1
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Nguyen GT, Schelling MA, Raju A, Buscher KA, Sritharan A, Sashital DG. CRISPR-Cas12a exhibits metal-dependent specificity switching. Nucleic Acids Res 2024:gkae613. [PMID: 39019776 DOI: 10.1093/nar/gkae613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
Cas12a is the immune effector of type V-A CRISPR-Cas systems and has been co-opted for genome editing and other biotechnology tools. The specificity of Cas12a has been the subject of extensive investigation both in vitro and in genome editing experiments. However, in vitro studies have often been performed at high magnesium ion concentrations that are inconsistent with the free Mg2+ concentrations that would be present in cells. By profiling the specificity of Cas12a orthologs at a range of Mg2+ concentrations, we find that Cas12a switches its specificity depending on metal ion concentration. Lowering Mg2+ concentration decreases cleavage defects caused by seed mismatches, while increasing the defects caused by PAM-distal mismatches. We show that Cas12a can bind seed mutant targets more rapidly at low Mg2+ concentrations, resulting in faster cleavage. In contrast, PAM-distal mismatches cause substantial defects in cleavage following formation of the Cas12a-target complex at low Mg2+ concentrations. We observe differences in Cas12a specificity switching between three orthologs that results in variations in the routes of phage escape from Cas12a-mediated immunity. Overall, our results reveal the importance of physiological metal ion conditions on the specificity of Cas effectors that are used in different cellular environments.
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Affiliation(s)
- Giang T Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Michael A Schelling
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Akshara Raju
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Kathryn A Buscher
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Aneisha Sritharan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
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2
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Jiao C, Peeck NL, Yu J, Ghaem Maghami M, Kono S, Collias D, Martinez Diaz SL, Larose R, Beisel CL. TracrRNA reprogramming enables direct PAM-independent detection of RNA with diverse DNA-targeting Cas12 nucleases. Nat Commun 2024; 15:5909. [PMID: 39003282 PMCID: PMC11246509 DOI: 10.1038/s41467-024-50243-x] [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: 10/17/2023] [Accepted: 07/04/2024] [Indexed: 07/15/2024] Open
Abstract
Many CRISPR-Cas immune systems generate guide (g)RNAs using trans-activating CRISPR RNAs (tracrRNAs). Recent work revealed that Cas9 tracrRNAs could be reprogrammed to convert any RNA-of-interest into a gRNA, linking the RNA's presence to Cas9-mediated cleavage of double-stranded (ds)DNA. Here, we reprogram tracrRNAs from diverse Cas12 nucleases, linking the presence of an RNA-of-interest to dsDNA cleavage and subsequent collateral single-stranded DNA cleavage-all without the RNA necessarily encoding a protospacer-adjacent motif (PAM). After elucidating nuclease-specific design rules, we demonstrate PAM-independent RNA detection with Cas12b, Cas12e, and Cas12f nucleases. Furthermore, rationally truncating the dsDNA target boosts collateral cleavage activity, while the absence of a gRNA reduces background collateral activity and enhances sensitivity. Finally, we apply this platform to detect 16 S rRNA sequences from five different bacterial pathogens using a universal reprogrammed tracrRNA. These findings extend tracrRNA reprogramming to diverse dsDNA-targeting Cas12 nucleases, expanding the flexibility and versatility of CRISPR-based RNA detection.
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Affiliation(s)
- Chunlei Jiao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Natalia L Peeck
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Mohammad Ghaem Maghami
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Sarah Kono
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Daphne Collias
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Sandra L Martinez Diaz
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Rachael Larose
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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3
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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:S1097-2765(24)00485-4. [PMID: 38955179 DOI: 10.1016/j.molcel.2024.06.007] [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: 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 Acidaminococcussp. 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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4
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Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
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Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
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5
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Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2024:10.1038/s41587-024-02224-0. [PMID: 38760567 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
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Affiliation(s)
- C C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - C M Wilson
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
| | | | - R Dai
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Q Chen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - N Teyssier
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - S Misiukiewicz
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - A Arab
- Arc Institute, Palo Alto, CA, USA
| | - T O'Loughlin
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - J C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - L A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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6
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Bhattacharya S, Agarwal A, Muniyappa K. Deciphering the Substrate Specificity Reveals that CRISPR-Cas12a Is a Bifunctional Enzyme with Both Endo- and Exonuclease Activities. J Mol Biol 2024; 436:168550. [PMID: 38575054 DOI: 10.1016/j.jmb.2024.168550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for genome-editing, with applications in biotechnology and medicine. However, significantly less is known about their substrate specificity, but such knowledge may provide instructive insights into their off-target cleavage and previously unrecognized mechanism of action. Here, we document that the Acidaminococcus sp. Cas12a (AsCas12a) binds preferentially, and independently of crRNA, to a suite of branched DNA structures, such as the Holliday junction (HJ), replication fork and D-loops, compared with single- or double-stranded DNA, and promotes their degradation. Further, our study revealed that AsCas12a binds to the HJ, specifically at the crossover region, protects it from DNase I cleavage and renders a pair of thymine residues in the HJ homologous core hypersensitive to KMnO4 oxidation, suggesting DNA melting and/or distortion. Notably, these structural changes enabled AsCas12a to resolve HJ into nonligatable intermediates, and subsequently their complete degradation. We further demonstrate that crRNA impedes HJ cleavage by AsCas12a, and that of Lachnospiraceae bacterium Cas12a, without affecting their DNA-binding ability. We identified a separation-of-function variant, which uncouples DNA-binding and DNA cleavage activities of AsCas12a. Importantly, we found robust evidence that AsCas12a endonuclease also has 3'-to-5' and 5'-to-3' exonuclease activity, and that these two activities synergistically promote degradation of DNA, yielding di- and mononucleotides. Collectively, this study significantly advances knowledge about the substrate specificity of AsCas12a and provides important insights into the degradation of different types of DNA substrates.
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Affiliation(s)
- Supreet Bhattacharya
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India.
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7
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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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8
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Hetzler Z, Marinakos SM, Lott N, Mohammad N, Lass-Napiorkowska A, Kolbe J, Turrentine L, Fields D, Overton L, Marie H, Hucknall A, Rammo O, George H, Wei Q. Adeno-associated virus genome quantification with amplification-free CRISPR-Cas12a. Gene Ther 2024; 31:304-313. [PMID: 38528117 DOI: 10.1038/s41434-024-00449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Efficient manufacturing of recombinant Adeno-Associated Viral (rAAV) vectors to meet rising clinical demand remains a major hurdle. One of the most significant challenges is the generation of large amounts of empty capsids without the therapeutic genome. There is no standardized analytical method to accurately quantify the viral genes, and subsequently the empty-to-full ratio, making the manufacturing challenges even more complex. We propose the use of CRISPR diagnostics (CRISPR-Dx) as a robust and rapid approach to determine AAV genome titers. We designed and developed the CRISPR-AAV Evaluation (CRAAVE) assay to maximize sensitivity, minimize time-to-result, and provide a potentially universal design for quantifying multiple transgene constructs encapsidated within different AAV serotypes. We also demonstrate an on-chip CRAAVE assay with lyophilized reagents to minimize end user assay input. The CRAAVE assay was able to detect AAV titers as low as 7e7 vg/mL with high precision (<3% error) in quantifying unknown AAV titers when compared with conventional quantitative PCR (qPCR) method. The assay only requires 30 min of assay time, shortening the analytical workflow drastically. Our results suggest CRISPR-Dx could be a promising tool for efficient rAAV genome titer quantification and has the potential to revolutionize biomanufacturing process analytical technology (PAT).
