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bioRxiv · 10.64898/2026.08.27.747560

Molecular origins of heterogeneous aging and spatial organization in RNA condensates

Mohanta, D.·Zhang, H.·Thirumalai, D.·Nguyen, H. T.
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Abstract

The molecular origins of aging of biomolecular condensates, which play a central role in cellular organization, is poorly understood. Here, we use coarse-grained molecular simulations to investigate how RNA sequence and chain connectivity govern condensate aging over extended timescales. Condensates formed by CAG-repeat RNA undergo pronounced aging characterized by progressive dynamical slowing, loss of ergodicity, and the emergence of two distinct relaxation timescales. Aging proceeds heterogeneously in space, giving rise to a dynamically arrested, solid-like core surrounded by a more fluid shell. We demonstrate that aging is driven by sequence-encoded base pairing that favors RNA expansion, alignment and the formation of a dense interchain interaction network. These structural changes lead to increased topological entanglement, stabilizing long-lived conformations and reinforcing dynamic arrest in the condensate interior. Strikingly, a scrambled sequence with identical composition remains largely liquid-like. Our results establish RNA sequence patterning as a key determinant not only of phase separation but also of condensate aging and spatial organization. These findings provide a molecular framework for understanding the persistence and solidification of repeat RNA assemblies observed in diseases and suggest general physical principles by which entangled polymer networks drive aging in biomolecular condensates.

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Mohanta, D., Zhang, H., Thirumalai, D., Nguyen, H. T.. 2026-08-27. Molecular origins of heterogeneous aging and spatial organization in RNA condensates. https://doi.org/10.64898/2026.08.27.747560

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