Abstract
The ability to identify single-nucleotide mutations is critical for probing cell biology and for precise detection of disease. However, the small differences in hybridization energy provided by single-base changes makes identification of these mutations challenging in living cells and complex reaction environments. Here, we report a class of de novo-designed prokaryotic riboregulators that provide ultraspecific RNA detection capabilities in vivo and in cell-free transcription-translation reactions. These single-nucleotide-specific programmable riboregulators (SNIPRs) provide over 100-fold differences in gene expression in response to target RNAs differing by a single nucleotide in E. coli and resolve single epitranscriptomic marks in vitro. By exploiting the programmable SNIPR design, we implement an automated design algorithm to develop riboregulators for a range of mutations associated with cancer, drug resistance, and genetic disorders. Integrating SNIPRs with portable paper-based cell-free reactions enables convenient isothermal detection of cancer-associated mutations from clinical samples and identification of Zika strains through unambiguous colorimetric reactions.
Original language | English (US) |
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Pages (from-to) | 1018-1032.e16 |
Journal | Cell |
Volume | 180 |
Issue number | 5 |
DOIs | |
State | Published - Mar 5 2020 |
Keywords
- colorimetric
- diagnostic
- isothermal
- mutation
- paper-based assay
- riboregulator
- specificity
ASJC Scopus subject areas
- General Biochemistry, Genetics and Molecular Biology