with Echinococcus granulosus, poses a significant challenge as a neglected tropical disease owing to the lack of any known effective treatment. Primarily affecting under-resourced, remote, and conflict-ridden regions, the disease is compounded by the limitations of current detection techniques, such as microscopy, physical imaging, ELISA, and qPCR, which are unsuitable for application in these areas. The emergence of CRISPR/Cas12a as a promising tool for nucleic acid detection, characterized by its unparalleled specificity, heightened sensitivity, and rapid detection time, offers a potential solution. In this study, we present a one-pot CRISPR/Cas12a detection method for E. granulosus (genotype G1, sheep strain) integrating recombinase polymerase amplification (RPA) with suboptimal protospacer adjacent motif (PAM) and structured CRISPR RNA (crRNA) to enhance reaction efficiency. The evaluation of the assay's performance using hydatid cyst spiked dog feces and the examination of 62 dog fecal samples collected from various regions of Western China demonstrate its efficacy. The assay permits visual observation of test results about 15 minutes under blue light and displays superior portability and reaction speed relative to qPCR, achieving a sensitivity level of 10 copies of standard plasmids of the target gene. Analytic specificity was verified against four tapeworm species (E. multilocularis, H. taeniaeformis, M. benedeni, and D. caninum) and two other helminths (T. canis and F. hepatica), with negative results also noted for Mesocestoides sp. This study presents a rapid, sensitive, and time-efficient DNA detection method for E. granulosus of hydatid cyst spiked and clinical dog feces, potential serving as an alternative tool for field detection. This novel assay is primarily used to diagnose the definitive host of E. granulosus. Further validation using a larger set of clinical fecal samples is warranted, along with additional exploration of more effective approaches for nucleic acid release.
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Affiliation(s)
- Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan, China.
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Foshan, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yule Zhou
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China; Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases at China CDC/Chinese Center for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory for Parasite and Vector Biology, Shanghai, China
| | - Jun Kui
- Huangzhong District Animal Husbandry and Veterinary Station, Xining, China
| | - Chunxia Zhang
- Qinghai Agri-animal Husbandry Vocational College, Huangyuan, China
| | - Xu Zhang
- School of Life Science and Engineering, Foshan University, Foshan, China
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3
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Huang S, Lou Y, Zheng L. Synergistic effect of split DNA activators of Cas12a with exon-unwinding and induced targeting effect. Nucleic Acids Res 2024:gkae766. [PMID: 39258555 DOI: 10.1093/nar/gkae766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/24/2024] [Accepted: 08/22/2024] [Indexed: 09/12/2024] Open
Abstract
CRISPR-Cas12a, an RNA-guided nuclease, has been repurposed for genome editing and molecular diagnostics due to its capability of cis-cleavage on target DNA and trans-cleavage on non-target single-strand DNA (ssDNA). However, the mechanisms underlying the activation of trans-cleavage activity of Cas12a, particularly in the context of split DNA activators, remain poorly understood. We elucidate the synergistic effect of these activators and introduce the concepts of induced targeting effect and exon-unwinding to describe the phenomenon. We demonstrate that upon binding of split DNA activators adjacent to the Protospacer Adjacent Motif (PAM) to the Cas12a ribonucleoprotein (Cas12a-RNP), a ternary complex form that can capture and interact with distal split DNA activators to achieve synergistic effects. Notably, if the distal activator is double-strand DNA (dsDNA), the complex initiates exon-unwinding, facilitating the RNA-guide sequence's access. Our findings provide a mechanistic insight into action of Cas12a and propose a model that could significantly advance our understanding of its function.
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Affiliation(s)
- Shen Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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4
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Soczek KM, Cofsky JC, Tuck OT, Shi H, Doudna JA. CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606079. [PMID: 39131396 PMCID: PMC11312533 DOI: 10.1101/2024.07.31.606079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a-RNA-DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA engineering begins with local helix distortion by transient CRISPR-Cas protein binding.
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Affiliation(s)
- Katarzyna M. Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Joshua C. Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
| | - Owen T. Tuck
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley; Berkeley, CA, USA
| | - Honglue Shi
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley CA, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley; Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley CA, USA
- Gladstone-UCSF Institute of Genomic Immunology; San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory; Berkeley, CA, USA
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5
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Strohkendl I, Saha A, Moy C, Nguyen AH, Ahsan M, Russell R, Palermo G, Taylor DW. Cas12a domain flexibility guides R-loop formation and forces RuvC resetting. Mol Cell 2024; 84:2717-2731.e6. [PMID: 38955179 PMCID: PMC11283365 DOI: 10.1016/j.molcel.2024.06.007] [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: 09/11/2023] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The specific nature of CRISPR-Cas12a makes it a desirable RNA-guided endonuclease for biotechnology and therapeutic applications. To understand how R-loop formation within the compact Cas12a enables target recognition and nuclease activation, we used cryo-electron microscopy to capture wild-type Acidaminococcus sp. Cas12a R-loop intermediates and DNA delivery into the RuvC active site. Stages of Cas12a R-loop formation-starting from a 5-bp seed-are marked by distinct REC domain arrangements. Dramatic domain flexibility limits contacts until nearly complete R-loop formation, when the non-target strand is pulled across the RuvC nuclease and coordinated domain docking promotes efficient cleavage. Next, substantial domain movements enable target strand repositioning into the RuvC active site. Between cleavage events, the RuvC lid conformationally resets to occlude the active site, requiring re-activation. These snapshots build a structural model depicting Cas12a DNA targeting that rationalizes observed specificity and highlights mechanistic comparisons to other class 2 effectors.
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Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Aakash Saha
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Catherine Moy
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Alexander-Hoi Nguyen
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA; Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; LIVESTRONG Cancer Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
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6
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Song R, Chen Z, Xiao H, Wang H. The CRISPR-Cas system in molecular diagnostics. Clin Chim Acta 2024; 561:119820. [PMID: 38901631 DOI: 10.1016/j.cca.2024.119820] [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: 05/22/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Robust, sensitive, and rapid molecular detection tools are essential prerequisites for disease diagnosis and epidemiological control. However, the current mainstream tests necessitate expensive equipment and specialized operators, impeding the advancement of molecular diagnostics. The CRISPR-Cas system is an integral component of the bacterial adaptive immune system, wherein Cas proteins recognize PAM sequences by binding to CRISPR RNA, subsequently triggering DNA or RNA cleavage. The discovery of the CRISPR-Cas system has invigorated molecular diagnostics. With further in-depth research on this system, its application in molecular diagnosis is flourishing. In this review, we provide a comprehensive overview of recent research progress on the CRISPR-Cas system, specifically focusing on its application in molecular diagnosis.
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Affiliation(s)
- Rao Song
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Zhongyi Chen
- Department of Pathology, Suining Central Hospital, Suining 629000, China
| | - Hongtao Xiao
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Haojun Wang
- Department of Pathology, Suining Central Hospital, Suining 629000, China.
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7
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Rosignoli S, Lustrino E, Conci A, Fabrizi A, Rinaldo S, Latella M, Enzo E, Prosseda G, De Rosa L, De Luca M, Paiardini A. AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach. Nucleic Acids Res 2024; 52:W29-W38. [PMID: 38795068 PMCID: PMC11223865 DOI: 10.1093/nar/gkae419] [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: 03/07/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/27/2024] Open
Abstract
Gene therapy of dominantly inherited genetic diseases requires either the selective disruption of the mutant allele or the editing of the specific mutation. The CRISPR-Cas system holds great potential for the genetic correction of single nucleotide variants (SNVs), including dominant mutations. However, distinguishing between single-nucleotide variations in a pathogenic genomic context remains challenging. The presence of a PAM in the disease-causing allele can guide its precise targeting, preserving the functionality of the wild-type allele. The AlPaCas (Aligning Patients to Cas) webserver is an automated pipeline for sequence-based identification and structural analysis of SNV-derived PAMs that satisfy this demand. When provided with a gene/SNV input, AlPaCas can: (i) identify SNV-derived PAMs; (ii) provide a list of available Cas enzymes recognizing the SNV (s); (iii) propose mutational Cas-engineering to enhance the selectivity towards the SNV-derived PAM. With its ability to identify allele-specific genetic variants that can be targeted using already available or engineered Cas enzymes, AlPaCas is at the forefront of advancements in genome editing. AlPaCas is open to all users without a login requirement and is freely available at https://schubert.bio.uniroma1.it/alpacas.
