Developing, Characterizing, and Modeling CRISPR-Based Point-of-Use Pathogen Diagnostics
Recent years have seen intense interest in the development of point-of-care nucleic acid diagnostic technologies to address the scaling limitations of laboratory-based approaches. Chief among these are combinations of isothermal amplification approaches with CRISPR-based detection and readouts of target products. Here, we contribute to the growing body of rapid, programmable point-of-care pathogen tests by developing and optimizing a one-pot NASBA-Cas13a nucleic acid detection assay. This test uses the isothermal amplification technique NASBA to amplify target viral nucleic acids, followed by the Cas13a-based detection of amplified sequences. We first demonstrate an in-house formulation of NASBA that enables the optimization of individual NASBA components. We then present design rules for NASBA primer sets and LbuCas13a guide RNAs for the fast and sensitive detection of SARS-CoV-2 viral RNA fragments, resulting in 20-200 aM sensitivity. Finally, we explore the combination of high-throughput assay condition screening with mechanistic ordinary differential equation modeling of the reaction scheme to gain a deeper understanding of the NASBA-Cas13a system. This work presents a framework for developing a mechanistic understanding of reaction performance and optimization that uses both experiments and modeling, which we anticipate will be useful in developing future nucleic acid detection technologies.
Authors
- Anne E. d’Aquino (ORCID: https://orcid.org/0000-0003-3264-4719)
- Joseph J. Muldoon (ORCID: https://orcid.org/0000-0003-3784-3565)
- Sasha Shirman (ORCID: https://orcid.org/0000-0001-5855-9470)
- Maria D. Cabezas (ORCID: https://orcid.org/0000-0002-0861-9735)
- Neda Bagheri (ORCID: https://orcid.org/0000-0003-0146-4627)
- Julius B. Lucks (ORCID: https://orcid.org/0000-0002-0619-6505)
- Grant A. Rybnicky
- Kate E. Dray (ORCID: https://orcid.org/0000-0002-2972-047X)
- Kathleen S. Dreyer (ORCID: https://orcid.org/0000-0002-2041-4118)
- Kosuke Seki (ORCID: https://orcid.org/0000-0002-0413-8184)
- Joshua N. Leonard (ORCID: https://orcid.org/0000-0003-4359-6126)
- Michael C. Jewett (ORCID: https://orcid.org/0000-0003-2948-6211)
- Jithin D. George (ORCID: https://orcid.org/0000-0002-2439-2411)
- Niall M. Mangan (ORCID: https://orcid.org/0000-0002-3491-8341)
- Khalid K. Alam (ORCID: https://orcid.org/0000-0002-2210-3962)
- Matthew S. Verosloff (ORCID: https://orcid.org/0000-0002-4519-633X)
- Jaeyoung K. Jung (ORCID: https://orcid.org/0000-0002-5180-0900)
Institutions
- Northwestern University (US)
- Gladstone Institutes (US)
- University of California, San Francisco (US)
- University of Washington (US)
- Stanford University (US)
Publication Details
- Journal
- ACS Synthetic Biology
- Published
- 2024-12-13
- DOI
- https://doi.org/10.1021/acssynbio.4c00469
- Citations
- 7
- Primary Topic
- CRISPR and Genetic Engineering
- Type
- article
- Field-Weighted Citation Impact
- 1.64
Funders
- National Science Foundation
- Bill and Melinda Gates Foundation
- John Simon Guggenheim Memorial Foundation
- Northwestern University
- University of Washington
- National Institutes of Health
- Directorate for Biological Sciences
- Chemistry of Life Processes Institute
- Office of Naval Research
- National Institute of Biomedical Imaging and Bioengineering
- Division of Graduate Education
- U.S. Naval Research Laboratory
- Air Force Office of Scientific Research