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Affiliation(s)
- Zach Hetzler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27606, USA
| | | | - Noah Lott
- Biomanufacturing, Training, and Education Center (BTEC), North Carolina State University, Raleigh, NC, 27606, USA
| | - Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27606, USA
| | | | - Jenna Kolbe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27606, USA
| | - Lauren Turrentine
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27606, USA
| | - Delaney Fields
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27606, USA
| | - Laurie Overton
- Biomanufacturing, Training, and Education Center (BTEC), North Carolina State University, Raleigh, NC, 27606, USA
| | | | | | | | | | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27606, USA.
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9
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Ci Q, He Y, Chen J. Novel Anti-CRISPR-Assisted CRISPR Biosensor for Exclusive Detection of Single-Stranded DNA (ssDNA). ACS Sens 2024; 9:1162-1167. [PMID: 38442486 PMCID: PMC10964243 DOI: 10.1021/acssensors.4c00201] [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: 01/26/2024] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
Nucleic acid analysis plays an important role in disease diagnosis and treatment. The discovery of CRISPR technology has provided novel and versatile approaches to the detection of nucleic acids. However, the most widely used CRISPR-Cas12a detection platforms lack the capability to distinguish single-stranded DNA (ssDNA) from double-stranded DNA (dsDNA). To overcome this limitation, we first employed an anti-CRISPR protein (AcrVA1) to develop a novel CRISPR biosensor to detect ssDNA exclusively. In this sensing strategy, AcrVA1 cut CRISPR guide RNA (crRNA) to inhibit the cleavage activity of the CRISPR-Cas12a system. Only ssDNA has the ability to recruit the cleaved crRNA fragment to recover the detection ability of the CRISPR-Cas12 biosensor, but dsDNA cannot accomplish this. By measuring the recovered cleavage activity of the CRISPR-Cas12a biosensor, our developed AcrVA1-assisted CRISPR biosensor is capable of distinguishing ssDNA from dsDNA, providing a simple and reliable method for the detection of ssDNA. Furthermore, we demonstrated our developed AcrVA1-assisted CRISPR biosensor to monitor the enzymatic activity of helicase and screen its inhibitors.
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Affiliation(s)
- Qiaoqiao Ci
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Yawen He
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Juhong Chen
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
- Department
of Bioengineering, University of California,
Riverside, Riverside, California 92521, United States
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10
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Saha A, Ahsan M, Arantes PR, Schmitz M, Chanez C, Jinek M, Palermo G. An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nat Commun 2024; 15:1473. [PMID: 38368461 PMCID: PMC10874386 DOI: 10.1038/s41467-024-45762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/01/2024] [Indexed: 02/19/2024] Open
Abstract
CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by a sequential mechanism in which initial cleavage of the non-target strand is followed by target strand cleavage. How the spatially distant DNA target strand traverses toward the RuvC catalytic core is presently not understood. Here, continuous tens of microsecond-long molecular dynamics and free-energy simulations reveal that an α-helical lid, located within the RuvC domain, plays a pivotal role in the traversal of the DNA target strand by anchoring the crRNA:target strand duplex and guiding the target strand toward the RuvC core, as also corroborated by DNA cleavage experiments. In this mechanism, the REC2 domain pushes the crRNA:target strand duplex toward the core of the enzyme, while the Nuc domain aids the bending and accommodation of the target strand within the RuvC core by bending inward. Understanding of this critical process underlying Cas12a activity will enrich fundamental knowledge and facilitate further engineering strategies for genome editing.
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Affiliation(s)
- Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Michael Schmitz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
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11
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Fu X, Sun J, Yu B, Ye Y, Sheng L, Ji J, Zheng J, Fan M, Shao J, Sun X. Investigating enzyme kinetics and fluorescence sensing strategy of CRISPR/Cas12a for foodborne pathogenic bacteria. Anal Chim Acta 2024; 1290:342203. [PMID: 38246741 DOI: 10.1016/j.aca.2024.342203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
Foodborne pathogenic bacteria are widespread in various foods, whose cross-contamination and re-contamination are critical influences on food safety. Rapid, accurate, and sensitive detection of foodborne pathogenic bacteria remains a topic of concern. CRISPR/Cas12a can recognize double-stranded DNA directly, showing great potential in nucleic acid detection. However, few studies have investigated the cleavage properties of CRISPR/Cas12a. In this study, the trans-cleavage properties of LbCas12a and AsCas12a were investigated to construct the detection methods for foodborne pathogenic bacteria. The highly sensitive fluorescent strategies for foodborne pathogens were constructed by analyzing the cleavage rates and properties of substrates at different substrate concentrations. Cas12a was activated in the presence of foodborne pathogenic target sequence was present, resulting in the cleavage of a single-stranded reporter ssDNA co-labelled by fluorescein quencher and fluorescein. The sensitivity and specificity of the Cas12a fluorescent strategy was investigated with Salmonella and Staphylococcus aureus as examples. The results showed that AsCas12a was slightly more capable of trans-cleavage than LbCas12a. The detection limits of AsCas12a for Salmonella and Staphylococcus aureus were 24.9 CFU mL-1 and 1.50 CFU mL-1, respectively. In all the seven bacteria, Staphylococcus aureus and Salmonella were accurately discriminated. The study provided a basis for constructing and improving the CRISPR/Cas12a fluorescence strategies. The AsCas12a-based detection strategy is expected to be a promising method for field detection.
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Affiliation(s)
- XuRan Fu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - JiaDi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Bingqian Yu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Yongli Ye
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Lina Sheng
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jian Ji
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jiayu Zheng
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Minghong Fan
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Jingdong Shao
- Comprehensive Technology Center of Zhangjiagang Customs, Zhangjiagang, Jiangsu, 215600, PR China
| | - XiuLan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
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12
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Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558350. [PMID: 37781594 PMCID: PMC10541102 DOI: 10.1101/2023.09.18.558350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
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13
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Kim CH, Lee WJ, Oh Y, Lee Y, Lee HK, Seong JB, Lim KS, Park SJ, Huh JW, Kim YH, Kim KM, Hur JK, Lee SH. Utilization of nicking properties of CRISPR-Cas12a effector for genome editing. Sci Rep 2024; 14:3352. [PMID: 38336977 PMCID: PMC10858195 DOI: 10.1038/s41598-024-53648-2] [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: 08/03/2023] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
The CRISPR-Cas nickase system for genome editing has attracted considerable attention owing to its safety, efficiency, and versatility. Although alternative effectors to Cas9 have the potential to expand the scope of genome editing, their application has not been optimized. Herein, we used an enhanced CRISPR-Cas12a nickase system to induce mutations by targeting genes in a human-derived cell line. The optimized CRISPR-Cas12a nickase system effectively introduced mutations into target genes under a specific directionality and distance between nickases. In particular, the single-mode Cas12a nickase system can induce the target-specific mutations with less DNA double-strand breaks. By inducing mutations in the Thymine-rich target genes in single- or dual-mode, Cas12a nickase compensates the limitations of Cas9 nickase and is expected to contribute to the development of future genome editing technologies.
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Grants
- KGM5282322, KGM4562323, KGM5382221 the Korea Research Institute of Bioscience and Biotechnology (KRIBB; Research Initiative Program)
- KGM5282322, KGM4562323, KGM5382221 the Korea Research Institute of Bioscience and Biotechnology (KRIBB; Research Initiative Program)
- KGM5282322, KGM4562323, KGM5382221 the Korea Research Institute of Bioscience and Biotechnology (KRIBB; Research Initiative Program)
- 2022R1A2C4001609, 2020R1C1C1010869, 2021M3A9I4024452 Korean Ministry of Education, Science and Technology
- 2022R1A2C4001609, 2020R1C1C1010869, 2021M3A9I4024452 Korean Ministry of Education, Science and Technology
- 2022R1A2C4001609, 2020R1C1C1010869, 2021M3A9I4024452 Korean Ministry of Education, Science and Technology
- (22A0203L1) the Korean Fund for Regenerative Medicine (KFRM) grant funded by the Korea government (the Ministry of Science and ICT, the Ministry of Health & Welfare).