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Affiliation(s)
- Serena Rosignoli
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
| | - Elisa Lustrino
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
| | - Alessio Conci
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alessandra Fabrizi
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
| | | | - Elena Enzo
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Gianni Prosseda
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Laura De Rosa
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Michele De Luca
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
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8
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Zhang X, Wang Y, Tang Y, Yang L, Zhao C, Yang G, Wang P, Gao S. A One-Step RPA-CRISPR Assay Using crRNA Based on Suboptimal Protospacer Adjacent Motif for Vibrio vulnificus Detection. Foodborne Pathog Dis 2024; 21:458-466. [PMID: 38551156 DOI: 10.1089/fpd.2023.0119] [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: 07/11/2024] Open
Abstract
Vibrio vulnificus is a hazardous foodborne pathogen responsible for approximately 95% of seafood-related deaths. This highlights the urgent requirement for specialized detection tools to be developed and used by food enterprises and food safety authorities. The DETECTR (DNA endonuclease targeted CRISPR trans reporter) system that combines CRISPR/Cas and recombinase polymerase amplification (RPA) has been utilized to develop a molecular detection assay for V. vulnificus. However, because the incompatibility between RPA and Cas12a cleavage has not been addressed, it is a two-step assay that lacks convenience and presents contamination risk. Here, we developed a one-step RPA-CRISPR assay for V. vulnificus using a special crRNA targeting a sequence with a suboptimal protospacer adjacent motif (PAM). The entire assay, conducted at 37°C, takes only 40-60 min, yields results visualized under blue light, and exhibits exceptional specificity and sensitivity (detecting 4 pathogen genome copies per reaction). This study offers a valuable tool for detecting V. vulnificus, aiding in foodborne infection prevention, and exemplifies one-step RPA-CRISPR assays managing Cas-cleavage activity through PAM adjustments.
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Affiliation(s)
- Xue Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Yue Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Yixin Tang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Lihong Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Chenjie Zhao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Guang Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
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9
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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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10
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Zhang J, Li Z, Guo C, Guan X, Avery L, Banach D, Liu C. Intrinsic RNA Targeting Triggers Indiscriminate DNase Activity of CRISPR-Cas12a. Angew Chem Int Ed Engl 2024; 63:e202403123. [PMID: 38516796 PMCID: PMC11073899 DOI: 10.1002/anie.202403123] [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: 02/13/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
The CRISPR-Cas12a system has emerged as a powerful tool for next-generation nucleic acid-based molecular diagnostics. However, it has long been believed to be effective only on DNA targets. Here, we investigate the intrinsic RNA-enabled trans-cleavage activity of AsCas12a and LbCas12a and discover that they can be directly activated by full-size RNA targets, although LbCas12a exhibits weaker trans-cleavage activity than AsCas12a on both single-stranded DNA and RNA substrates. Remarkably, we find that the RNA-activated Cas12a possesses higher specificity in recognizing mutated target sequences compared to DNA activation. Based on these findings, we develop the "Universal Nuclease for Identification of Virus Empowered by RNA-Sensing" (UNIVERSE) assay for nucleic acid testing. We incorporate a T7 transcription step into this assay, thereby eliminating the requirement for a protospacer adjacent motif (PAM) sequence in the target. Additionally, we successfully detect multiple PAM-less targets in HIV clinical samples that are undetectable by the conventional Cas12a assay based on double-stranded DNA activation, demonstrating unrestricted target selection with the UNIVERSE assay. We further validate the clinical utility of the UNIVERSE assay by testing both HIV RNA and HPV 16 DNA in clinical samples. We envision that the intrinsic RNA targeting capability may bring a paradigm shift in Cas12a-based nucleic acid detection and further enhance the understanding of CRISPR-Cas biochemistry.
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Affiliation(s)
- Jiongyu Zhang
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Chong Guo
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Xin Guan
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lori Avery
- Department of Pathology and Laboratory Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - David Banach
- Department of Medicine, Division of Infectious Diseases, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
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11
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Nalefski EA, Kooistra RM, Parikh I, Hedley S, Rajaraman K, Madan D. Determinants of CRISPR Cas12a nuclease activation by DNA and RNA targets. Nucleic Acids Res 2024; 52:4502-4522. [PMID: 38477377 PMCID: PMC11077072 DOI: 10.1093/nar/gkae152] [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: 05/31/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The RNA-guided CRISPR-associated (Cas) enzyme Cas12a cleaves specific double-stranded (ds-) or single-stranded (ss-) DNA targets (in cis), unleashing non-specific ssDNA cleavage (in trans). Though this trans-activity is widely coopted for diagnostics, little is known about target determinants promoting optimal enzyme performance. Using quantitative kinetics, we show formation of activated nuclease proceeds via two steps whereby rapid binding of Cas12a ribonucleoprotein to target is followed by a slower allosteric transition. Activation does not require a canonical protospacer-adjacent motif (PAM), nor is utilization of such PAMs predictive of high trans-activity. We identify several target determinants that can profoundly impact activation times, including bases within the PAM (for ds- but not ssDNA targets) and sequences within and outside those complementary to the spacer, DNA topology, target length, presence of non-specific DNA, and ribose backbone itself, uncovering previously uncharacterized cleavage of and activation by RNA targets. The results provide insight into the mechanism of Cas12a activation, with direct implications on the role of Cas12a in bacterial immunity and for Cas-based diagnostics.
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Affiliation(s)
| | | | | | | | | | - Damian Madan
- Global Health Labs, Inc, Bellevue, WA 98007, USA
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12
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Rananaware SR, Meister KS, Shoemaker GM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Karalkar VN, Lange IH, Pizzano BLM, Chang M, Ahmadimashhadi MR, Flannery SJ, Nguyen LT, Wang GP, Jain PK. PAM-free diagnostics with diverse type V CRISPR-Cas systems. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306194. [PMID: 38746294 PMCID: PMC11092703 DOI: 10.1101/2024.05.02.24306194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.
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13
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Ren K, Zhou F, Zhang F, Yin M, Zhu Y, Wang S, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z. Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs. Cell Res 2024; 34:370-385. [PMID: 38575718 PMCID: PMC11061315 DOI: 10.1038/s41422-024-00952-1] [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: 01/15/2024] [Accepted: 03/09/2024] [Indexed: 04/06/2024] Open
Abstract
CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.
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Affiliation(s)
- Kuan Ren
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Fengxia Zhou
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
| | - Mingyu Yin
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Shouyu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yan Chen
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Tengjin Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zixuan Wu
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jiale He
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Anqi Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Changyou Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- New Cornerstone Science Laboratory, Shenzhen, Guangdong, China.
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14
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Zaman QU, Raza A, Lozano-Juste J, Chao L, Jones MGK, Wang HF, Varshney RK. Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops. Trends Biotechnol 2024; 42:560-574. [PMID: 37993299 DOI: 10.1016/j.tibtech.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson-Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits. DNA-free and off-target-free GEd crops with defined characteristics can help to achieve sustainable global food security under a changing climate, but need alignment of international regulations to operate in existing supply chains.
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Affiliation(s)
- Qamar U Zaman
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China; Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia 46022, Spain
| | - Li Chao
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Michael G K Jones
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia
| | - Hua-Feng Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia.
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15
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Bagheri N, Chamorro A, Idili A, Porchetta A. PAM-Engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications. Angew Chem Int Ed Engl 2024; 63:e202319677. [PMID: 38284432 DOI: 10.1002/anie.202319677] [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: 12/19/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
The RNA-programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio-engineering strategies are required to achieve control over Cas12a activity. Here, we show that Toehold Switch DNA hairpins, presenting a rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used to control Cas12a in response to molecular inputs. Reconfiguring the Toehold Switch DNA from a hairpin to a duplex conformation through a strand displacement reaction provides an effective means to modulate the accessibility of the PAM, thereby controlling the binding and cleavage activities of Cas12a. Through this approach, we showcase the potential to trigger downstream Cas12a activity by leveraging proximity-based strand displacement reactions in response to target binding. By utilizing the trans-cleavage activity of Cas12a as a signal transduction method, we demonstrate the versatility of our approach for sensing applications. Our system enables rapid, one-pot detection of IgG antibodies and small molecules with high sensitivity and specificity even within complex matrices. Besides the bioanalytical applications, the switchable PAM-engineered Toehold Switches serve as programmable tools capable of regulating Cas12a-based targeting and DNA processing in response to molecular inputs and hold promise for a wide array of biotechnological applications.
