Mostly Biomathematics Lunchtime Seminar

---

RNA structure affects its interactions: From condensates to CRISPR-Cas13

Speaker: Dr. Ofer Kimchi, Princeton University

Location: Warren Weaver Hall 1314

Date: Tuesday, March 4, 2025, 12:45 p.m.

Synopsis:

Nucleic acid interactions underlie almost all of modern biology, both in cells (transcription, RNA viruses, miRNA) and in the lab (PCR, FISH, CRISPR). In principle, these interactions are straightforward, determined by sequence complementarity. In practice, however, the competition between intramolecular RNA structure and intermolecular RNA-RNA interactions can lead to surprising phenomena. I will illustrate how this plays out in RNA-based condensates implicated in human neurological disorders, and in the Cas13 system, a CRISPR enzyme targeting single-stranded RNA. In the former system, I will show that the competition with intramolecular structure leads to a surprising reentrant transition, and I will describe our solution for a complete sequence-space phase diagram for repeat-RNA condensates. I will then show how similar principles are at play in a very different context that involves protein-RNA interactions, the Cas13 system. We developed a massively multiplexed screen to probe how intramolecular RNA structure affects Cas13, revealing a strand-displacement process underlying Cas13 activation. We then leveraged this strand-displacement reaction to enhance Cas13 mismatch discrimination by an order of magnitude, setting a new standard for Cas13-based RNA detection and viral diagnostics.