Accelerated Simulations Reveal Physicochemical Factors Governing Stability and Composition of RNA Clusters

D Aierken, JA Joseph - Journal of Chemical Theory and …, 2024 - ACS Publications
Under certain conditions, RNA repeat sequences phase separate, yielding protein-free
biomolecular condensates. Importantly, RNA repeat sequences have also been implicated …

Odd–even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

H Maity, HT Nguyen, N Hori, D Thirumalai - Proceedings of the National …, 2023 - pnas.org
Low-complexity nucleotide repeat sequences, which are implicated in several neurological
disorders, undergo liquid–liquid phase separation (LLPS) provided the number of repeat …

Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning

V Ramachandran, DA Potoyan - Biophysical Journal, 2024 - cell.com
Conformational dynamics of RNA plays important roles in a variety of cellular functions such
as transcriptional regulation, catalysis, scaffolding, and sensing. Recently, RNAs with low …

Small CAG Repeat RNA Forms a Duplex Structure with Sticky Ends That Promote RNA Condensation

L Wan, C Zhang, Y Liu, J Zhang, L He… - Journal of the …, 2025 - ACS Publications
Biomolecular condensation lays the foundation of forming biologically important
membraneless organelles, but abnormal condensation processes are often associated with …

[PDF][PDF] Biomolecular Condensates Can Enhance Homotypic RNA Clustering

TS Mahendran, GM Wadsworth, A Singh, R Gupta… - bioRxiv, 2025 - researchgate.net
Intracellular aggregation of repeat expanded RNA has been implicated in many
neurological disorders. Here, we study the role of biomolecular condensates on irreversible …

Understanding the self-assembly and molecular structure of mRNA lipid nanoparticles at real size: Insights from the ultra-large-scale simulation

R Wang, Y Zhang, H Zhong, J Zang, W Wang… - International Journal of …, 2025 - Elsevier
Messenger RNA (mRNA) encapsulated in lipid nanoparticles (LNPs) represents a cutting-
edge delivery technology that played a pivotal role during the COVID-19 pandemic and in …

Impact of linker length on biomolecular condensate formation

T GrandPre, Y Zhang, AGT Pyo, B Weiner, JL Li… - PRX Life, 2023 - APS
Biomolecular condensates are membraneless organelles formed via phase separation of
macromolecules, typically consisting of bond-forming “stickers” connected by flexible …

Interplay between self-assembly and phase separation in a polymer-complex model

T Li, WB Rogers, WM Jacobs - Physical Review E, 2023 - APS
We present a theoretical model for predicting the phase behavior of polymer solutions in
which phase separation competes with oligomerization. Specifically, we consider scenarios …

Competition between self-assembly and phase separation governs high-temperature condensation of a DNA liquid

O Hegde, T Li, A Sharma, M Borja, WM Jacobs… - Physical review …, 2024 - APS
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low
concentrations also promote phase separation at high concentrations. Here we study a …

Effects of linker length on phase separation: lessons from the Rubisco-EPYC1 system of the algal pyrenoid

T GrandPre, Y Zhang, AGT Pyo, B Weiner, JL Li… - …, 2023 - pmc.ncbi.nlm.nih.gov
Biomolecular condensates are membraneless organelles formed via phase separation of
macromolecules, typically consisting of bond-forming “stickers” connected by flexible …