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Affiliation(s)
- Neda Bagheri
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alejandro Chamorro
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Andrea Idili
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
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16
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Sun L, Zhang T, Lan X, Zhang N, Wang R, Ma S, Zhao P, Xia Q. High-Throughput Screening of PAM-Flexible Cas9 Variants for Expanded Genome Editing in the Silkworm ( Bombyx mori). INSECTS 2024; 15:241. [PMID: 38667371 PMCID: PMC11050708 DOI: 10.3390/insects15040241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Genome editing provides novel opportunities for the precise genome engineering of diverse organisms. Significant progress has been made in the development of genome-editing tools for Bombyx mori (B. mori) in recent years. Among these, CRISPR/Cas9, which is currently the most commonly used system in lepidopteran insects, recognizes NGG protospacer adjacent motif (PAM) sequences within the target locus. However, Cas9 lacks the ability to target all gene loci in B. mori, indicating the need for Cas9 variants with a larger editing range. In this study, we developed a high-throughput screening platform to validate Cas9 variants at all possible recognizable and editable PAM sites for target sequences in B. mori. This platform enabled us to identify PAM sites that can be recognized by both xCas9 3.7 and SpCas9-NG variants in B. mori and to assess their editing efficiency. Cas9 shows PAM sites every 13 base pairs in the genome, whereas xCas9 3.7 and SpCas9-NG have an average distance of 3.4 and 3.6 base pairs, respectively, between two specific targeting sites. Combining the two Cas9 variants could significantly expand the targeting range of the genome, accelerate research on the B. mori genome, and extend the high-throughput rapid screening platform to other insects, particularly those lacking suitable NGG PAM sequences.
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Affiliation(s)
- Le Sun
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Tong Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Xinhui Lan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Na Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Ruolin Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
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17
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Li X, Dang Z, Tang W, Zhang H, Shao J, Jiang R, Zhang X, Huang F. Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a. BIOSENSORS 2024; 14:145. [PMID: 38534252 DOI: 10.3390/bios14030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.
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Affiliation(s)
- Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jianwei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rui Jiang
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
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18
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Sun Q, Lin H, Li Y, Yuan L, Li B, Ma Y, Wang H, Deng X, Chen H, Tang S. A photocontrolled one-pot isothermal amplification and CRISPR-Cas12a assay for rapid detection of SARS-CoV-2 Omicron variants. Microbiol Spectr 2024; 12:e0364523. [PMID: 38319081 PMCID: PMC10913417 DOI: 10.1128/spectrum.03645-23] [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: 10/14/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
CRISPR-Cas technology has widely been applied to detect single-nucleotide mutation and is considered as the next generation of molecular diagnostics. We previously reported the combination of nucleic acid amplification (NAA) and CRISPR-Cas12a system to distinguish major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. However, the mixture of NAA and CRISPR-Cas12a reagents in one tube could interfere with the efficiency of NAA and CRISPR-Cas12a cleavage, which in turn affects the detection sensitivity. In the current study, we employed a novel photoactivated CRISPR-Cas12a strategy integrated with recombinase polymerase amplification (RPA) to develop one-pot RPA/CRISPR-Cas12a genotyping assay for detecting SARS-CoV-2 Omicron sub-lineages. The new system overcomes the potential inhibition of RPA due to early CRISPR-Cas12a activation and cleavage of the target template in traditional one-pot assay using photocleavable p-RNA, a complementary single-stranded RNA to specifically bind crRNA and precisely block Cas12a activation. The detection can be finished in one tube at 39℃ within 1 h and exhibits a low limit of detection of 30 copies per reaction. Our results demonstrated that the photocontrolled one-pot RPA/CRISPR-Cas12a assay could effectively identify three signature mutations in the spike gene of SARS-CoV-2 Omicron variant, namely, R346T, F486V, and 49X, and distinguish Omicron BA.1, BA.5.2, and BF.7 sub-lineages. Furthermore, the assay achieved a sensitivity of 97.3% and a specificity of 100.0% and showed a concordance of 98.3% with Sanger sequencing results.IMPORTANCEWe successfully developed one-pot recombinase polymerase amplification/CRISPR-Cas12a genotyping assay by adapting photocontrolled CRISPR-Cas technology to optimize the conditions of nucleic acid amplification and CRISPR-Cas12a-mediated detection. This innovative approach was able to quickly distinguish severe acute respiratory syndrome coronavirus 2 Omicron variants and can be readily modified for detecting any nucleic acid mutations. The assay system demonstrates excellent clinical performance, including rapid detection, user-friendly operations, and minimized risk of contamination, which highlights its promising potential as a point-of-care testing for wide applications in resource-limiting settings.
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Affiliation(s)
- Qian Sun
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongqing Lin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuan Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Liping Yuan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Baisheng Li
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Yunan Ma
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Hongliang Chen
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
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19
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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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20
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Nguyen LT, Macaluso NC, Rakestraw NR, Carman DR, Pizzano BLM, Hautamaki RC, Rananaware SR, Roberts IE, Jain PK. Harnessing noncanonical crRNAs to improve functionality of Cas12a orthologs. Cell Rep 2024; 43:113777. [PMID: 38358883 PMCID: PMC11031708 DOI: 10.1016/j.celrep.2024.113777] [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: 07/09/2023] [Revised: 12/04/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
There is a broad diversity among Cas12a endonucleases that possess nucleic acid detection and gene-editing capabilities, but few are studied extensively. Here, we present an exhaustive investigation of 23 Cas12a orthologs, with a focus on their cis- and trans-cleavage activities in combination with noncanonical crRNAs. Through biochemical assays, we observe that some noncanonical crRNA:Cas12a effector complexes outperform their corresponding wild-type crRNA:Cas12a. Cas12a can recruit crRNA with modifications such as loop extensions and split scaffolds. Moreover, the tolerance of Cas12a to noncanonical crRNA is also observed in mammalian cells through the formation of indels. We apply the adaptability of Cas12a:crRNA complexes to detect SARS-CoV-2 in clinical nasopharyngeal swabs, saliva samples, and tracheal aspirates. Our findings further expand the toolbox for next-generation CRISPR-based diagnostics and gene editing.
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Affiliation(s)
- Long T Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Nicolas C Macaluso
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Noah R Rakestraw
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Dylan R Carman
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Brianna L M Pizzano
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Raymond C Hautamaki
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, USA
| | | | - Isabel E Roberts
- Department of Chemical Engineering, John and Marcia Price College of Engineering, University of Utah, Salt Lake City, UT, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA; Health Cancer Center, University of Florida, Gainesville, FL, USA.
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21
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Ke Y, Zhang S, Gao Y, Chen X, He J, Chen Y, Zhang Q, Ding X. Engineered CRISPRa System for Precise and Multiplex Gene Regulation Using a Hybrid dCas12a Variant and Hairpin-Spacer crRNAs. Anal Chem 2024; 96:2637-2642. [PMID: 38305901 DOI: 10.1021/acs.analchem.3c05318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a nucleases have emerged as a promising alternative to CRISPR-Cas9 in gene editing and expression regulation. However, the adoption of Cas12a has been hindered due to general off-target activities and limited efficiency. Here, we utilized a hybrid engineered Cas12a variant and hairpin-spacer crRNAs (h-CAP) to enhance the specificity and efficiency of the CRISPR-Cas12a system. Leveraging the h-CAP strategy, we demonstrate both single-base-specific and multiplex gene expression regulation in human cells.
