Aug 2026· Current Opinion in Structural Biology· Vol 101, pp.
103356
· 0 citations· 68 references
Medicine
TL;DR
This minireview examines how RNA shapes the formation, composition, and material properties of biomolecular condensates, highlighting the molecular grammar encoded in RNA sequence, length and valency, structure, and chemical modifications.
Abstract
The crowded intracellular milieu shapes the thermodynamics and kinetics of biochemical reactions. RNA, an abundant and structurally versatile polymer, contributes to this crowding by acting both as a physical agent that restricts diffusion and enhances excluded volume, and as a sequence- and structure-specific scaffold driving multivalent RNA-RNA and RNA-protein interactions. These properties position RNA as a biologically active determinant of intracellular organization, distinct from inert synthetic crowders and purely structural scaffolds. This minireview examines how RNA shapes the formation, composition, and material properties of biomolecular condensates, highlighting the molecular grammar encoded in RNA sequence, length and valency, structure, and chemical modifications. We discuss how concentration-dependent, biphasic effects of RNA on condensate assembly can tip the balance between functional compartmentalization and pathological liquid-to-solid transitions implicated in neurodegenerative disease and cancer. Finally, we outline challenges in defining RNA-specific thresholds and translating structural insights into therapeutic strategies for mitigating aberrant RNA-mediated crowding.
This work examines the physicochemical principles underlying RNA-mediated crowding, focusing on how sequence-driven multivalency, structural topology, and network connectivity govern molecular organization.
Jonathan Fiorentino, Michele Monti, Laura Broglia et al.· Current Opinion in Structura...· 0 citations
Crowding-aware structural biology, including in-cell nuclear magnetic resonance, cryo-electron microscopy of condensates, single-molecule methods, and thermodynamic-kinetic modelling, will be important for resolving physiologically relevant intermediates.
Tejas Nikam, Shashi Prakash Patel, S. Saraf et al.· Current Opinion in Structura...· 1 citation
RNA molecules populate complex structural landscapes that are continuously reshaped throughout the RNA lifecycle by equilibrium and non-equilibrium processes. Resolving these structural landscapes represents a central challenge in RNA biochemistry. We review recent advances in RNA chemical probing, sequencing, and computational deconvolution technologies that are revolutionizing our ability to measure the complexities of RNA folding in cells and the deep involvement of these complexities in RNA functional mechanisms. We highlight new methods for deconvolving structural ensembles, distinguishing isoform-specific architectures using long-read sequencing, capturing co-transcriptional folding intermediates in vivo, and measuring higher-order RNA structures while also underscoring remaining challenges. We conclude by outlining future directions in probe development, sequencing, and integrative modeling, and discuss how resolving RNA structural ensembles with increasingly high resolution will likely reveal new therapeutic opportunities to selectively target functional RNA heterogeneity.
Anthony M. Mustoe, D. Incarnato· Current Opinion in Structura...· 0 citations
It is demonstrated that single-molecule mass measurements with mass photometry can capture RNA-protein interactions in phase-separated protein systems and can distinguish between charge neutralization, which drives coacervation, and complex formation, which mediates phase re-entry, making it a highly complementary tool for the study of RNA-mediated phase separation.
Axel Leppert, Jesper Shiapan, Irena Papageorgiou et al.· bioRxiv· 0 citations
Supramolecular assemblies regulated by small biomolecules, such as nucleotides, provide key insights into biological organization, particularly in protein aggregation, which is linked to neurodegenerative diseases. While the role of nucleotides as a stabilizer and biological hydrotrope is well-established, their interaction with biological assembly is inherently paradoxical. Furthermore, the interaction of nucleotides with the transient intermediates of self-assembly of proteins and peptides remains largely unexplored. Here, l-phenylalanine (Phe) is employed as a minimal model to investigate nucleotide-mediated regulation in both native and metal-stabilized assemblies. In native Phe assemblies, ATP and ADP exhibit a concentration-dependent disruption of fibrillar morphology, whereas AMP offers a minimal influence. In contrast, within cation-mediated metastable assemblies, nucleotides actively redirect the assembly pathways. Phosphate multiplicity dictates structural outcomes: ATP and ADP stabilize compact spherical-like architectures, while AMP promotes fibrillar aggregates. Mechanistic analysis, supported by imaging techniques and zeta potential, reveals synergistic contributions from multivalent phosphate interaction and nucleoside-mediated interactions.
Suman Choudhury, Priyanka Nath, Huma Tabassum et al.· Journal of Physical Chemistr...· 0 citations
Aminoglycoside antibiotics bind RNA with high affinity through networks of amine and hydroxyl contacts, yet whether this multivalent binding can drive macroscopic RNA phase transitions has never been tested. Here we show that aminoglycosides are a class of small-molecule RNA condensers, and we take neomycin B (neoB), an FDA-approved member of the family, as a representative drug through which to dissect the mechanism. NeoB induces concentration-dependent phase separation of poly(A), poly(U), and total E. coli RNA, and kanamycin, apramycin, and gentamicin condense RNA as well. Condensate size and density are tunable by pH and ionic strength, which independently modulate neoB protonation and screening of interdroplet repulsion. NeoB forms more stable condensates than spermine despite spermine’s larger effective charge at physiological pH, whereas the amine-free polyol fucitol fails to condense RNA. Molecular dynamics simulations attribute neoB’s greater efficiency to additional hydrogen bonds donated by its hydroxyl groups. The chemical complexity that aminoglycosides evolved for RNA recognition thus also drives a macroscopic RNA phase transition that may contribute to bactericidal activity and cellular toxicity.
Julian von Hofe, Mechi Chen, Christine Choi et al.· bioRxiv· 0 citations
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