SensEDNA: An innovative optical CRISPR platform for rapid environmental DNA monitoring

Abstract

Biodiversity loss is at an all-time high increasing the need for simple and rapid species monitoring systems. Management and conservation of fish species within aquatic environments requires knowledge of distribution, traditionally gained through visual detection and counting. These methods are expensive, time consuming and can lead to harm of the species of interest. Environmental DNA (eDNA) offers a solution to this through detection of DNA that may be shed into the environment by a given target species. Integrating eDNA based molecular assays to a biosensor device enables onsite sample testing for rapid species assessment.

Herein, a portable fluorometer with incubating capabilities (SensEDNA) was custom designed and built to conduct the simultaneous incubation and fluorescent detection steps required for isothermal eDNA detection. The system features three optical cells to enable triplicate analysis. Each optical cell is set to incubate at 37 °C and control within 0.5 °C. Fluorescence detection with excitation at 485 nm and emission at 535 nm was integrated and optimised to provide highest signal/noise ratio while minimising fluorescence bleaching. The system comprises a simple LED/high pass filter/photodiode configuration and is controlled by a Wixel board. This affordable and user-friendly optical detection platform, coupled with RPA-CRISPR-Cas, provides a crucial step towards on-site single species identification from eDNA.