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Hajian R, Balderston S, Tran T, deBoer T, Etienne J, Sandhu M, Wauford NA, Chung JY, Nokes J, Athaiya M, Paredes J, Peytavi R, Goldsmith B, Murthy N, Conboy IM, Aran K. Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng 2019; 3:427-437. [PMID: 31097816 PMCID: PMC6556128 DOI: 10.1038/s41551-019-0371-x] [Citation(s) in RCA: 324] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 02/19/2019] [Indexed: 12/25/2022]
Abstract
Most methods for the detection of nucleic acids require many reagents and expensive and bulky instrumentation. Here, we report the development and testing of a graphene-based field-effect transistor that uses clustered regularly interspaced short palindromic repeats (CRISPR) technology to enable the digital detection of a target sequence within intact genomic material. Termed CRISPR-Chip, the biosensor uses the gene-targeting capacity of catalytically deactivated CRISPR-associated protein 9 (Cas9) complexed with a specific single-guide RNA and immobilized on the transistor to yield a label-free nucleic-acid-testing device whose output signal can be measured with a simple handheld reader. We used CRISPR-Chip to analyse DNA samples collected from HEK293T cell lines expressing blue fluorescent protein, and clinical samples of DNA with two distinct mutations at exons commonly deleted in individuals with Duchenne muscular dystrophy. In the presence of genomic DNA containing the target gene, CRISPR-Chip generates, within 15 min, with a sensitivity of 1.7 fM and without the need for amplification, a significant enhancement in output signal relative to samples lacking the target sequence. CRISPR-Chip expands the applications of CRISPR-Cas9 technology to the on-chip electrical detection of nucleic acids.
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Affiliation(s)
- Reza Hajian
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Thanhtra Tran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Tara deBoer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jessy Etienne
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Mandeep Sandhu
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Noreen A Wauford
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jing-Yi Chung
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Mitre Athaiya
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Jacobo Paredes
- Tecnun, School of Engineering, University of Navarra, San Sebastián, Spain
| | | | | | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Irina M Conboy
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Nanosens Innovations, San Diego, CA, USA.
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Cox KJ, Subramanian HKK, Samaniego CC, Franco E, Choudhary A. A universal method for sensitive and cell-free detection of CRISPR-associated nucleases. Chem Sci 2019; 10:2653-2662. [PMID: 30996981 PMCID: PMC6419926 DOI: 10.1039/c8sc03426e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/28/2018] [Indexed: 12/18/2022] Open
Abstract
A multitude of biological applications for CRISPR-associated (Cas) nucleases have propelled the development of robust cell-based methods for quantitation of on- and off-target activities of these nucleases. However, emerging applications of these nucleases require cell-free methods that are simple, sensitive, cost effective, high throughput, multiplexable, and generalizable to all classes of Cas nucleases. Current methods for cell-free detection are cumbersome, expensive, or require sophisticated sequencing technologies, hindering their widespread application beyond the field of life sciences. Developing such cell-free assays is challenging for multiple reasons, including that Cas nucleases are single-turnover enzymes that must be present in large excess over their substrate and that different classes of Cas nucleases exhibit wildly different operating mechanisms. Here, we report the development of a cell-free method wherein Cas nuclease activity is amplified via an in vitro transcription reaction that produces a fluorescent RNA:small-molecule adduct. We demonstrate that our method is sensitive, detecting activity from low nanomolar concentrations of several families of Cas nucleases, and can be conducted in a high-throughput microplate fashion with a simple fluorescent-based readout. We provide a mathematical framework for quantifying the activities of these nucleases and demonstrate two applications of our method, namely the development of a logic circuit and the characterization of an anti-CRISPR protein. We anticipate our method will be valuable to those studying Cas nucleases and will allow the application of Cas nuclease beyond the field of life sciences.
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Affiliation(s)
- Kurt J Cox
- Chemical Biology and Therapeutics Science , Broad Institute of MIT and Harvard , 415 Main Street, Rm 3012 , Cambridge , MA 02142 , USA . ; ; Tel: +1 617 714 7445
- Department of Medicine , Harvard Medical School , Boston , MA 02115 , USA
- Divisions of Renal Medicine and Engineering , Brigham and Women's Hospital , Boston , MA 02115 , USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering , University of California - Riverside , Riverside , CA - 92521 , USA . ; Tel: +1 951 827 2442
| | - Christian Cuba Samaniego
- Department of Mechanical Engineering , University of California - Riverside , Riverside , CA - 92521 , USA . ; Tel: +1 951 827 2442
| | - Elisa Franco
- Department of Mechanical Engineering , University of California - Riverside , Riverside , CA - 92521 , USA . ; Tel: +1 951 827 2442
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science , Broad Institute of MIT and Harvard , 415 Main Street, Rm 3012 , Cambridge , MA 02142 , USA . ; ; Tel: +1 617 714 7445
- Department of Medicine , Harvard Medical School , Boston , MA 02115 , USA
- Divisions of Renal Medicine and Engineering , Brigham and Women's Hospital , Boston , MA 02115 , USA
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