The canonical purpose of RNA is to produce proteins.1 Despite this, up to 97 percent of the RNA produced in cells does not get translated.2 These non-coding RNA sequences have varied functions, including regulating gene expression, post-transcriptional modification, and interacting with epigenetic factors.3 They may also bind proteins to modulate their activity,4 but a comprehensive understanding of RNA structures and how they interact with specific amino acid sequences is lacking due to the overwhelming scale of biomacromolecules, often requiring crystallographic analysis.
Here, we show that a novel short peptide5 based on the intrinsically disordered region of the RNA-binding protein Nucleolin interacts with, templates, and stabilizes short natural sequences of RNA to form non-canonical secondary structures; the i-motif and G-quadruplex. This peptide discriminates binding at a single-nucleotide mutation, is selective for RNA over DNA, and is competitive with endogenous chaperones. Our system leverages the intrinsic disorder of peptides to define RNA structure selectively, providing a unique pathway to RNA folding that stabilizes disease-relevant secondary structures. This work underscores the potential for future RNA therapies and nanotechnologies to be built on structural complementarity, rather than translational efficiency, by understanding RNA-peptide interactions at the molecular level.