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Affiliation(s)
- Chan Hyoung Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Wi-Jae Lee
- 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
| | - Youngjeon Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Hyomin K Lee
- Department of Medicine, Major in Medical Genetics, Graduate School, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jung Bae Seong
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
| | - Kyung-Seob Lim
- Futuristic Animal Resource and Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Sang Je Park
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
| | - Kyoung Mi Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea.
| | - Junho K Hur
- Department of Genetics, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea.
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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14
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Nguyen GT, Schelling MA, Buscher KA, Sritharan A, Sashital DG. CRISPR-Cas12a exhibits metal-dependent specificity switching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.29.569287. [PMID: 38076861 PMCID: PMC10705449 DOI: 10.1101/2023.11.29.569287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Cas12a is the immune effector of type V-A CRISPR-Cas systems and has been co-opted for genome editing and other biotechnology tools. The specificity of Cas12a has been the subject of extensive investigation both in vitro and in genome editing experiments. However, in vitro studies have often been performed at high magnesium ion concentrations that are inconsistent with the free Mg2+ concentrations that would be present in cells. By profiling the specificity of Cas12a orthologs at a range of Mg2+ concentrations, we find that Cas12a switches its specificity depending on metal ion concentration. Lowering Mg2+ concentration decreases cleavage defects caused by seed mismatches, while increasing the defects caused by PAM-distal mismatches. We show that Cas12a can bind seed mutant targets more rapidly at low Mg2+ concentrations, resulting in faster cleavage. In contrast, PAM-distal mismatches cause substantial defects in cleavage following formation of the Cas12a-target complex at low Mg2+ concentrations. We observe differences in Cas12a specificity switching between three orthologs that results in variations in the routes of phage escape from Cas12a-mediated immunity. Overall, our results reveal the importance of physiological metal ion conditions on the specificity of Cas effectors that are used in different cellular environments.
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Affiliation(s)
- Giang T. Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Equal contribution
| | - Michael A. Schelling
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Equal contribution
| | - Kathryn A. Buscher
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Current address: Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aneisha Sritharan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Current address: Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dipali G. Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
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15
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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: 0] [Impact Index Per Article: 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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16
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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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17
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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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18
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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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19
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Avaro AS, Santiago JG. A critical review of microfluidic systems for CRISPR assays. LAB ON A CHIP 2023; 23:938-963. [PMID: 36601854 DOI: 10.1039/d2lc00852a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Reviewed are nucleic acid detection assays that incorporate clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics and microfluidic devices and techniques. The review serves as a reference for researchers who wish to use CRISPR-Cas systems for diagnostics in microfluidic devices. The review is organized in sections reflecting a basic five-step workflow common to most CRISPR-based assays. These steps are analyte extraction, pre-amplification, target recognition, transduction, and detection. The systems described include custom microfluidic chips and custom (benchtop) chip control devices for automated assays steps. Also included are partition formats for digital assays and lateral flow biosensors as a readout modality. CRISPR-based, microfluidics-driven assays offer highly specific detection and are compatible with parallel, combinatorial implementation. They are highly reconfigurable, and assays are compatible with isothermal and even room temperature operation. A major drawback of these assays is the fact that reports of kinetic rates of these enzymes have been highly inconsistent (many demonstrably erroneous), and the low kinetic rate activity of these enzymes limits achievable sensitivity without pre-amplification. Further, the current state-of-the-art of CRISPR assays is such that nearly all systems rely on off-chip assays steps, particularly off-chip sample preparation.
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Affiliation(s)
- Alexandre S Avaro
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA.
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20
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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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21
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Ma E, Chen K, Shi H, Stahl EC, Adler B, Trinidad M, Liu J, Zhou K, Ye J, Doudna J. Improved genome editing by an engineered CRISPR-Cas12a. Nucleic Acids Res 2022; 50:12689-12701. [PMID: 36537251 PMCID: PMC9825149 DOI: 10.1093/nar/gkac1192] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2-18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.
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Affiliation(s)
- Enbo Ma
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kai Chen
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Ben Adler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Junjie Liu
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kaihong Zhou
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jinjuan Ye
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Gladstone Institutes, University of California, San Francisco, CA 94114, USA
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22
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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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23
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Hall PM, Inman JT, Fulbright RM, Le TT, Brewer JJ, Lambert G, Darst SA, Wang MD. Polarity of the CRISPR roadblock to transcription. Nat Struct Mol Biol 2022; 29:1217-1227. [PMID: 36471058 PMCID: PMC9758054 DOI: 10.1038/s41594-022-00864-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/12/2022] [Indexed: 12/12/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) utility relies on a stable Cas effector complex binding to its target site. However, a Cas complex bound to DNA may be removed by motor proteins carrying out host processes and the mechanism governing this removal remains unclear. Intriguingly, during CRISPR interference, RNA polymerase (RNAP) progression is only fully blocked by a bound endonuclease-deficient Cas (dCas) from the protospacer adjacent motif (PAM)-proximal side. By mapping dCas-DNA interactions at high resolution, we discovered that the collapse of the dCas R-loop allows Escherichia coli RNAP read-through from the PAM-distal side for both Sp-dCas9 and As-dCas12a. This finding is not unique to RNAP and holds for the Mfd translocase. This mechanistic understanding allowed us to modulate the dCas R-loop stability by modifying the guide RNAs. This work highlights the importance of the R-loop in dCas-binding stability and provides valuable mechanistic insights for broad applications of CRISPR technology.
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Affiliation(s)
- Porter M Hall
- Biophysics Program, Cornell University, Ithaca, NY, USA
| | - James T Inman
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
| | - Robert M Fulbright
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
| | - Tung T Le
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
| | - Joshua J Brewer
- Laboratory of Molecular Biophysics, Rockefeller University, New York, NY, USA
| | - Guillaume Lambert
- Department of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, Rockefeller University, New York, NY, USA
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA.
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA.
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24
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Wang JY, Pausch P, Doudna JA. Structural biology of CRISPR-Cas immunity and genome editing enzymes. Nat Rev Microbiol 2022; 20:641-656. [PMID: 35562427 DOI: 10.1038/s41579-022-00739-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2022] [Indexed: 12/20/2022]
Abstract
CRISPR-Cas systems provide resistance against foreign mobile genetic elements and have a wide range of genome editing and biotechnological applications. In this Review, we examine recent advances in understanding the molecular structures and mechanisms of enzymes comprising bacterial RNA-guided CRISPR-Cas immune systems and deployed for wide-ranging genome editing applications. We explore the adaptive and interference aspects of CRISPR-Cas function as well as open questions about the molecular mechanisms responsible for genome targeting. These structural insights reflect close evolutionary links between CRISPR-Cas systems and mobile genetic elements, including the origins and evolution of CRISPR-Cas systems from DNA transposons, retrotransposons and toxin-antitoxin modules. We discuss how the evolution and structural diversity of CRISPR-Cas systems explain their functional complexity and utility as genome editing tools.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick Pausch
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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25
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Wörle E, Newman A, D’Silva J, Burgio G, Grohmann D. Allosteric activation of CRISPR-Cas12a requires the concerted movement of the bridge helix and helix 1 of the RuvC II domain. Nucleic Acids Res 2022; 50:10153-10168. [PMID: 36107767 PMCID: PMC9508855 DOI: 10.1093/nar/gkac767] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/19/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Nucleases derived from the prokaryotic defense system CRISPR-Cas are frequently re-purposed for gene editing and molecular diagnostics. Hence, an in-depth understanding of the molecular mechanisms of these enzymes is of crucial importance. We focused on Cas12a from Francisella novicida (FnCas12a) and investigated the functional role of helix 1, a structural element that together with the bridge helix (BH) connects the recognition and the nuclease lobes of FnCas12a. Helix 1 is structurally connected to the lid domain that opens upon DNA target loading thereby activating the active site of FnCas12a. We probed the structural states of FnCas12a variants altered in helix 1 and/or the bridge helix using single-molecule FRET measurements and assayed the pre-crRNA processing, cis- and trans-DNA cleavage activity. We show that helix 1 and not the bridge helix is the predominant structural element that confers conformational stability of FnCas12a. Even small perturbations in helix 1 lead to a decrease in DNA cleavage activity while the structural integrity is not affected. Our data, therefore, implicate that the concerted remodeling of helix 1 and the bridge helix upon DNA binding is structurally linked to the opening of the lid and therefore involved in the allosteric activation of the active site.
