Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics

Nguyen, Hung T.; Hori, Naoto; Thirumalai, D.

Abstract

Although it is known that RNA undergoes liquid–liquid phase separation, the interplay between the molecular driving forces and the emergent features of the condensates, such as their morphologies and dynamic properties, is not well understood. We introduce a coarse-grained model to simulate phase separation of trinucleotide repeat RNAs, which are implicated in neurological disorders. After establishing that the simulations reproduce key experimental findings, we show that once recruited inside the liquid droplets, the monomers transition from hairpin-like structures to extended states. Interactions between the monomers in the condensates result in the formation of an intricate and dense intermolecular network, which severely restrains the fluctuations and mobilities of the RNAs inside large droplets. In the largest densely packed high-viscosity droplets, the mobility of RNA chains is best characterized by reptation, reminiscent of the dynamics in polymer melts. Our work provides a microscopic framework for understanding liquid–liquid phase separation in RNA, which is not easily discernible in current experiments.

Citation

Nguyen, H. T., Hori, N., & Thirumalai, D. (2022). Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics. Nature Chemistry, https://doi.org/10.1038/s41557-022-00934-z

• Journal Article Type: Article
• Acceptance Date: Mar 24, 2022
• Online Publication Date: May 2, 2022
• Publication Date: May 2, 2022
• Deposit Date: May 2, 2022
• Publicly Available Date: Nov 3, 2022
• Journal: Nature Chemistry
• Print ISSN: 1755-4330
• Electronic ISSN: 1755-4349
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• DOI: https://doi.org/10.1038/s41557-022-00934-z
• Keywords: General Chemical Engineering; General Chemistry
• Public URL: https://nottingham-repository.worktribe.com/output/7765455
• Publisher URL: https://www.nature.com/articles/s41557-022-00934-z