Abstract

Pathological protein misfolding and aggregation underlie many devastating human diseases, yet strategies to selectively neutralize aggregation-prone protein states without perturbing their normal functions remain limited. Here we identify loosely structured circular RNA (cRNA) aptamers, circT3 and its minimized 116-nt variant circT3-M3, as superb sub-stoichiometric RNA chaperones that suppress pathological assembly of TAR DNA-binding protein 43 (TDP-43), a defining feature of amyotrophic lateral sclerosis and frontotemporal dementia, in vitro and in cells. Rather than acting through simple stoichiometric sequestration, these cRNA aptamers engage TDP-43 transiently and iteratively through functionally and pathologically important residues in the RRM1 domain. Such interaction enables a single cRNA aptamer to promote rapid and multiple RRM1-dependent homomeric assembly, thereby stabilizing TDP-43 in a soluble oligomeric state to outcompete the C-terminal prion-like domain-driven condensation and supersaturation. Together, our findings establish cRNA aptamers as highly efficient subcellular RNA chaperones with exceptionally potent low-dose activity and highlight their promise as next-generation RNA therapeutics for certain protein-aggregation disorders.