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Affiliation(s)
- Elisabeth Wörle
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Anthony Newman
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Jovita D’Silva
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Gaetan Burgio
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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26
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Naqvi MM, Lee L, Montaguth OET, Diffin FM, Szczelkun MD. CRISPR-Cas12a-mediated DNA clamping triggers target-strand cleavage. Nat Chem Biol 2022; 18:1014-1022. [PMID: 35836018 PMCID: PMC9395263 DOI: 10.1038/s41589-022-01082-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/08/2022] [Indexed: 01/19/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a is widely used for genome editing and diagnostics, so it is important to understand how RNA-guided DNA recognition activates the cleavage of the target strand (TS) following non-target-strand (NTS) cleavage. Here we used single-molecule magnetic tweezers, gel-based assays and nanopore sequencing to explore DNA unwinding and cleavage. In addition to dynamic and heterogenous R-loop formation, we also directly observed transient double-stranded DNA unwinding downstream of the 20-bp heteroduplex and, following NTS cleavage, formation of a hyperstable 'clamped' Cas12a-DNA intermediate necessary for TS cleavage. Annealing of a 4-nucleotide 3' CRISPR RNA overhang to the unwound TS downstream of the heteroduplex inhibited clamping and slowed TS cleavage by ~16-fold. Alanine substitution of a conserved aromatic amino acid in the REC2 subdomain that normally caps the R-loop relieved this inhibition but favoured stabilisation of unwound states, suggesting that the REC2 subdomain regulates access of the 3' CRISPR RNA to downstream DNA.
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Affiliation(s)
- Mohsin M Naqvi
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Laura Lee
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Oscar E Torres Montaguth
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, UK.
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27
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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28
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Huyke DA, Ramachandran A, Bashkirov VI, Kotseroglou EK, Kotseroglou T, Santiago JG. Enzyme Kinetics and Detector Sensitivity Determine Limits of Detection of Amplification-Free CRISPR-Cas12 and CRISPR-Cas13 Diagnostics. Anal Chem 2022; 94:9826-9834. [PMID: 35759403 DOI: 10.1021/acs.analchem.2c01670] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Interest in CRISPR-Cas12 and CRISPR-Cas13 detection continues to increase as these detection schemes enable the specific recognition of nucleic acids. The fundamental sensitivity limits of these schemes (and their applicability in amplification-free assays) are governed by kinetic rates. However, these kinetic rates remain poorly understood, and their reporting has been inconsistent. We quantify kinetic parameters for several enzymes (LbCas12a, AsCas12a, AapCas12b, LwaCas13a, and LbuCas13a) and their corresponding limits of detection (LoD). Collectively, we present quantification of enzyme kinetics for 14 guide RNAs (gRNAs) and nucleic acid targets for a total of 50 sets of kinetic rate parameters and 25 LoDs. We validate the self-consistency of our measurements by comparing trends and limiting behaviors with a Michaelis-Menten trans-cleavage reaction kinetics model. For our assay conditions, activated Cas12 and Cas13 enzymes exhibit trans-cleavage catalytic efficiencies between order 105 and 106 M-1 s-1. For assays that use fluorescent reporter molecules (ssDNA and ssRNA) for target detection, the kinetic rates at the current assay conditions result in an amplification-free LoD in the picomolar range. The results suggest that successful detection of target requires cleavage (by an activated CRISPR enzyme) of the order of at least 0.1% of the fluorescent reporter molecules. This fraction of reporters cleaved is required to differentiate the signal from the background, and we hypothesize that this required fraction is largely independent of the detection method (e.g., endpoint vs reaction velocity) and detector sensitivity. Our results demonstrate the fundamental nature by which kinetic rates and background signal limit LoDs and thus highlight areas of improvement for the emerging field of CRISPR diagnostics.
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Affiliation(s)
- Diego A Huyke
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ashwin Ramachandran
- Department of Aeronautics & Astronautics, Stanford University, Stanford, California 94305, United States
| | | | | | | | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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29
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Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
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Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
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30
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Huang CJ, Adler BA, Doudna JA. A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression. Mol Cell 2022; 82:2148-2160.e4. [PMID: 35659325 DOI: 10.1016/j.molcel.2022.04.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/14/2022] [Accepted: 04/14/2022] [Indexed: 12/26/2022]
Abstract
Used widely for genome editing, CRISPR-Cas enzymes provide RNA-guided immunity to microbes by targeting foreign nucleic acids for cleavage. We show here that the native activity of CRISPR-Cas12c protects bacteria from phage infection by binding to DNA targets without cleaving them, revealing that antiviral interference can be accomplished without chemical attack on the invader or general metabolic disruption in the host. Biochemical experiments demonstrate that Cas12c is a site-specific ribonuclease capable of generating mature CRISPR RNAs (crRNAs) from precursor transcripts. Furthermore, we find that crRNA maturation is essential for Cas12c-mediated DNA targeting. These crRNAs direct double-stranded DNA binding by Cas12c using a mechanism that precludes DNA cutting. Nevertheless, Cas12c represses transcription and can defend bacteria against lytic bacteriophage infection when targeting an essential phage gene. Together, these results show that Cas12c employs targeted DNA binding to provide antiviral immunity in bacteria, providing a native DNase-free pathway for transient antiviral immunity.
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Affiliation(s)
- Carolyn J Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin A Adler
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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31
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Kim H, Lee WJ, Kim CH, Oh Y, Gwon LW, Lee H, Song W, Hur JK, Lim KS, Jeong KJ, Nam KH, Won YS, Lee KR, Lee Y, Kim YH, Huh JW, Jun BH, Lee DS, Lee SH. Highly specific chimeric DNA-RNA-guided genome editing with enhanced CRISPR-Cas12a system. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:353-362. [PMID: 35505967 PMCID: PMC9035383 DOI: 10.1016/j.omtn.2022.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/27/2022] [Indexed: 12/02/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a system is composed of a Cas12a effector that acts as a DNA-cleaving endonuclease and a crispr RNA (crRNA) that guides the effector to the target DNA. It is considered a key molecule for inducing target-specific gene editing in various living systems. Here, we improved the efficiency and specificity of the CRISPR-Cas12a system through protein and crRNA engineering. In particular, to optimize the CRISPR-Cas12a system at the molecular level, we used a chimeric DNA-RNA guide chemically similar to crRNA to maximize target sequence specificity. Compared with the wild-type (wt)-Cas12a system, when using enhanced Cas12a system (en-Cas12a), the efficiency and target specificity improved on average by 2.58 and 2.77 times, respectively. In our study, when the chimeric DNA-RNA-guided en-Cas12a effector was used, the gene-editing efficiency and accuracy were simultaneously increased. These findings could contribute to highly accurate genome editing, such as human gene therapy, in the near future.