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Affiliation(s)
- Yuqing Ke
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Shuang Zhang
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Yingying Gao
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Xiaoxiang Chen
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Jie He
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Youming Chen
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Qiang Zhang
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Xianting Ding
- Nantong First People's Hospital and Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Nantong 226006, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
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22
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Xia X, Chen Q, Zuo T, Liang Z, Xu G, Wei F, Yang J, Hu Q, Zhao Z, Tang BZ, Cen Y. DNA Robots for CRISPR/Cas12a Activity Management and Universal Platforms for Biosensing. Anal Chem 2024; 96:2620-2627. [PMID: 38217497 DOI: 10.1021/acs.analchem.3c05210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
The CRISPR/Cas12a system is a revolutionary genome editing technique that is widely employed in biosensing and molecular diagnostics. However, there are few reports on precisely managing the trans-cleavage activity of Cas12a by simple modification since the traditional methods to manage Cas12a often require difficult and rigorous regulation of core components. Hence, we developed a novel CRISPR/Cas12a regulatory mechanism, named DNA Robots for Enzyme Activity Management (DREAM), by introducing two simple DNA robots, apurinic/apyrimidinic site (AP site) or nick on target activator. First, we revealed the mechanism of how the DREAM strategy precisely regulated Cas12a through different binding affinities. Second, the DREAM strategy was found to improve the selectivity of Cas12a for identifying base mismatch. Third, a modular biosensor for base excision repair enzymes based on the DREAM strategy was developed by utilizing diversified generation ways of DNA robots, and a multi-signal output platform such as fluorescence, colorimetry, and visual lateral flow strip was constructed. Furthermore, we extended logic sensing circuits to overcome the barrier that Cas12a could not detect simultaneously in a single tube. Overall, the DREAM strategy not only provided new prospects for programmable Cas12a biosensing systems but also enabled portable, specific, and humanized detection with great potential for molecular diagnostics.
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Affiliation(s)
- Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Tongshan Zuo
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhigang Liang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zheng Zhao
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
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23
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Pietralla J, Capdeville N, Schindele P, Puchta H. Optimizing ErCas12a for efficient gene editing in Arabidopsis thaliana. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:401-412. [PMID: 37864303 PMCID: PMC10826985 DOI: 10.1111/pbi.14194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/24/2023] [Accepted: 09/23/2023] [Indexed: 10/22/2023]
Abstract
The ErCas12a nuclease, also known as MAD7, is part of a CRISPR/Cas system from Eubacterium rectale and distantly related to Cas12a nucleases. As it shares only 31% sequence homology with the commonly used AsCas12a, its intellectual property may not be covered by the granted patent rights for Cas12a nucleases. Thus, ErCas12a became an attractive alternative for practical applications. However, the editing efficiency of ErCas12a is strongly target sequence- and temperature-dependent. Therefore, optimization of the enzyme activity through protein engineering is especially attractive for its application in plants, as they are cultivated at lower temperatures. Based on the knowledge obtained from the optimization of Cas12a nucleases, we opted to improve the gene editing efficiency of ErCas12a by introducing analogous amino acid exchanges. Interestingly, neither of these mutations analogous to those in the enhanced or Ultra versions of AsCas12a resulted in significant editing enhancement of ErCas12a in Arabidopsis thaliana. However, two different mutations, V156R and K172R, in putative alpha helical structures of the enzyme showed a detectable improvement in editing. By combining these two mutations, we obtained an improved ErCas12a (imErCas12a) variant, showing several-fold increase in activity in comparison to the wild-type enzyme in Arabidopsis. This variant yields strong editing efficiencies at 22 °C which could be further increased by raising the cultivation temperature to 28 °C and even enabled editing of formerly inaccessible targets. Additionally, no enhanced off-site activity was detected. Thus, imErCas12a is an economically attractive and efficient alternative to other CRISPR/Cas systems for plant genome engineering.
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Affiliation(s)
- Janine Pietralla
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
| | - Niklas Capdeville
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
| | - Patrick Schindele
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
| | - Holger Puchta
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
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24
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Dampier W, Berman R, Nonnemacher MR, Wigdahl B. Computational analysis of cas proteins unlocks new potential in HIV-1 targeted gene therapy. Front Genome Ed 2024; 5:1248982. [PMID: 38239625 PMCID: PMC10794619 DOI: 10.3389/fgeed.2023.1248982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction: The human immunodeficiency virus type 1 (HIV-1) pandemic has been slowed with the advent of anti-retroviral therapy (ART). However, ART is not a cure and as such has pushed the disease into a chronic infection. One potential cure strategy that has shown promise is the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas gene editing system. It has recently been shown to successfully edit and/or excise the integrated provirus from infected cells and inhibit HIV-1 in vitro, ex vivo, and in vivo. These studies have primarily been conducted with SpCas9 or SaCas9. However, additional Cas proteins are discovered regularly and modifications to these known proteins are being engineered. The alternative Cas molecules have different requirements for protospacer adjacent motifs (PAMs) which impact the possible targetable regions of HIV-1. Other modifications to the Cas protein or gRNA handle impact the tolerance for mismatches between gRNA and the target. While reducing off-target risk, this impacts the ability to fully account for HIV-1 genetic variability. Methods: This manuscript strives to examine these parameter choices using a computational approach for surveying the suitability of a Cas editor for HIV-1 gene editing. The Nominate, Diversify, Narrow, Filter (NDNF) pipeline measures the safety, broadness, and effectiveness of a pool of potential gRNAs for any PAM. This technique was used to evaluate 46 different potential Cas editors for their HIV therapeutic potential. Results: Our examination revealed that broader PAMs that improve the targeting potential of editors like SaCas9 and LbCas12a have larger pools of useful gRNAs, while broader PAMs reduced the pool of useful SpCas9 gRNAs yet increased the breadth of targetable locations. Investigation of the mismatch tolerance of Cas editors indicates a 2-missmatch tolerance is an ideal balance between on-target sensitivity and off-target specificity. Of all of the Cas editors examined, SpCas-NG and SPRY-Cas9 had the highest number of overall safe, broad, and effective gRNAs against HIV. Discussion: Currently, larger proteins and wider PAMs lead to better targeting capacity. This implies that research should either be targeted towards delivering longer payloads or towards increasing the breadth of currently available small Cas editors. With the discovery and adoption of additional Cas editors, it is important for researchers in the HIV-1 gene editing field to explore the wider world of Cas editors.
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Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
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25
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Badon IW, Oh Y, Kim HJ, Lee SH. Recent application of CRISPR-Cas12 and OMEGA system for genome editing. Mol Ther 2024; 32:32-43. [PMID: 37952084 PMCID: PMC10787141 DOI: 10.1016/j.ymthe.2023.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
In 2012, it was discovered that precise gene editing could be induced in target DNA using the reprogrammable characteristics of the CRISPR system. Since then, several studies have investigated the potential of the CRISPR system to edit various biological organisms. For the typical CRISPR system obtained from bacteria and archaea, many application studies have been conducted and have spread to various fields. To date, orthologs with various characteristics other than CRISPR-Cas9 have been discovered and are being intensively studied in the field of gene editing. CRISPR-Cas12 and its varied orthologs are representative examples of genome editing tools and have superior properties in terms of in vivo target gene editing compared with Cas9. Recently, TnpB and Fanzor of the OMEGA (obligate mobile element guided activity) system were identified to be the ancestor of CRISPR-Cas12 on the basis of phylogenetic analysis. Notably, the compact sizes of Cas12 and OMEGA endonucleases allow adeno-associated virus (AAV) delivery; hence, they are set to challenge Cas9 for in vivo gene therapy. This review is focused on these RNA-guided reprogrammable endonucleases: their structure, biochemistry, off-target effects, and applications in therapeutic gene editing.
