Folding Stability and Self-Association of a Triplet-Repeat (CAG)20 RNA Hairpin in Cytomimetic Media

RNA molecules with trinucleotide repeat expansions are involved in the pathology of various neurodegenerative diseases, such as Huntington's disease. A central research objective is to understand how trinucleotide repeat RNAs fold and function in disease progression. Studies that investigate the sequence structure, stability and self-assembly of such RNAs mainly focused on invitro methods in dilute aqueous solution. Functional studies in cells reveal further aspects of transport, protein association or assembly in phase separated compartments. Our study aims to understand governing factors for folding stability of trinucleotide repeats on the cellular level by assessing the influence of key components of the cellular medium invitro. We investigate (CAG)(20) RNA in complex and cytomimetic media using Fast Relaxation Imaging. Using distinct cosolutes we analyze the different enthalpic and entropic contributions that determine folding stability. We find a remarkable destabilization and aggregation of the RNA in cellular lysate that can be attributed to specific and non-specific interactions with the unfolded state.

Automated summary

Research has focused on the relationship between RNA molecules with trinucleotide repeat expansions and neurodegenerative diseases, primarily aiming to understand how they fold and function in disease progression. Functional studies in cells can reveal additional aspects of RNA behavior, while invitro studies mainly focus on sequence structure, stability, and self-assembly. Specific interactions with the unfolded state have been found to contribute to destabilization and aggregation of RNA in cellular lysate.