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32
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McGaw C, Garrity AJ, Munoz GZ, Haswell JR, Sengupta S, Keston-Smith E, Hunnewell P, Ornstein A, Bose M, Wessells Q, Jakimo N, Yan P, Zhang H, Alfonse LE, Ziblat R, Carte JM, Lu WC, Cerchione D, Hilbert B, Sothiselvam S, Yan WX, Cheng DR, Scott DA, DiTommaso T, Chong S. Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing. Nat Commun 2022; 13:2833. [PMID: 35595757 PMCID: PMC9122993 DOI: 10.1038/s41467-022-30465-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
The CRISPR-Cas type V-I is a family of Cas12i-containing programmable nuclease systems guided by a short crRNA without requirement for a tracrRNA. Here we present an engineered Type V-I CRISPR system (Cas12i), ABR-001, which utilizes a tracr-less guide RNA. The compact Cas12i effector is capable of self-processing pre-crRNA and cleaving dsDNA targets, which facilitates versatile delivery options and multiplexing, respectively. We apply an unbiased mutational scanning approach to enhance initially low editing activity of Cas12i2. The engineered variant, ABR-001, exhibits broad genome editing capability in human cell lines, primary T cells, and CD34+ hematopoietic stem and progenitor cells, with both robust efficiency and high specificity. In addition, ABR-001 achieves a high level of genome editing when delivered via AAV vector to HEK293T cells. This work establishes ABR-001 as a versatile, specific, and high-performance platform for ex vivo and in vivo gene therapy.
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Affiliation(s)
- Colin McGaw
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Anthony J Garrity
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Gabrielle Z Munoz
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Jeffrey R Haswell
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Sejuti Sengupta
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Elise Keston-Smith
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | | | - Alexa Ornstein
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Mishti Bose
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Quinton Wessells
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Noah Jakimo
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Paul Yan
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Huaibin Zhang
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Lauren E Alfonse
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Roy Ziblat
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Jason M Carte
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Wei-Cheng Lu
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Derek Cerchione
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Brendan Hilbert
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | | | - Winston X Yan
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - David R Cheng
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - David A Scott
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Tia DiTommaso
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA.
| | - Shaorong Chong
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
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33
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Cofsky JC, Knott GJ, Gee CL, Doudna JA. Crystal structure of an RNA/DNA strand exchange junction. PLoS One 2022; 17:e0263547. [PMID: 35436289 PMCID: PMC9015157 DOI: 10.1371/journal.pone.0263547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/29/2022] Open
Abstract
Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types-an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5'/DNA-3' strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.
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Affiliation(s)
- Joshua C. Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Gavin J. Knott
- Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christine L. Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
- Gladstone Institutes, University of California, San Francisco, San Francisco, California, United States of America
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34
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Fuchs RT, Curcuru JL, Mabuchi M, Noireterre A, Weigele PR, Sun Z, Robb GB. Characterization of Cme and Yme thermostable Cas12a orthologs. Commun Biol 2022; 5:325. [PMID: 35388146 PMCID: PMC8986864 DOI: 10.1038/s42003-022-03275-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR-Cas12a proteins are RNA-guided endonucleases that cleave invading DNA containing target sequences adjacent to protospacer adjacent motifs (PAM). Cas12a orthologs have been repurposed for genome editing in non-native organisms by reprogramming them with guide RNAs to target specific sites in genomic DNA. After single-turnover dsDNA target cleavage, multiple-turnover, non-specific single-stranded DNA cleavage in trans is activated. This property has been utilized to develop in vitro assays to detect the presence of specific DNA target sequences. Most applications of Cas12a use one of three well-studied enzymes. Here, we characterize the in vitro activity of two previously unknown Cas12a orthologs. These enzymes are active at higher temperatures than widely used orthologs and have subtle differences in PAM preference, on-target cleavage, and trans nuclease activity. Together, our results enable refinement of Cas12a-based in vitro assays especially when elevated temperature is desirable.
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Affiliation(s)
- Ryan T Fuchs
- New England Biolabs Inc, Ipswich, MA, 01938, USA
| | | | | | - Audrey Noireterre
- New England Biolabs Inc, Ipswich, MA, 01938, USA
- Département de Biologie Cellulaire (BICEL), Université de Genève, CH - 1211, Genève 4, Switzerland
| | | | - Zhiyi Sun
- New England Biolabs Inc, Ipswich, MA, 01938, USA
| | - G Brett Robb
- New England Biolabs Inc, Ipswich, MA, 01938, USA.
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35
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Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA. CRISPR-Cas9 bends and twists DNA to read its sequence. Nat Struct Mol Biol 2022; 29:395-402. [PMID: 35422516 PMCID: PMC9189902 DOI: 10.1038/s41594-022-00756-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/01/2022] [Indexed: 12/28/2022]
Abstract
In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that Cas9 sharply bends and undertwists DNA on PAM binding, thereby flipping DNA nucleotides out of the duplex and toward the guide RNA for sequence interrogation. Cryogenic-electron microscopy (cryo-EM) structures of Cas9-RNA-DNA complexes trapped at different states of the interrogation pathway, together with solution conformational probing, reveal that global protein rearrangement accompanies formation of an unstacked DNA hinge. Bend-induced base flipping explains how Cas9 'reads' snippets of DNA to locate target sites within a vast excess of nontarget DNA, a process crucial to both bacterial antiviral immunity and genome editing. This mechanism establishes a physical solution to the problem of complementarity-guided DNA search and shows how interrogation speed and local DNA geometry may influence genome editing efficiency.
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Affiliation(s)
- Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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36
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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37
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Nguyen LT, Macaluso NC, Pizzano BLM, Cash MN, Spacek J, Karasek J, Miller MR, Lednicky JA, Dinglasan RR, Salemi M, Jain PK. A thermostable Cas12b from Brevibacillus leverages one-pot discrimination of SARS-CoV-2 variants of concern. EBioMedicine 2022; 77:103926. [PMID: 35290826 PMCID: PMC8917962 DOI: 10.1016/j.ebiom.2022.103926] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Current SARS-CoV-2 detection platforms lack the ability to differentiate among variants of concern (VOCs) in an efficient manner. CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated) based detection systems have the potential to transform the landscape of COVID-19 diagnostics due to their programmability; however, most of these methods are reliant on either a multi-step process involving amplification or elaborate guide RNA designs. METHODS Three Cas12b proteins from Alicyclobacillus acidoterrestris (AacCas12b), Alicyclobacillus acidiphilus (AapCas12b), and Brevibacillus sp. SYP-B805 (BrCas12b) were expressed and purified, and their thermostability was characterised by differential scanning fluorimetry, cis-, and trans-cleavage activities over a range of temperatures. The BrCas12b was then incorporated into a reverse transcription loop-mediated isothermal amplification (RT-LAMP)-based one-pot reaction system, coined CRISPR-SPADE (CRISPR Single Pot Assay for Detecting Emerging VOCs). FINDINGS Here we describe a complete one-pot detection reaction using a thermostable Cas12b effector endonuclease from Brevibacillus sp. to overcome these challenges detecting and discriminating SARS-CoV-2 VOCs in clinical samples. CRISPR-SPADE was then applied for discriminating SARS-CoV-2 VOCs, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) and validated in 208 clinical samples. CRISPR-SPADE achieved 92·8% sensitivity, 99·4% specificity, and 96·7% accuracy within 10-30 min for discriminating the SARS-CoV-2 VOCs, in agreement with S gene sequencing, achieving a positive and negative predictive value of 99·1% and 95·1%, respectively. Interestingly, for samples with high viral load (Ct value ≤ 30), 100% accuracy and sensitivity were attained. To facilitate dissemination and global implementation of the assay, a lyophilised version of one-pot CRISPR-SPADE reagents was developed and combined with an in-house portable multiplexing device capable of interpreting two orthogonal fluorescence signals. INTERPRETATION This technology enables real-time monitoring of RT-LAMP-mediated amplification and CRISPR-based reactions at a fraction of the cost of a qPCR system. The thermostable Brevibacillus sp. Cas12b offers relaxed primer design for accurately detecting SARS-CoV-2 VOCs in a simple and robust one-pot assay. The lyophilised reagents and simple instrumentation further enable rapid deployable point-of-care diagnostics that can be easily expanded beyond COVID-19. FUNDING This project was funded in part by the United States-India Science & Technology Endowment Fund- COVIDI/247/2020 (P.K.J.), Florida Breast Cancer Foundation- AGR00018466 (P.K.J.), National Institutes of Health- NIAID 1R21AI156321-01 (P.K.J.), Centers for Disease Control and Prevention- U01GH002338 (R.R.D., J.A.L., & P.K.J.), University of Florida, Herbert Wertheim College of Engineering (P.K.J.), University of Florida Vice President Office of Research and CTSI seed funds (M.S.), and University of Florida College of Veterinary Medicine and Emerging Pathogens Institute (R.R.D.).
