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The application of CRISPR‐Cas for single species identification from environmental DNA

Williams, Molly-Ann orcid logoORCID: 0000-0002-7795-8001, O'Grady, Joyce, Ball, Bernard, Carlsson, Jens orcid logoORCID: 0000-0002-9262-5627, de Eyto, Elvira orcid logoORCID: 0000-0003-2281-2491, McGinnity, Philip orcid logoORCID: 0000-0001-5199-5632, Jennings, Eleanor orcid logoORCID: 0000-0002-9344-2056, Regan, Fiona orcid logoORCID: 0000-0002-8273-9970 and Parle-McDermott, Anne orcid logoORCID: 0000-0002-1533-3209 (2019) The application of CRISPR‐Cas for single species identification from environmental DNA. Molecular Ecology Resources, 19 (5). pp. 1106-1114. ISSN 1755-0998

Abstract
We report the first application of CRISPR‐Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their envi‐ronment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows noninvasive monitoring with increased specificity and sensi‐tivity. Current methods primarily employ PCR‐based techniques to detect a given species from eDNA samples, posing a logistical challenge for on‐site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR‐Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof‐of‐concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (<2.5 hr). This approach simplifies the challenge of building a biosensor device for rapid target species detection in the field and can be easily adapted to detect any species from eDNA samples from a variety of sources enhancing the capabilities of eDNA as a tool for monitoring biodiversity.
Metadata
Item Type:Article (Published)
Refereed:Yes
Uncontrolled Keywords:Freshwater; Biosensor; Environmental; Salmon, CRISPR-Cas; eDNA
Subjects:Physical Sciences > Chemical detectors
DCU Faculties and Centres:DCU Faculties and Schools > Faculty of Science and Health > School of Biotechnology
DCU Faculties and Schools > Faculty of Science and Health > School of Chemical Sciences
Research Initiatives and Centres > Water Institute
Publisher:Wiley Blankwell
Official URL:http://doi.org/10.1111/1755-0998.13045
Copyright Information:© 2016 Wiley
Use License:This item is licensed under a Creative Commons Attribution-NonCommercial-Share Alike 3.0 License. View License
ID Code:24151
Deposited On:17 Jan 2020 14:06 by Fran Callaghan . Last Modified 16 Feb 2022 15:46
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