Biology subjects

Voets, I. K.

Publications and source records attributed to Voets, I. K..

3 recordsLinked to original sources

bioRxiv2024

Selective ion binding and uptake shape the microenvironment of biomolecular condensates

Biomolecular condensates modulate various ion-dependent cellular processes and can regulate subcellular ion distributions by selective uptake of ions. However, the molecular grammar governing condensate-ion interactions is poorly understood. Here, we use NMR spectroscopy of ions and model condensate components to quantify and spatially resolve selective ion binding to condensates and show that these interactions follow the law of matching water affinities, resulting in strong binding between proteins and chaotropic anions, and between nucleic acids and kosmotropic cations. Ion uptake into condensates directly follows binding affinities, resulting in selective uptake of strong-binding ions, but exclusion of weak-binding ions. Ion binding further shapes the condensate microenvironment by altering the composition, viscosity and interface potential. Such changes can have profound effects on biochemical processes taking place inside condensates, as we show for RNA duplex formation. Our findings provide a new perspective on the role of condensate-ion interactions in cellular bio- and electrochemistry and may aid design of condensate-targeting therapeutics.

biophysics↗

bioRxiv2023

DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

Owing to its longevity and extremely high information density, DNA has emerged as an attractive medium for archival data storage. Scalable parallel random access of information is a desirable property of any storage system. For DNA-based storage systems, however, this yet has to be robustly established. Here we develop thermoconfined PCR, a novel method that enables multiplexed, repeated random access of compartmentalized DNA files. Our strategy is based on stable localization of biotin-functionalized oligonucleotides inside microcapsules with temperature-dependent membrane permeability. At low temperatures, microcapsules are permeable to enzymes, primers, and amplified products, while at high temperatures membrane collapse prevents molecular crosstalk during amplification. We demonstrate that our platform outperforms non-compartmentalized DNA storage with respect to repeated random access and reducing amplification bias during multiplex PCR. Using fluorescent sorting, we additionally demonstrate sample pooling and data retrieval by barcoding of microcapsules. Our thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access of archival DNA files.

synthetic biology↗

bioRxiv2022

Direct evidence for pinning of single, ice-bound antifreeze proteins by subzero nanoscopy

Ice-binding by antifreeze proteins (AFPs) reduces freezing temperatures and arrests ice-crystal ripening, making AFPs essential for survival in ice-laden environments and attractive as biocompatible antifreezes. Whilst their activity was identified over 50 years ago, the physical mechanisms are still debated because experimental insights at the molecular scale remain elusive. Here we introduce optical nanoscopy to resolve the ice/water interfacial dynamics of single AFPs. Using this method, we demonstrate pinning of individual proteins. Surprisingly, this quasi-permanent pinning is lost when freezing point depression activity is inhibited by a single mutation in the ice-binding site. These findings provide direct experimental evidence for the adsorption-inhibition paradigm, pivotal to all theoretical descriptions of activity and offer new insights in the molecular mechanisms by which these biological antifreezes function.

biophysics↗