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Affiliation(s)
- Long T Nguyen
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Nicolas C Macaluso
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Brianna L M Pizzano
- Department of Agricultural and Biological Engineering, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, USA
| | - Melanie N Cash
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Jan Spacek
- Sparsek S.R.O., Příkop 838/6, Zábrdovice, Brno 60200, Czech Republic
| | - Jan Karasek
- SCIERING S.R.O., Příkop 838/6, Zábrdovice, Brno 62100, Czech Republic
| | - Megan R Miller
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - John A Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Rhoel R Dinglasan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Piyush K Jain
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
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38
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Son H, Park J, Choi YH, Jung Y, Lee JW, Bae S, Lee S. Exploring the dynamic nature of divalent metal ions involved in DNA cleavage by CRISPR-Cas12a. Chem Commun (Camb) 2022; 58:1978-1981. [PMID: 35045150 DOI: 10.1039/d1cc04446j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12a has been widely used in genome editing and nucleic acid detection. In both of these applications, Cas12a cleaves target DNA in a divalent metal ion-dependent manner. However, when and how metal ions contribute to the cleavage reaction is unclear. Here, using a single-molecule FRET assay, we reveal that these metal ions are necessary for stabilising cleavage-competent conformations and that they are easily exchangeable, suggesting that they are dynamically coordinated.
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Affiliation(s)
- Heyjin Son
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
| | - Jaeil Park
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea. .,Department of Physics and Optoelectronics Convergence Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - You Hee Choi
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea. .,Ministry of Food and Drug Safety (MFDS), Cheongju 28159, Republic of Korea
| | - Youngri Jung
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Joong-Wook Lee
- Department of Physics and Optoelectronics Convergence Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
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39
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Fu R, He W, Dou J, Villarreal OD, Bedford E, Wang H, Hou C, Zhang L, Wang Y, Ma D, Chen Y, Gao X, Depken M, Xu H. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Nat Commun 2022; 13:474. [PMID: 35078987 PMCID: PMC8789861 DOI: 10.1038/s41467-022-28028-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022] Open
Abstract
The specificity of CRISPR/Cas9 genome editing is largely determined by the sequences of guide RNA (gRNA) and the targeted DNA, yet the sequence-dependent rules underlying off-target effects are not fully understood. To systematically explore the sequence determinants governing CRISPR/Cas9 specificity, here we describe a dual-target system to measure the relative cleavage rate between off- and on-target sequences (off-on ratios) of 1902 gRNAs on 13,314 synthetic target sequences, and reveal a set of sequence rules involving 2 factors in off-targeting: 1) a guide-intrinsic mismatch tolerance (GMT) independent of the mismatch context; 2) an "epistasis-like" combinatorial effect of multiple mismatches, which are associated with the free-energy landscape in R-loop formation and are explainable by a multi-state kinetic model. These sequence rules lead to the development of MOFF, a model-based predictor of Cas9-mediated off-target effects. Moreover, the "epistasis-like" combinatorial effect suggests a strategy of allele-specific genome editing using mismatched guides. With the aid of MOFF prediction, this strategy significantly improves the selectivity and expands the application domain of Cas9-based allele-specific editing, as tested in a high-throughput allele-editing screen on 18 cancer hotspot mutations.
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Affiliation(s)
- Rongjie Fu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Jinzhuang Dou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Oscar D Villarreal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Ella Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Helen Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Connie Hou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Liang Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Dacheng Ma
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Martin Depken
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands
| | - Han Xu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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40
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Inconsistent treatments of the kinetics of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) impair assessment of its diagnostic potential. QRB DISCOVERY 2022. [PMID: 37529278 PMCID: PMC10392624 DOI: 10.1017/qrd.2022.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
The scientific and technological advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is one of the most exciting developments of the past decade, particularly in the field of gene editing. The technology has two essential components, (1) a guide RNA to match a targeted gene and (2) a CRISPR-associated protein (e.g. Cas 9, Cas12 or Cas13) that acts as an endonuclease to specifically cut DNA. This specificity and reconfigurable nature of CRISPR has also spurred intense academic and commercial interest in the development of CRISPR-based molecular diagnostics. CRISPR Cas12 and Cas13 orthologs are most commonly applied to diagnostics, and these cleave and become activated by DNA and RNA targets, respectively. Despite the intense research interest, the limits of detection (LoDs) and applications of CRISP-based diagnostics remain an open question. A major reason for this is that reports of kinetic rates have been widely inconsistent, and the vast majority of these reports contain gross errors including violations of basic conservation and kinetic rate laws. It is the intent of this Perspective to bring attention to these issues and to identify potential improvements in the manner in which CRISPR kinetic rates and assay LoDs are reported and compared. The CRISPR field would benefit from verifications of self-consistency of data, providing sufficient data for reproduction of experiments, and, in the case of reports of novel assay LoDs, concurrent reporting of the associated kinetic rate constants. The early development of CRISPR-based diagnostics calls for self-reflection and urges us to proceed with caution.
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Zhang F, Huang Z. Mechanistic insights into the versatile class II CRISPR toolbox. Trends Biochem Sci 2021; 47:433-450. [PMID: 34920928 DOI: 10.1016/j.tibs.2021.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
The constantly expanding group of class II CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated) effectors and their engineered variants exhibit distinct editing modes and efficiency, fidelity, target range, and molecular size. Their enormous diversity of capabilities provides a formidable toolkit for a large array of technologies. We review the structural and biochemical mechanisms of versatile effector proteins from class II CRISPR-Cas systems to provide mechanistic insights into their target specificity, protospacer adjacent motif (PAM) restriction, and activity regulation, and discuss possible strategies to enhance genome-engineering tools in terms of accuracy, efficiency, applicability, and controllability.
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Affiliation(s)
- Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China.
