Cell-free biosensors for rapid detection of water contaminants

• Published in: Nature biotechnology Vol. 38; no. 12; pp. 1451 - 1459
• Main Authors: Jung, Jaeyoung K., Alam, Khalid K., Verosloff, Matthew S., Capdevila, Daiana A., Desmau, Morgane, Clauer, Phillip R., Lee, Jeong Wook, Nguyen, Peter Q., Pastén, Pablo A., Matiasek, Sandrine J., Gaillard, Jean-François, Giedroc, David P., Collins, James J., Lucks, Julius B.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2020; Nature Publishing Group
• Subjects: 631/337/572; 631/45/500; 631/553/552; Agriculture; Allosteric properties; Antibiotics; Aptamers; Aptamers, Nucleotide - metabolism; Bioengineering; Bioinformatics; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biosensing Techniques - methods; Biosensors; Biotechnology; Chemical contaminants; Circuits; Contaminants; Crosstalk; Deoxyribonucleic acid; DNA; Drinking water; Engineering; Environmental monitoring; Evaluation; Fluorescence; Freeze Drying; Gene expression; Genes, Reporter; Laboratories; Life Sciences; Ligands; Metals; Metals - metabolism; Municipal water supplies; Pathogens; Protein engineering; Proteins; Ribonucleic acid; RNA; RNA - metabolism; RNA polymerase; Small Molecule Libraries - chemistry; Synthetic biology; Transcription factors; Transcription Factors - metabolism; Transcription, Genetic; United States; Water monitoring; Water Pollutants, Chemical - analysis; Water pollution; Water quality; Water supply; United States
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/s41587-020-0571-7

Lack of access to safe drinking water is a global problem, and methods to reliably and easily detect contaminants could be transformative. We report the development of a cell-free in vitro transcription system that uses RNA Output Sensors Activated by Ligand Induction (ROSALIND) to detect contaminants in water. A combination of highly processive RNA polymerases, allosteric protein transcription factors and synthetic DNA transcription templates regulates the synthesis of a fluorescence-activating RNA aptamer. The presence of a target contaminant induces the transcription of the aptamer, and a fluorescent signal is produced. We apply ROSALIND to detect a range of water contaminants, including antibiotics, small molecules and metals. We also show that adding RNA circuitry can invert responses, reduce crosstalk and improve sensitivity without protein engineering. The ROSALIND system can be freeze-dried for easy storage and distribution, and we apply it in the field to test municipal water supplies, demonstrating its potential use for monitoring water quality. Water contaminants are detected with freeze-dried, regulated in vitro transcription reactions.