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Abstract Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. It utilizes a CRISPR RNA (crRNA) to target RNA sequences and trigger a composite active site formed by two ‘Higher Eukaryotes and Prokaryotes Nucleotide’ (HEPN) domains, cleaving any solvent-exposed RNA. In this system, an intriguing form of allosteric communication controls the RNA cleavage activity, yet its molecular details are unknown. Here, multiple-microsecond molecular dynamics simulations are combined with graph theory to decipher this intricate activation mechanism. We show that the binding of a target RNA acts as an allosteric effector, by amplifying the communication signals over the dynamical noise through interactions of the crRNA at the buried HEPN1-2 interface. By introducing a novel Signal-to-Noise Ratio (SNR) of communication efficiency, we reveal critical allosteric residues—R377, N378, and R973—that rearrange their interactions upon target RNA binding. Alanine mutation of these residues is shown to select target RNA over an extended complementary sequence beyond guide-target duplex for RNA cleavage, establishing the functional significance of these hotspots. Collectively our findings offer a fundamental understanding of the Cas13a mechanism of action and pave new avenues for the development of highly selective RNA-based cleavage and detection tools.
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This content will become publicly available on February 1, 2026
RNA communication between organisms inspires innovative eco-friendly strategies for disease control
Evidence shows that RNA trafficking is a key communication mechanism across kingdoms and species, but how RNAs are secreted and trafficked and how they function within the recipient organisms remain unclear. Here, we discuss how understanding inter-organismal RNA communication can assist in disease management in both agriculture and medicine.
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- Award ID(s):
- 1922642
- PAR ID:
- 10635130
- Publisher / Repository:
- Nature reviews molecular cell biolog
- Date Published:
- Journal Name:
- Nature Reviews Molecular Cell Biology
- Volume:
- 26
- Issue:
- 2
- ISSN:
- 1471-0072
- Page Range / eLocation ID:
- 81 to 82
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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