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Affiliation(s)
- Isabel Wen Badon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ho-Joong Kim
- Department of Chemistry, Chosun University, Gwangju 61452, Republic of Korea.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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26
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Lin C, Chen F, Huang D, Li W, He C, Tang Y, Li X, Liu C, Han L, Yang Y, Zhu Y, Chen R, Shi Y, Xia C, Yan Z, Du H, Huang L. A universal all-in-one RPA-Cas12a strategy with de novo autodesigner and its application in on-site ultrasensitive detection of DNA and RNA viruses. Biosens Bioelectron 2023; 239:115609. [PMID: 37611446 DOI: 10.1016/j.bios.2023.115609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/23/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023]
Abstract
Revolutionary all-in-one RPA-CRISPR assays are rapidly becoming the most sought-after tools for point-of-care testing (POCT) due to their high sensitivity and ease of use. Despite the availability of one-pot methods for specific targets, the development of more efficient methods for new targets remains a significant challenge. In this study, we present a rapid and universal approach to establishing an all-in-one RPA-Cas12a method CORDSv2 based on rational balancing amplification and Cas12a cleavage, which achieves ultrasensitive detection of several targets, including SARS-CoV-2, ASFV, HPV16, and HPV18. CORDSv2 demonstrates a limit of detection (LOD) of 0.6 cp/μL and 100% sensitivity for SARS-CoV-2, comparable to qPCR. Combining with our portable device(hippo-CORDS), it has a visual detection LOD of 6 cp/μL and a sensitivity up to 100% for SARS-CoV-2 and 97% for Ct<35 ASFV samples, surpassing most one-pot visual methods. To simplify and accelerate the process for new targets, we also develop a de novo autodesigner by which the optimal couples of primers and crRNA can be selected rapidly. As a universal all-in-one RPA-CRISPR method for on-site testing, CORDSv2 becomes an attractive choice for rapid and accurate diagnosis in resource-limited settings.
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Affiliation(s)
- Cailing Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Feng Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Dongchao Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Wenyan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Changsheng He
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Experimental Animal Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yingjun Tang
- WENS Foodstuff Group Co., Ltd., Yunfu, 527400, China
| | - Xueping Li
- Guangzhou Yoyoung Bio-tech Company, Guangzhou, 510300, China
| | - Can Liu
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, 528000, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 515150, China
| | - Liya Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yunpeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yongchong Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ruikang Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yuanju Shi
- Guangzhou Yoyoung Bio-tech Company, Guangzhou, 510300, China
| | - Chenglai Xia
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, 528000, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 515150, China
| | - Zhibin Yan
- Guangdong Provincial Key Laboratory of Optical Information Materials and Technology & Institute of Electronic Paper Displays, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou, 510006, PR China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Fangrui Institute of Innovative Drugs, South China University of Technology, Guangzhou, 510006, China.
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27
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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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28
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Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination. Nucleic Acids Res 2023; 51:8730-8743. [PMID: 37522352 PMCID: PMC10484686 DOI: 10.1093/nar/gkad636] [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: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The finding sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
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Affiliation(s)
- Jaideep Singh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Kevin G Liu
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Aleique Allen
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Jiang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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29
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Wang M, Chen M, Wu X, Huang X, Yu B. CRISPR applications in cancer diagnosis and treatment. Cell Mol Biol Lett 2023; 28:73. [PMID: 37674114 PMCID: PMC10481571 DOI: 10.1186/s11658-023-00483-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/17/2023] [Indexed: 09/08/2023] Open
Abstract
Cancer remains a significant global health challenge, necessitating the exploration of novel and more precise therapeutic options beyond conventional treatments. In this regard, clustered regularly interspaced short palindromic repeats (CRISPR) systems have emerged as highly promising tools for clinical gene editing applications. The CRISPR family encompasses diverse CRISPR-associated (Cas) proteins that possess the ability to recognize specific target sequences. The initial CRISPR system consisted of the Cas9 protein and a single-guide RNA, which guide Cas9 to the desired target sequence, facilitating precise double-stranded cleavage. In addition to the traditional cis-cleavage activity, the more recently discovered Cas12 and Cas13 proteins exhibit trans-cleavage activity, which expands their potential applications in cancer diagnosis. In this review, we provide an overview of the functional characteristics of Cas9, Cas12, and Cas13. Furthermore, we highlight the latest advancements and applications of these CRISPR systems in cancer gene therapy and molecular diagnosis. We also emphasize the importance of understanding the strengths and limitations of each CRISPR system to maximize their clinical utility. By providing a comprehensive overview of the current state of CRISPR technology in cancer research, we aim to inspire further exploration and innovation in this rapidly evolving field.
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Affiliation(s)
- Mingxia Wang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Menghui Chen
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Xia Wu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Xinbo Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| | - Bo Yu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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Cheng M, Tan C, Xiang B, Lin W, Cheng B, Peng X, Yang Y, Lin Y. Chain hybridization-based CRISPR-lateral flow assay enables accurate gene visual detection. Anal Chim Acta 2023; 1270:341437. [PMID: 37311609 DOI: 10.1016/j.aca.2023.341437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
Visualized gene detection based on the CRISPR-Cas12/CRISPR-Cas13 technology and lateral flow assay device (CRISPR-LFA) has shown great potential in point-of-care testing sector. Current CRISPR-LFA methodology mainly utilizes conventional immuno-based LFA test strips, which could visualize whether the reporter probe is trans-cleaved by Cas protein, indicating the target positive detection. However, conventional CRISPR-LFA usually produces false-positive results in target negative assay. Herein, a nucleic acid Chain Hybridization-based Lateral Flow Assay platform, named CHLFA, has been developed to achieve the CRISPR-CHLFA concept. Different from the conventional CRISPR-LFA, the proposed CRISPR-CHLFA system was established based on the nucleic acid hybridization between the GNP-probe embedded in test strips and ssDNA (or ssRNA) reporter from CRISPR (LbaCas12a or LbuCas13a) reaction, which eliminated the requirement of immunoreaction in conventional immuno-based LFA. The assay realized the detection of 1-10 copy of target gene per reaction within 50 min. The CRISPR-CHLFA system achieved highly accurate visual detection of target negative samples, thus overcoming the false-positive problem that often produced in assays using conventional CRISPR-LFA. The CRISPR-CHLFA platform was further adopted for the visual detection of marker gene from SASR-CoV-2 Omicron variant and Mycobacterium tuberculosis (MTB), respectively, and 100% accuracy for the analysis of clinical specimens (45 SASR-CoV-2 specimens and 20 MTB specimens) was obtained. The proposed CRISPR-CHLFA system could provide an alternative platform for the development of POCT biosensors and can be widely adopted in accurate and visualized gene detection.
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Affiliation(s)
- Meng Cheng
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Caiwei Tan
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Xiang
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weihong Lin
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bolin Cheng
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuechun Peng
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yihao Yang
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yongping Lin
- Department of Laboratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China.
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31
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Hu Z, Sun A, Yang J, Naz G, Sun G, Li Z, Gogo Liu JJ, Zhang S, Zhang X. Regulation of the CRISPR-Cas12a system by methylation and demethylation of guide RNA. Chem Sci 2023; 14:5945-5955. [PMID: 37293662 PMCID: PMC10246701 DOI: 10.1039/d3sc00629h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
Chemical modifications of CRISPR-Cas nucleases help decrease off-target editing and expand the biomedical applications of CRISPR-based gene manipulation tools. Here, we found that epigenetic modifications of guide RNA, such as m6A and m1A methylation, can effectively inhibit both the cis- and trans-DNA cleavage activities of CRISPR-Cas12a. The underlying mechanism is that methylations destabilize the secondary and tertiary structure of gRNA which prevents the assembly of the Cas12a-gRNA nuclease complex, leading to decreased DNA targeting ability. A minimum of three adenine methylated nucleotides are required to completely inhibit the nuclease activity. We also demonstrate that these effects are reversible through the demethylation of gRNA by demethylases. This strategy has been used in the regulation of gene expression, demethylase imaging in living cells and controllable gene editing. The results demonstrate that the methylation-deactivated and demethylase-activated strategy is a promising tool for regulation of the CRISPR-Cas12a system.
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Affiliation(s)
- Zhian Hu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Ao Sun
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
| | - Jinlei Yang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Gul Naz
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Gongwei Sun
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
| | - Jun-Jie Gogo Liu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
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Huang X, Zhou J, Yang D, Zhang J, Xia X, Chen YE, Xu J. Decoding CRISPR-Cas PAM recognition with UniDesign. Brief Bioinform 2023; 24:bbad133. [PMID: 37078688 PMCID: PMC10199764 DOI: 10.1093/bib/bbad133] [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: 12/20/2022] [Revised: 02/09/2023] [Accepted: 03/16/2023] [Indexed: 04/21/2023] Open
Abstract
The critical first step in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (CRISPR-Cas) protein-mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the protein's PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR-Cas engineering to relax or tighten PAM requirements for subsequent applications. Here, we describe a universal computational protein design framework (UniDesign) for designing protein-nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM-PIAA interactions for eight Cas9 and two Cas12a proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs of all Cas proteins. In turn, given natural PAMs, the computationally redesigned PIAA residues largely recapitulated the native PIAAs (74% and 86% in terms of identity and similarity, respectively). These results demonstrate that UniDesign faithfully captures the mutual preference between natural PAMs and native PIAAs, suggesting it is a useful tool for engineering CRISPR-Cas and other nucleic acid-interacting proteins. UniDesign is open-sourced at https://github.com/tommyhuangthu/UniDesign.