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42
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Son H, Park J, Hwang I, Jung Y, Bae S, Lee S. Mg 2+-dependent conformational rearrangements of CRISPR-Cas12a R-loop complex are mandatory for complete double-stranded DNA cleavage. Proc Natl Acad Sci U S A 2021; 118:e2113747118. [PMID: 34853172 PMCID: PMC8670479 DOI: 10.1073/pnas.2113747118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas12a, an RNA-guided DNA targeting endonuclease, has been widely used for genome editing and nucleic acid detection. As part of the essential processes for both of these applications, the two strands of double-stranded DNA are sequentially cleaved by a single catalytic site of Cas12a, but the mechanistic details that govern the generation of complete breaks in double-stranded DNA remain to be elucidated. Here, using single-molecule fluorescence resonance energy transfer assay, we identified two conformational intermediates that form consecutively following the initial cleavage of the nontarget strand. Specifically, these two intermediates are the result of further unwinding of the target DNA in the protospacer-adjacent motif (PAM)-distal region and the subsequent binding of the target strand to the catalytic site. Notably, the PAM-distal DNA unwound conformation was stabilized by Mg2+ ions, thereby significantly promoting the binding and cleavage of the target strand. These findings enabled us to propose a Mg2+-dependent kinetic model for the mechanism whereby Cas12a achieves cleavage of the target DNA, highlighting the presence of conformational rearrangements for the complete cleavage of the double-stranded DNA target.
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Affiliation(s)
- Heyjin Son
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jaeil Park
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Injoo Hwang
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Youngri Jung
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea;
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43
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Tang Y, Gao L, Feng W, Guo C, Yang Q, Li F, Le XC. The CRISPR-Cas toolbox for analytical and diagnostic assay development. Chem Soc Rev 2021; 50:11844-11869. [PMID: 34611682 DOI: 10.1039/d1cs00098e] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems have revolutionized biological and biomedical sciences in many ways. The last few years have also seen tremendous interest in deploying the CRISPR-Cas toolbox for analytical and diagnostic assay development because CRISPR-Cas is one of the most powerful classes of molecular machineries for the recognition and manipulation of nucleic acids. In the short period of development, many CRISPR-enabled assays have already established critical roles in clinical diagnostics, biosensing, and bioimaging. We describe in this review the recent advances and design principles of CRISPR mediated analytical tools with an emphasis on the functional roles of CRISPR-Cas machineries as highly efficient binders and molecular scissors. We highlight the diverse engineering approaches for molecularly modifying CRISPR-Cas machineries and for devising better readout platforms. We discuss the potential roles of these new approaches and platforms in enhancing assay sensitivity, specificity, multiplexity, and clinical outcomes. By illustrating the biochemical and analytical processes, we hope this review will help guide the best use of the CRISPR-Cas toolbox in detecting, quantifying and imaging biologically and clinically important molecules and inspire new ideas, technological advances and engineering strategies for addressing real-world challenges such as the on-going COVID-19 pandemic.
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Affiliation(s)
- Yanan Tang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Lu Gao
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Wei Feng
- Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Chen Guo
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Qianfan Yang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Feng Li
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China. .,Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, T6G 2G3, Canada
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44
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Nguyen LT, Macaluso NC, Pizzano BLM, Cash MN, Spacek J, Karasek J, Dinglasan RR, Salemi M, Jain PK. A Thermostable Cas12b from Brevibacillus Leverages One-pot Detection of SARS-CoV-2 Variants of Concern. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.10.15.21265066. [PMID: 34704101 PMCID: PMC8547533 DOI: 10.1101/2021.10.15.21265066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Current SARS-CoV-2 detection platforms lack the ability to differentiate among variants of concern (VOCs) in an efficient manner. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) has the potential to transform diagnostics due to its programmability. However, many of the CRISPR-based detection methods are reliant on either a multi-step process involving amplification or elaborate guide RNA designs. A complete one-pot detection reaction using alternative Cas effector endonucleases has been proposed to overcome these challenges. Yet, current approaches using Alicyclobacillus acidiphilus Cas12b (AapCas12b) are limited by its thermal instability at optimum reverse transcription loop-mediated isothermal amplification (RT-LAMP) reaction temperatures. Herein, we demonstrate that a novel Cas12b from Brevibacillus sp. SYP-B805 (referred to as BrCas12b) has robust trans-cleavage activity at ideal RT-LAMP conditions. A competitive profiling study of BrCas12b against Cas12b homologs from other bacteria genera underscores the potential of BrCas12b in the development of new diagnostics. As a proof-of-concept, we incorporated BrCas12b into an RT-LAMP-mediated one-pot reaction system, coined CRISPR-SPADE (CRISPR Single Pot Assay for Detecting Emerging VOCs) to enable rapid, differential detection of SARS-CoV-2 VOCs, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) in 205 clinical samples. Notably, a BrCas12b detection signal was observed within 1-3 minutes of amplification, achieving an overall 98.1% specificity, 91.2% accuracy, and 88.1% sensitivity within 30 minutes. Significantly, for samples with high viral load (C t value ≤ 30), 100% accuracy and sensitivity were attained. To facilitate dissemination and global implementation of the assay, we combined the lyophilized one-pot reagents with a portable multiplexing device capable of interpreting fluorescence signals at a fraction of the cost of a qPCR system. With relaxed design requirements, one-pot detection, and simple instrumentation, this assay has the capability to advance future diagnostics.
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45
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Wu Y, Yuan Q, Zhu Y, Gao X, Song J, Yin Z. Improving FnCas12a Genome Editing by Exonuclease Fusion. CRISPR J 2021; 3:503-511. [PMID: 33346706 DOI: 10.1089/crispr.2020.0073] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Among current reported Cas12a orthologs, Francisella novicida Cas12a (FnCas12a) is less restricted by protospacer adjacent motif (PAM). However, the activity of FnCas12a nuclease is relatively low or undetectable in human cells, limiting its application as desirable genome engineering tools. Here, we describe TEXT (Tethering EXonuclease T5 with FnCas12a)-a fusion strategy that significantly increased the knockout efficiency of FnCas12a in human cells at multiple genomic loci in three different cell lines. TEXT results in higher insertion and deletion efficiency than FnCas12a under different spacer lengths from 18 nt to 23 nt. Deep sequencing shows that TEXT substantially increased the deletion frequency and deletion size at the targeted locus. Compared to other Cas12a orthologs, including AsCas12a and LbCas12a, TEXT achieves the highest on-targeting efficiency and shows minimal off-targeting effects at all tested sites. TEXT enhances the activity of FnCas12a nuclease and expands its targeting scope and efficiency in human cell genome engineering.
