Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima

Synth Syst Biotechnol. 2022 Mar 30;7(2):791-801. doi: 10.1016/j.synbio.2022.03.003. eCollection 2022 Jun.


Nucleic acid sensing is a 3 decades old but still challenging area of application for different biological sub-domains, from pathogen detection to single cell transcriptomics analysis. The many applications of nucleic acid detection and identification are mostly carried out by PCR techniques, sequencing, and their derivatives used at large scale. However, these methods' limitations on speed, cost, complexity and specificity have motivated the development of innovative detection methods among which nucleic acid biosensing technologies seem promising. Toehold switches are a particular class of RNA sensing devices relying on a conformational switch of secondary structure induced by the pairing of the detected trigger RNA with a de novo designed synthetic sensing mRNA molecule. Here we describe a streamlined methodology enabling the development of such a sensor for the RNA-mediated detection of an endangered plant species in a cell-free reaction system. We applied this methodology to help identify the rosewood Dalbergia maritima, a highly trafficked wood, whose protection is limited by the capacity of the authorities to distinguish protected logs from other unprotected but related species. The streamlined pipeline presented in this work is a versatile framework enabling cheap and rapid development of new sensors for custom RNA detection.

Keywords: Biosensor; CITES, Convention on International Trade in Endangered Species of Wild Fauna and Flore; CUHK, Chinese University of Hong Kong; MEFL, Molecules of Equivalent Fluorescein; MFE, Minimum free energy; MatK, Maturase K; RBS, Ribosome binding site; RbcL, Ribulose bisphosphate carboxylase large chain; Riboregulator; Rosewood; Toehold switch; TrnL-UAA, Transfer RNA Leucine UAA.