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Affiliation(s)
- Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jun Zhou
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Xiaofeng Xia
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab 129, Wynnewood, PA 19096, USA
| | - Yuqing Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
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Chen K, Dai L, Zhao J, Deng M, Song L, Bai D, Wu Y, Zhou X, Yang Y, Yang S, Zhao L, Chen X, Xie G, Li J. Temperature-boosted PAM-less activation of CRISPR-Cas12a combined with selective inhibitors enhances detection of SNVs with VAFs below 0.01. Talanta 2023; 261:124674. [PMID: 37201341 DOI: 10.1016/j.talanta.2023.124674] [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: 03/14/2023] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 05/20/2023]
Abstract
The precise identification of rare single nucleotide variations (SNVs) concomitant with excess wild-type DNA is a valuable method for minimally invasive disease diagnosis and early prediction of drug responsiveness. Selective enrichment of mutant variants via strand displacement reaction offers an ideal approach of SNVs analysis but fails to differentiate wildtype from mutants with variant allele fraction (VAF) < 0.01%. Here, we demonstrate that integration of PAM-less CRISPR-Cas12a and adjacent mutation-enhanced inhibition of wild-type alleles enables highly sensitive measurement of SNVs well below the 0.01% VAF threshold. Raising the reaction temperature to the upper limit of LbaCas12a helps to boost PAM-less activation of collateral DNase activity, which can be further enhanced using PCR additives, leading to ideal discriminative performance for single point mutations. Along with selective inhibitors bearing additional adjacent mutation, it allowed detection of model EGFR L858R mutants down to 0.001% with high sensitivity and specificity. Preliminary investigation on adulterated genomic samples prepared in two different ways also suggests that it can accurately measure ultralow-abundance SNVs extracted directly from clinical samples. We believe that our design, which combines the superior SNV enrichment capability of strand displacement reaction and unparalleled programmability of CRISPR-Cas12a, has the potential to significantly advance current SNV profiling technologies.
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Affiliation(s)
- Kena Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ling Dai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Jie Zhao
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Mengjun Deng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - You Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xi Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shuangshuang Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Lin Zhao
- The Department of Emergency & Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Xueping Chen
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Junjie Li
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
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Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA Unwinding Equilibrium Serves as a Checkpoint for CRISPR-Cas12a Target Discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541046. [PMID: 37292754 PMCID: PMC10245671 DOI: 10.1101/2023.05.16.541046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The data sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
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Jiao J, Liu Y, Yang M, Zheng J, Liu C, Ye W, Song S, Bai T, Song C, Wang M, Shi J, Wan R, Zhang K, Hao P, Feng J, Zheng X. The engineered CRISPR-Mb2Cas12a variant enables sensitive and fast nucleic acid-based pathogens diagnostics in the field. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37069831 DOI: 10.1111/pbi.14051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Existing CRISPR/Cas12a-based diagnostic platforms offer accurate and vigorous monitoring of nucleic acid targets, but have the potential to be further optimized for more efficient detection. Here, we profiled 16 Cas12a orthologs, focusing on their trans-cleavage activity and their potential as diagnostic enzymes. We observed the Mb2Cas12a has more robust trans-cleavage activity than other orthologs, especially at lower temperatures. An engineered Mb2Cas12a-RRVRR variant presented robust trans-cleavage activity and looser PAM constraints. Moreover, we found the existing one-pot assay, which simultaneously performed Recombinase Polymerase Amplification (RPA) and Cas12a reaction in one system, resulted in the loss of single-base discrimination during diagnosis. Therefore, we designed a reaction vessel that physically separated the RPA and Cas12a steps while maintaining a closed system. This isolated but closed system made diagnostics more sensitive and specific and effectively prevented contamination. This shelved Mb2Cas12a-RRVRR variant-mediated assay detected various targets in less than 15 min and exhibited equal or greater sensitivity than qPCR when detecting bacterial pathogens, plant RNA viruses and genetically modified crops. Overall, our findings further improved the efficiency of the current CRISPR-based diagnostic system and undoubtedly have great potential for highly sensitive and specific detection of multiple sample types.
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Affiliation(s)
- Jian Jiao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Yiqi Liu
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Mengli Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jingcheng Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenxiu Ye
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Shangwei Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Tuanhui Bai
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Chunhui Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Miaomiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jiangli Shi
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Ran Wan
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Kunxi Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Pengbo Hao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
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36
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Fang L, Yang L, Han M, Xu H, Ding W, Dong X. CRISPR-cas technology: A key approach for SARS-CoV-2 detection. Front Bioeng Biotechnol 2023; 11:1158672. [PMID: 37214290 PMCID: PMC10198440 DOI: 10.3389/fbioe.2023.1158672] [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: 02/09/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
The CRISPR (Clustered Regularly Spaced Short Palindromic Repeats) system was first discovered in prokaryotes as a unique immune mechanism to clear foreign nucleic acids. It has been rapidly and extensively used in basic and applied research owing to its strong ability of gene editing, regulation and detection in eukaryotes. Hererin in this article, we reviewed the biology, mechanisms and relevance of CRISPR-Cas technology and its applications in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. CRISPR-Cas nucleic acid detection tools include CRISPR-Cas9, CRISPR-Cas12, CRISPR-Cas13, CRISPR-Cas14, CRISPR nucleic acid amplification detection technology, and CRISPR colorimetric readout detection system. The above CRISPR technologies have been applied to the nucleic acid detection, including SARS-CoV-2 detection. Common nucleic acid detection based on CRISPR derivation technology include SHERLOCK, DETECTR, and STOPCovid. CRISPR-Cas biosensing technology has been widely applied to point-of-care testing (POCT) by targeting recognition of both DNA molecules and RNA Molecules.
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Affiliation(s)
- Lijuan Fang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Lusen Yang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Mingyue Han
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Huimei Xu
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Wenshuai Ding
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Xuejun Dong
- Medical Laboratory, Zhejiang University Shaoxing Hospital, Shaoxing, China
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Liu Z, Gong G, Li Y, Xu Q, Akimbekov N, Zha J, Wu X. Peptidoglycan-Targeting Staphylolytic Enzyme Lysostaphin as a Novel and Efficient Protease toward Glycine-Rich Flexible Peptide Linkers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5293-5301. [PMID: 36967580 DOI: 10.1021/acs.jafc.3c00189] [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: 06/18/2023]
Abstract
Glycine-rich flexible peptide linkers have been widely adopted in fusion protein engineering; however, they can hardly be cleaved for the separation of fusion partners unless specific protease recognition sites are introduced. Herein, we report the use of the peptidoglycan-targeting staphylolytic enzyme lysostaphin to directly digest the glycine-rich flexible linkers of various lengths including oligoglycine linkers and (G4S)x linkers, without the incorporation of extra amino acids. Using His-MBP-linker-LbCpf1 as a model substrate, we show that both types of linkers could be digested by lysostaphin, and the digestion efficiency improved with increasing linker length. The enzyme LbCpf1 retained full activity after tag removal. We further demonstrated that the proteolytic activity of lysostaphin could be well maintained under different environmental conditions and in the presence of a series of chemical reagents at various concentrations that are frequently used in protein purification and stabilization. In addition, such a digestion strategy could also be applied to remove the SUMO domain linked to LwCas13a via an octaglycine linker. This study extends the applications of lysostaphin beyond an antimicrobial reagent and demonstrates its potential as a novel, efficient, and robust protease for protein engineering.
