Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation
Date
2025-11-24
Journal Title
Journal ISSN
Volume Title
Publisher
Nucleic Acids Research
Abstract
CRISPR activation is a powerful tool to upregulate a vast array of genes in many different contexts. However, there are few dynamic CRISPR transcriptional programs, which limit its usage in the creation of living biosensors, self-regulating microbial factories, or conditional therapeutics. Here, we address this limitation by embedding a molecular switch directly into a guide RNA to create a combined sensor–actuator called a metabolite-responsive scaffold RNA (MR-scRNA). We demonstrate the regulatory potential for MR-sc RNAs by conditionally activating genes in three different kingdoms of life. We create MR-scRNAs responsive to two distinct metabolites, theophylline and tryptophan, by swapping the molecular switch used. MR-scRNAs respond quickly in a dose-dependent manner specifically to their target metabolite and enhance biochemical production when used as a dynamic regulator of pathway enzyme expression. The broad functionality and ease of design of the MR-scRNAs offer a promising tool for dynamic cellular regulation.
Description
This article was originally published in Nucleic Acids Research. The version of record is available at: https://doi.org/10.1093/nar/gkaf1290
© The Author(s) 2025. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
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Citation
Anthony M Stohr, Helena Hansen, Blake Richards, Hayeon Park, Antonio G Goncalves, Ayushi Agrawal, Mark Blenner, Wilfred Chen, Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation, Nucleic Acids Research, Volume 53, Issue 21, 26 November 2025, gkaf1290, https://doi.org/10.1093/nar/gkaf1290