ROSALIND: Rapid Detection of Chemical Contaminants with In Vitro Transcription Factor-Based Biosensors

Jaeyoung K Jung; Khalid K Alam; Julius B Lucks

doi:10.1007/978-1-0716-1998-8_20

ROSALIND: Rapid Detection of Chemical Contaminants with In Vitro Transcription Factor-Based Biosensors

Methods Mol Biol. 2022:2433:325-342. doi: 10.1007/978-1-0716-1998-8_20.

Authors

Jaeyoung K Jung^{1

2

3}, Khalid K Alam⁴, Julius B Lucks^{5

6

7

8

9}

Affiliations

¹ Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
² Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
³ Center for Water Research, Northwestern University, Evanston, IL, USA.
⁴ Stemloop, Inc., Evanston, IL, USA.
⁵ Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. jblucks@northwestern.edu.
⁶ Center for Synthetic Biology, Northwestern University, Evanston, IL, USA. jblucks@northwestern.edu.
⁷ Center for Water Research, Northwestern University, Evanston, IL, USA. jblucks@northwestern.edu.
⁸ Stemloop, Inc., Evanston, IL, USA. jblucks@northwestern.edu.
⁹ Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA. jblucks@northwestern.edu.

PMID: 34985754
DOI: 10.1007/978-1-0716-1998-8_20

Abstract

ROSALIND (RNA Output Sensors Activated by Ligand Induction) is an in vitro biosensing system that detects small molecules using regulated transcription reactions. It consists of three key components: (1) RNA polymerases, (2) allosteric protein transcription factors, and (3) synthetic DNA transcription templates that together regulate the synthesis of a fluorescence-activating RNA aptamer. The system can detect a wide range of chemicals including antibiotics, small molecules, and metal ions. We have demonstrated that ROSALIND can be lyophilized and transported at ambient conditions for water testing on-site. Here, we describe how to set up a ROSALIND reaction for detecting various chemical contaminants in water using a model transcription factor as well as how to build a new ROSALIND sensor.

Keywords: Allosteric transcription factors; Biosensors; Cell-free synthetic biology; In vitro transcription; RNA aptamer; Water quality monitoring.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aptamers, Nucleotide* / chemistry
Biosensing Techniques*
Metals
RNA / metabolism
Transcription Factors / metabolism

Substances

Aptamers, Nucleotide
Metals
Transcription Factors
RNA