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Affiliation(s)
- Zhiqiang Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Yanni Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Nuraly Akimbekov
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
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Sasnauskas G, Tamulaitiene G, Druteika G, Carabias A, Silanskas A, Kazlauskas D, Venclovas Č, Montoya G, Karvelis T, Siksnys V. TnpB structure reveals minimal functional core of Cas12 nuclease family. Nature 2023; 616:384-389. [PMID: 37020015 DOI: 10.1038/s41586-023-05826-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 04/07/2023]
Abstract
The widespread TnpB proteins of IS200/IS605 transposon family have recently emerged as the smallest RNA-guided nucleases capable of targeted genome editing in eukaryotic cells1,2. Bioinformatic analysis identified TnpB proteins as the likely predecessors of Cas12 nucleases3-5, which along with Cas9 are widely used for targeted genome manipulation. Whereas Cas12 family nucleases are well characterized both biochemically and structurally6, the molecular mechanism of TnpB remains unknown. Here we present the cryogenic-electron microscopy structures of the Deinococcus radiodurans TnpB-reRNA (right-end transposon element-derived RNA) complex in DNA-bound and -free forms. The structures reveal the basic architecture of TnpB nuclease and the molecular mechanism for DNA target recognition and cleavage that is supported by biochemical experiments. Collectively, these results demonstrate that TnpB represents the minimal structural and functional core of the Cas12 protein family and provide a framework for developing TnpB-based genome editing tools.
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Affiliation(s)
- Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gytis Druteika
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Arturo Carabias
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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39
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Zhang HX, Zhang C, Lu S, Tong X, Zhang K, Yin H, Zhang Y. Cas12a-based one-pot SNP detection with high accuracy. CELL INSIGHT 2023; 2:100080. [PMID: 37193068 PMCID: PMC10134196 DOI: 10.1016/j.cellin.2023.100080] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 05/18/2023]
Abstract
CRISPR-Cas12a based one-pot detection system has been used in nucleic acid detection and diagnosis. However, it is not sensitive enough to distinguish single nucleotide polymorphisms (SNP), which has greatly restricted its application. To overcome these limitations, we engineered a LbCas12a variant with enhanced sensitivity against SNP, named seCas12a (sensitive Cas12a). SeCas12a-based one-pot SNP detection system is a versatile platform that could use both canonical and non-canonical PAM, and was almost not limited by mutation types to distinguish SNPs located between position 1 to 17. The use of truncated crRNA further improved SNP specificity of seCas12a. Mechanistically, we found only when the cis-cleavage was at low level between 0.01min-1 and 0.0006 min-1, a good signal-to-noise ratio can be achieved in one-pot test. SeCas12a-based one-pot SNP detection system was applied to detect pharmacogenomic SNPs in human clinical samples. Of thirteen donors tested in two different SNPs, the seCas12a mediated one-pot system could faithfully detect the SNPs in 30 min with 100% accuracy.
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Affiliation(s)
- Hong-Xia Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Caixiang Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Shuhan Lu
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Xiaohan Tong
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Kun Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Hao Yin
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
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40
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Jianwei L, Jobichen C, Machida S, Meng S, Read RJ, Hongying C, Jian S, Yuan YA, Sivaraman J. Structures of apo Cas12a and its complex with crRNA and DNA reveal the dynamics of ternary complex formation and target DNA cleavage. PLoS Biol 2023; 21:e3002023. [PMID: 36917574 PMCID: PMC10013913 DOI: 10.1371/journal.pbio.3002023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/06/2023] [Indexed: 03/15/2023] Open
Abstract
Cas12a is a programmable nuclease for adaptive immunity against invading nucleic acids in CRISPR-Cas systems. Here, we report the crystal structures of apo Cas12a from Lachnospiraceae bacterium MA2020 (Lb2) and the Lb2Cas12a+crRNA complex, as well as the cryo-EM structure and functional studies of the Lb2Cas12a+crRNA+DNA complex. We demonstrate that apo Lb2Cas12a assumes a unique, elongated conformation, whereas the Lb2Cas12a+crRNA binary complex exhibits a compact conformation that subsequently rearranges to a semi-open conformation in the Lb2Cas12a+crRNA+DNA ternary complex. Notably, in solution, apo Lb2Cas12a is dynamic and can exist in both elongated and compact forms. Residues from Met493 to Leu523 of the WED domain undergo major conformational changes to facilitate the required structural rearrangements. The REC lobe of Lb2Cas12a rotates 103° concomitant with rearrangement of the hinge region close to the WED and RuvC II domains to position the RNA-DNA duplex near the catalytic site. Our findings provide insight into crRNA recognition and the mechanism of target DNA cleavage.
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Affiliation(s)
- Li Jianwei
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Satoru Machida
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sun Meng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Chen Hongying
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Shi Jian
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yuren Adam Yuan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - J. Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
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41
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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. RESEARCH SQUARE 2023:rs.3.rs-2549171. [PMID: 36824842 PMCID: PMC9949221 DOI: 10.21203/rs.3.rs-2549171/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
CRISPR is a prominent bioengineering tool and the type V CRISPR-associated protein complex, Cas12a, is widely used in diagnostic platforms due to its innate ability to cleave DNA substrates. Here we demonstrate that Cas12a can also be programmed to directly detect RNA substrates without the need for reverse transcription or strand displacement. We discovered that while the PAM-proximal "seed" region of the crRNA exclusively recognizes DNA for initiating trans-cleavage, the PAM-distal region or 3'-end of the crRNA can tolerate both RNA and DNA substrates. Utilizing this property, we developed a method named Split Activators for Highly Accessible RNA Analysis or 'SAHARA' to detect RNA sequences at the PAM-distal region of the crRNA by merely supplying a short ssDNA or a PAM containing dsDNA to the seed region. Notably, SAHARA is Mg2+ concentration- and pH-dependent, and it was observed to work robustly at room temperature with multiple orthologs of Cas12a. SAHARA also displayed a significant improvement in the specificity for target recognition as compared to the wild-type CRISPR-Cas12a, at certain positions along the crRNA. By employing SAHARA we achieved amplification-free detection of picomolar concentrations of miRNA-155 and hepatitis C virus RNA. Finally, SAHARA can use a PAM-proximal DNA as a switch to control the trans-cleavage activity of Cas12a for the detection of both DNA and RNA targets. With this, multicomplex arrays can be made to detect distinct DNA and RNA targets with pooled crRNA/Cas12a complexes. 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)
- Santosh R. Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Emma K. Vesco
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Grace M. Shoemaker
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Swapnil S. Anekar
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | | | - Katelyn S. Meister
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Nicolas C. Macaluso
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Long T. Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Piyush K. Jain
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
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42
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Wang Y, Qi T, Liu J, Yang Y, Wang Z, Wang Y, Wang T, Li M, Li M, Lu D, Chang ACY, Yang L, Gao S, Wang Y, Lan F. A highly specific CRISPR-Cas12j nuclease enables allele-specific genome editing. SCIENCE ADVANCES 2023; 9:eabo6405. [PMID: 36763662 PMCID: PMC9917002 DOI: 10.1126/sciadv.abo6405] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
The CRISPR-Cas system can treat autosomal dominant diseases by nonhomologous end joining (NHEJ) gene disruption of mutant alleles. However, many single-nucleotide mutations cannot be discriminated from wild-type alleles by current CRISPR-Cas systems. Here, we functionally screened six Cas12j nucleases and determined Cas12j-8 as an ideal genome editor with a hypercompact size. Cas12j-8 displayed comparable activity to AsCas12a and Un1Cas12f1. Cas12j-8 is a highly specific nuclease sensitive to single-nucleotide mismatches in the protospacer adjacent motif (PAM)-proximal region. We experimentally proved that Cas12j-8 enabled allele-specific disruption of genes with a single-nucleotide polymorphism (SNP). Cas12j-8 recognizes a simple TTN PAM that provides for high target site density. In silico analysis reveals that Cas12j-8 enables allele-specific disruption of 25,931 clinically relevant variants in the ClinVar database, and 485,130,147 SNPs in the dbSNP database. Therefore, Cas12j-8 would be particularly suitable for therapeutic applications.
