Biology subjects

von Hofe, J.

Publications and source records attributed to von Hofe, J..

3 recordsLinked to original sources

bioRxiv2026

An aminoglycoside antibiotic drives RNA phase separation

AbstractAminoglycoside 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 neomycin B (neoB), an FDA-approved aminoglycoside, induces concentration-dependent phase separation of poly(A), poly(U), and total E. coli RNA. Condensate size and density are tunable by pH and ionic strength, which modulate neoB protonation and screening of interdroplet repulsion independently. Comparison with spermine shows that neoB produces more stable condensates despite spermine carrying at least as much effective charge at physiological pH. Fucitol, a hydroxyl-rich polyol lacking amines, fails to condense RNA, showing that cationic amine groups are required and cannot be replaced by hydroxyl groups. Molecular dynamics simulations attribute the greater condensation efficiency of neoB to additional hydrogen bonds donated by its hydroxyl groups. These results reveal that the chemical complexity of aminoglycosides, evolved for tight RNA recognition, also drives a macroscopic RNA phase transition. RNA condensation may contribute to aminoglycoside bactericidal activity and cellular toxicity.

biochemistry↗

bioRxiv2026

A tunable aqueous architecture modulates functionaloutput in biomolecular condensates

Biomolecular condensates organize cellular biochemistry, yet the principles governing their internal solvent architectures remain poorly understood. Most current models focus on macromolecular scaffolds while treating the solvent as a passive, spatially uniform background. Here, we introduce Condensate Spatial Topography via Emission Lifetimes (ConSTEL) to map the continuous solvent polarity landscape inside biomolecular condensates. Using PopZ as a model system, we show that the condensate interior contains a persistent, tunable mosaic of aqueous environments whose apparent polarity, reported by Nile Red fluorescence lifetimes, is organized by thermodynamic state and chemical cues. This microphase-separated solvent architecture defines distinct mesoscale rheological regimes, with intermediate aqueous niches supporting fast, confined tracer motion and highly polar or non-polar extremes forming a slower, viscoelastic mesh. We further demonstrate that drug-like small molecules partition non-uniformly across this landscape according to their physicochemical properties, and that exceeding local solubility limits drives "reciprocal sculpting", in which mismatched guests remodel the host solvent architecture. Together, these results highlight internal solvent organization as an active, tunable determinant of condensate material properties, molecular transport, and partitioning, and suggest that predictive models of condensate function and pharmacology would benefit from incorporating the spatial arrangement of solvent environments alongside bulk composition.

biochemistry↗

bioRxiv2025

Multivalency controls the growth and dynamics of a biomolecular condensate

Biomolecular condensates are essential for cellular organization and function, yet understanding how chemical and physical factors govern their formation and dynamics has been limited by a lack of non-invasive measurement techniques. Conventional microscopy methods often rely on fluorescent labeling and sub-strate immobilization, which can perturb the intrinsic properties of condensates. To overcome these challenges, we apply label-free, contact-free holographic video microscopy to study the behavior of a condensate-forming protein in vitro. This technique enables rapid, high-throughput, and precise measurements of individual condensate diameters and refractive indexes, providing unprecedented insight into size distributions and dense-phase macromolecular concentrations over time. Using this method, we investigate the kinetics of droplet growth, aging, and equilibrium dynamics in the model condensate-forming protein PopZ. By systematically varying the concentration and valence of cations, we uncover how multivalent ions influence condensate organization and dynamics, a hypothesis we further test using super-resolution microscopy. Our findings reveal that PopZ droplet growth deviates from classical models such as Smoluchowski coalescence and Ostwald ripening. Instead, we show that condensate growth is consistent with gelation at the critical overlap concentration. Holographic microscopy offers significant advantages over traditional techniques, such as differential interference contrast (DIC) microscopy, delivering reproducible measurements and capturing condensate dynamics with unparalleled precision. This work highlights the power of holographic microscopy to probe the material properties and mechanistic underpinnings of biomolecular condensates, paving the way for deeper insights into their roles in synthetic systems.

biophysics↗