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Affiliation(s)
- Yongqiang Wu
- Gene Editing Research Center, Hebei University of Science and Technology, Shijiazhuang, PR China; Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Qichen Yuan
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA; Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Yufeng Zhu
- Institute for Science and Technology Development, Hebei University of Science and Technology, Shijiazhuang, PR China; Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Xiang Gao
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China; Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Jiabao Song
- Department of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang, China; and Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Ziru Yin
- Periodical Press, Hebei University of Science and Technology, Shijiazhuang, PR China
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46
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Nalefski EA, Patel N, Leung PJY, Islam Z, Kooistra RM, Parikh I, Marion E, Knott GJ, Doudna JA, Le Ny ALM, Madan D. Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics. iScience 2021; 24:102996. [PMID: 34505008 PMCID: PMC8411246 DOI: 10.1016/j.isci.2021.102996] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 07/14/2021] [Accepted: 08/13/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial CRISPR systems provide acquired immunity against invading nucleic acids by activating RNA-programmable RNases and DNases. Cas13a and Cas12a enzymes bound to CRISPR RNA (crRNA) recognize specific nucleic acid targets, initiating cleavage of the targets as well as non-target (trans) nucleic acids. Here, we examine the kinetics of single-turnover target and multi-turnover trans-nuclease activities of both enzymes. High-turnover, non-specific Cas13a trans-RNase activity is coupled to rapid binding of target RNA. By contrast, low-turnover Cas12a trans-nuclease activity is coupled to relatively slow cleavage of target DNA, selective for DNA over RNA, indifferent to base identity, and preferential for single-stranded substrates. Combining multiple crRNA increases detection sensitivity of targets, an approach we use to quantify pathogen DNA in samples from patients suspected of Buruli ulcer disease. Results reveal that these enzymes are kinetically adapted to play distinct roles in bacterial adaptive immunity and show how kinetic analysis can be applied to CRISPR-based diagnostics. Cas13a HEPN trans-RNase activation is directly coupled to rapid target RNA binding Cas12a RuvC trans-nuclease activity is coupled to slow target DNA cleavage Individual crRNA generate widely varying levels of targeted trans-cleavage Pooling multiple crRNA allows pathogen quantification without target amplification
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Affiliation(s)
- Eric A Nalefski
- Global Health Labs, Bellevue, WA 98007, USA.,Center for In Vitro Diagnostics, Intellectual Ventures Global Good Fund, Bellevue, WA 98007, USA
| | | | - Philip J Y Leung
- Global Health Labs, Bellevue, WA 98007, USA.,Center for In Vitro Diagnostics, Intellectual Ventures Global Good Fund, Bellevue, WA 98007, USA
| | - Zeba Islam
- Global Health Labs, Bellevue, WA 98007, USA
| | - Remy M Kooistra
- Global Health Labs, Bellevue, WA 98007, USA.,Center for In Vitro Diagnostics, Intellectual Ventures Global Good Fund, Bellevue, WA 98007, USA
| | | | | | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94704, USA.,Monash Biomedicine Discovery Institute, Department of Chemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94704, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94704, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94704, USA.,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Anne-Laure M Le Ny
- Global Health Labs, Bellevue, WA 98007, USA.,Center for In Vitro Diagnostics, Intellectual Ventures Global Good Fund, Bellevue, WA 98007, USA
| | - Damian Madan
- Global Health Labs, Bellevue, WA 98007, USA.,Center for In Vitro Diagnostics, Intellectual Ventures Global Good Fund, Bellevue, WA 98007, USA
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47
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Verosloff MS, Shapiro SJ, Hawkins EM, Alpay E, Verma D, Stanfield EG, Kreindler L, Jain S, McKay B, Hubbell SA, Hendriks CG, Blizard BA, Broughton JP, Chen JS. CRISPR-Cas enzymes: The toolkit revolutionizing diagnostics. Biotechnol J 2021; 17:e2100304. [PMID: 34505742 DOI: 10.1002/biot.202100304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/11/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022]
Abstract
The programmable nature of sequence-specific targeting by CRISPR-Cas nucleases has revolutionized a wide range of genomic applications and is now emerging as a method for nucleic acid detection. We explore how the diversity of CRISPR systems and their fundamental mechanisms have given rise to a wave of new methods for target recognition and readout. These cross-disciplinary advances found at the intersection of CRISPR biology and engineering have led to the ability to rapidly generate solutions for emerging global challenges like the COVID-19 pandemic. We further discuss the advances and potential for CRISPR-based detection to have an impact across a continuum of diagnostic applications.
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Affiliation(s)
| | | | | | - Emel Alpay
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | - Deepika Verma
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | | | | | - Sonal Jain
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | - Bridget McKay
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | | | | | | | | | - Janice S Chen
- Mammoth Biosciences, Inc., Brisbane, California, USA
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48
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Torres Montaguth OE, Cross SJ, Ingram KWA, Lee L, Diffin FM, Szczelkun MD. ENDO-Pore: high-throughput linked-end mapping of single DNA cleavage events using nanopore sequencing. Nucleic Acids Res 2021; 49:e118. [PMID: 34417616 PMCID: PMC8599736 DOI: 10.1093/nar/gkab727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/05/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022] Open
Abstract
Mapping the precise position of DNA cleavage events plays a key role in determining the mechanism and function of endonucleases. ENDO-Pore is a high-throughput nanopore-based method that allows the time resolved mapping single molecule DNA cleavage events in vitro. Following linearisation of a circular DNA substrate by the endonuclease, a resistance cassette is ligated recording the position of the cleavage event. A library of single cleavage events is constructed and subjected to rolling circle amplification to generate concatemers. These are sequenced and used to produce accurate consensus sequences. To identify the cleavage site(s), we developed CSI (Cleavage Site Investigator). CSI recognizes the ends of the cassette ligated into the cleaved substrate and triangulates the position of the dsDNA break. We firstly benchmarked ENDO-Pore using Type II restriction endonucleases. Secondly, we analysed the effect of crRNA length on the cleavage pattern of CRISPR Cas12a. Finally, we mapped the time-resolved DNA cleavage by the Type ISP restriction endonuclease LlaGI that introduces random double-strand breaks into its DNA substrates.
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Affiliation(s)
- Oscar E Torres Montaguth
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Stephen J Cross
- Wolfson Bioimaging Facility, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Kincaid W A Ingram
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Laura Lee
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
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49
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Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA. DNA interference states of the hypercompact CRISPR-CasΦ effector. Nat Struct Mol Biol 2021; 28:652-661. [PMID: 34381246 PMCID: PMC8496406 DOI: 10.1038/s41594-021-00632-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/24/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-CasΦ, a small RNA-guided enzyme found uniquely in bacteriophages, achieves programmable DNA cutting as well as genome editing. To investigate how the hypercompact enzyme recognizes and cleaves double-stranded DNA, we determined cryo-EM structures of CasΦ (Cas12j) in pre- and post-DNA-binding states. The structures reveal a streamlined protein architecture that tightly encircles the CRISPR RNA and DNA target to capture, unwind and cleave DNA. Comparison of the pre- and post-DNA-binding states reveals how the protein rearranges for DNA cleavage upon target recognition. On the basis of these structures, we created and tested mutant forms of CasΦ that cut DNA up to 20-fold faster relative to wild type, showing how this system may be naturally attenuated to improve the fidelity of DNA interference. The structural and mechanistic insights into how CasΦ binds and cleaves DNA should allow for protein engineering for both in vitro diagnostics and genome editing.
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Affiliation(s)
- Patrick Pausch
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Dominik A Herbst
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor A Tsuchida
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
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50
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Wörle E, Jakob L, Schmidbauer A, Zinner G, Grohmann D. Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions. Nucleic Acids Res 2021; 49:5278-5293. [PMID: 34009379 PMCID: PMC8136826 DOI: 10.1093/nar/gkab286] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/26/2022] Open
Abstract
The widespread and versatile prokaryotic CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats and associated Cas proteins) constitute powerful weapons against foreign nucleic acids. Recently, the single-effector nuclease Cas12a that belongs to the type V CRISPR-Cas system was added to the Cas enzymes repertoire employed for gene editing purposes. Cas12a is a bilobal enzyme composed of the REC and Nuc lobe connected by the wedge, REC1 domain and bridge helix (BH). We generated BH variants and integrated biochemical and single-molecule FRET (smFRET) studies to elucidate the role of the BH for the enzymatic activity and conformational flexibility of Francisella novicida Cas12a. We demonstrate that the BH impacts the trimming activity and mismatch sensitivity of Cas12a resulting in Cas12a variants with improved cleavage accuracy. smFRET measurements reveal the hitherto unknown open and closed state of apo Cas12a. BH variants preferentially adopt the open state. Transition to the closed state of the Cas12a-crRNA complex is inefficient in BH variants but the semi-closed state of the ternary complex can be adopted even if the BH is deleted in its entirety. Taken together, these insights reveal that the BH is a structural element that influences the catalytic activity and impacts conformational transitions of FnCas12a.
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Affiliation(s)
- Elisabeth Wörle
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Leonhard Jakob
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Schmidbauer
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Gabriel Zinner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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