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Affiliation(s)
- Yao Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Tao Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jingtong Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yuan Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Ziwen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ying Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tianyi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Miaomiao Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Mingqing Li
- Laboratory for Reproductive Immunology, NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Shanghai Medical School, Fudan University, Shanghai 200080, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing 400020, China
| | - Alex Chia Yu Chang
- Department of Cardiology and Shanghai Institute Precision Medicine, Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200125, China
| | - Li Yang
- Center for Molecular Medicine, Children’s Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Feng Lan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
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43
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Three novel Cas12a orthologs with robust DNA cleavage activity suitable for nucleic acid detection. Gene 2023; 852:147055. [PMID: 36400115 DOI: 10.1016/j.gene.2022.147055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
Developing rapid and accurate pathogen detection methods is increasingly important, and CRISPR-Cas system can be optimized for this purpose. CRISPR-Cas12a is a single RNA-guided endonuclease system with the potential for nucleic acid detection. There is a broad diversity among Cas12a nucleases with robust detection capability. Herein, we characterised three Cas12a orthologs (ObCas12a, MbCas12a, and ScCas12a), including cis- and trans-cleavage activities, the identification of PAM, single-base resolution ability, and the application for nucleic acid detection. These Cas12a orthologs displayed robust cis- and trans-cleavage activities, and performed well in terms of specificity and sensitivity for nucleic acid detection. Furthermore, they have subtle differences in single-base resolution and recognised PAM sites in vitro. Therefore, these Cas12a nucleases are candidate proteins for CRISPR-based diagnostic methods. Addition of these enzymes to the nucleic acid detection toolbox will further expand the utility of this powerful technology.
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44
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.525716. [PMID: 36778248 PMCID: PMC9915489 DOI: 10.1101/2023.01.29.525716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CRISPR is a prominent bioengineering tool and the type V CRISPR-associated protein complex, Cas12a, is widely used in diagnostic platforms due to its innate ability to cleave DNA substrates. Here we demonstrate that Cas12a can also be programmed to directly detect RNA substrates without the need for reverse transcription or strand displacement. We discovered that while the PAM-proximal "seed" region of the crRNA exclusively recognizes DNA for initiating trans- cleavage, the PAM-distal region or 3'-end of the crRNA can tolerate both RNA and DNA substrates. Utilizing this property, we developed a method named Split Activators for Highly Accessible RNA Analysis or 'SAHARA' to detect RNA sequences at the PAM-distal region of the crRNA by merely supplying a short ssDNA or a PAM containing dsDNA to the seed region. Notably, SAHARA is Mg 2+ concentration- and pH-dependent, and it was observed to work robustly at room temperature with multiple orthologs of Cas12a. SAHARA also displayed a significant improvement in the specificity for target recognition as compared to the wild-type CRISPR-Cas12a, at certain positions along the crRNA. By employing SAHARA we achieved amplification-free detection of picomolar concentrations of miRNA-155 and hepatitis C virus RNA. Finally, SAHARA can use a PAM-proximal DNA as a switch to control the trans-cleavage activity of Cas12a for the detection of both DNA and RNA targets. With this, multicomplex arrays can be made to detect distinct DNA and RNA targets with pooled crRNA/Cas12a complexes. 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. Abstract Figure
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Affiliation(s)
- Santosh R. Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Emma K. Vesco
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Grace M. Shoemaker
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Swapnil S. Anekar
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | | | - Katelyn S. Meister
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Nicolas C. Macaluso
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Long T. Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Piyush K. Jain
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
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45
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Feng W, Zhang H, Le XC. Signal Amplification by the trans-Cleavage Activity of CRISPR-Cas Systems: Kinetics and Performance. Anal Chem 2023; 95:206-217. [PMID: 36625124 PMCID: PMC9835055 DOI: 10.1021/acs.analchem.2c04555] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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46
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Chen Q, Gul I, Liu C, Lei Z, Li X, Raheem MA, He Q, Haihui Z, Leeansyah E, Zhang CY, Pandey V, Du K, Qin P. CRISPR-Cas12-based field-deployable system for rapid detection of synthetic DNA sequence of the monkeypox virus genome. J Med Virol 2023; 95:e28385. [PMID: 36478250 DOI: 10.1002/jmv.28385] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/21/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
The global outbreak of the monkeypox virus (MPXV) highlights the need for rapid and cost-effective MPXV detection tools to effectively monitor and control the monkeypox disease. Herein, we demonstrated a portable CRISPR-Cas-based system for naked-eye detection of MPXV. The system harnesses the high selectivity of CRISPR-Cas12 and the isothermal nucleic acid amplification potential of recombinase polymerase amplification. It can detect both the current circulating MPXV clade and the original clades. We reached a limit of detection (LoD) of 22.4 aM (13.5 copies/µl) using a microtiter plate reader, while the visual LoD of the system is 75 aM (45 copies/µl) in a two-step assay, which is further reduced to 25 aM (15 copies/µl) in a one-pot system. We compared our results with quantitative polymerase chain reaction and obtained satisfactory consistency. For clinical application, we demonstrated a sensitive and precise visual detection method with attomolar sensitivity and a sample-to-answer time of 35 min.
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Affiliation(s)
- Qun Chen
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Ijaz Gul
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Changyue Liu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Zhengyang Lei
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Xingyu Li
- Department of Hepatobiliary and Pancreatic Surgery II, The Third Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China
| | - Muhammad A Raheem
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Qian He
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Zhang Haihui
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Edwin Leeansyah
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Can Y Zhang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Vijay Pandey
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, P. R. China.,Tsinghua Shenzhen International Graduate School, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, P. R. China
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47
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Enabling Precision Medicine with CRISPR-Cas Genome Editing Technology: A Translational Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:315-339. [DOI: 10.1007/978-981-19-5642-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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48
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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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49
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Green CM, Spangler J, Susumu K, Stenger DA, Medintz IL, Díaz SA. Quantum Dot-Based Molecular Beacons for Quantitative Detection of Nucleic Acids with CRISPR/Cas(N) Nucleases. ACS NANO 2022; 16:20693-20704. [PMID: 36378103 DOI: 10.1021/acsnano.2c07749] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Strategies utilizing the CRISPR/Cas nucleases Cas13 and Cas12 have shown great promise in the development of highly sensitive and rapid diagnostic assays for the detection of pathogenic nucleic acids. The most common approaches utilizing fluorophore-quencher molecular beacons require strand amplification strategies or highly sensitive optical setups to overcome the limitations of the readout. Here, we demonstrate a flexible strategy for assembling highly luminescent and colorimetric quantum dot-nucleic acid hairpin (QD-HP) molecular beacons for use in CRISPR/Cas diagnostics. This strategy utilizes a chimeric peptide-peptide nucleic acid (peptide-PNA) to conjugate fluorescently labeled DNA or RNA hairpins to ZnS-coated QDs. QDs are particularly promising alternatives for molecular beacons due to their greater brightness, strong UV absorbance with large emission offset, exceptional photostability, and potential for multiplexing due to their sharp emission peaks. Using Förster resonance energy transfer (FRET), we have developed ratiometric reporters capable of pM target detection (without nucleotide amplification) for both target DNA and RNA, and we further demonstrated their capabilities for multiplexing and camera-phone detection. The flexibility of this system is imparted by the dual functionality of the QD as both a FRET donor and a central nanoscaffold for arranging nucleic acids and fluorescent acceptors on its surface. This method also provides a generalized approach that could be applied for use in other CRISPR/Cas nuclease systems.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Joseph Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
- Jacobs Corporation, Hanover, Maryland21076, United States
| | - David A Stenger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
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50
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Nguyen GT, Dhingra Y, Sashital DG. Miniature CRISPR-Cas12 endonucleases - Programmed DNA targeting in a smaller package. Curr Opin Struct Biol 2022; 77:102466. [PMID: 36170778 PMCID: PMC10114186 DOI: 10.1016/j.sbi.2022.102466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/11/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
CRISPR-associated (Cas) endonucleases specifically target and cleave RNA or DNA based on complementarity to a guide RNA. Cas endonucleases - including Cas9, Cas12a, and Cas13 - have been adopted for a wide array of biotechnological tools, including gene editing, transcriptional modulation, and diagnostics. These tools are facilitated by ready reprogramming of guide RNA sequences and the varied nucleic acid binding and cleavage activities observed across diverse Cas endonucleases. However, the large size of most Cas endonucleases (950-1400 amino acids) can restrict applications. The recent discovery of miniature Cas endonucleases (400-800 amino acids) provides the potential to overcome this limitation. Here, we review recent advances in understanding the structural mechanisms of two miniature Cas endonucleases, Cas12f and Cas12j.
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Affiliation(s)
- Giang T Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50010, USA. https://twitter.com/GiangNg12638532
| | - Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50010, USA. https://twitter.com/yukti__dhingra
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50010, USA.
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