Biology subjects

Drees, C.

Publications and source records attributed to Drees, C..

4 recordsLinked to original sources

bioRxiv2025

Stable Synthetic Organelles from Aqueous Two-Phase Systemswith Access to the Cell Translation Machinery

Cells compartmentalize vital processes in membrane-less organelles to gain spatiotemporal control of metabolism, signaling, and for protection under stress. While such compartments can be manipulated or even de novo designed with genetic engineering of cells, the transfer and operation of exogenous synthetic compartments for intracellular engineering is challenged by developing pathways for implantation into the cell, stability issues, toxicity, ability to maintain compartmentalization, and access to cellular machinery. Here we introduce dextran-lipid droplets as versatile exogenous synthetic compartments, that are readily uptaken by model cancer and immune cells and are stable inside cells for days. Furthermore, the droplets can encapsulate nucleic acids with high efficiency, are non-toxic and endosomal escape occurs when formulated with ionizable lipids, as shown by reporter protein translation of an mRNA hosted inside the organelles. We propose that such synthetic microreactors implanted into the cells will become an important bioengineering tool to incorporate more complex and bioorthogonal molecular systems into cells.

synthetic biology↗

bioRxiv2025

Synthetic Aptamer Mechanoreceptors Enable Cell-SpecificForce Sensing and Temporal Control via DNA Circuits

Cells interpret mechanical cues from their microenvironment with spatiotemporal precision to guide adaptive behaviors. However, engineering synthetic mechanosensing systems with both cell-specificity and programmability remains challenging, especially when targeting ubiquitous classical mechanoreceptors. Here, we introduce an all-DNA mechanosensing platform based on aptamers that transmit force through noncanonical surface receptors. Aptamer-receptor recognition acts as a molecular gate for force transduction, enabling the design of mechanoprobes with cell-type selectivity. These probes interpret diverse mechanical inputs via distinct mechanisms, including actomyosin-driven contractility and membrane ruffling during macropinocytosis. By integrating aptamer mechanoprobes with upstream DNA reaction networks, we achieve reversible and temporally programmable mechanoresponses. This modular, all-nucleic-acid system offers a general framework for constructing tunable mechanotransduction circuits. It expands the design space for synthetic mechanobiology and provides new opportunities for autonomous, multi-layered mechanical-biochemical regulation in tissue engineering, morphogenesis, and dynamic cell programming.

synthetic biology↗

bioRxiv2025

A Versatile Toolbox for Nanoscale Interrogation of Multiprotein Assemblies inside Living Cells

Quantitative analysis of protein interactions and the formation of higher-order assemblies in living cells remains a major challenge. Here, we introduce a versatile nanopatterning toolbox that employs capillary nanostamping of functionalized polymers to generate high contrast bio-functionalized nanodot arrays (bNDAs) with diameters below 500 nm. By leveraging orthogonal adaptor designs, we achieve robust immobilization of diverse fluorescent protein fusions, enabling simultaneous and selective recruitment of cytosolic and membrane-associated proteins into discrete nanodomains. This approach of forming cytosolic nanodot arrays (cNDAs) provides striking capabilities for dissecting cytosolic multiprotein complexes with molecular precision. Focusing on the assembly of the multimeric myddosome complex, we demonstrate density-dependent recruitment and co-localization of the core components MyD88, IRAK4, IRAK1, and TRAF6 within cNDAs. Super-resolution microscopy reveals distinct nanoscale clustering of MyD88 and IRAK4 and uncovers the ultrastructural architecture of IRAK4 oligomers. These analyses highlight the spatial organization and hierarchical assembly of the myddosome at the nanoscale in the native cellular context. Collectively, our findings establish cNDAs as a powerful platform for reconstituting and analyzing intricate multiprotein assemblies in live cells, offering new opportunities for elucidating the principles of complex protein networks.

biophysics↗

bioRxiv2024

Nuclease-Resistant L-DNA Tension Probes Enable Long-TermForce Mapping of Single Cells and Cell Consortia

DNA-based tension probes with precisely programmable force response provide important insights into cellular mechanosensing. However, their degradability in cell culture limits their use for long-term imaging, for instance, when cells migrate, divide, and differentiate. This is a critical limitation for providing insights into mechanobiology for these longer-term processes. Here, we present DNA-based tension probes that are entirely designed based on the stereoisomer of biological D-DNA, i.e., L-DNA. We demonstrate that L-DNA tension probes are essentially indestructible by nucleases and provide days-long imaging without significant loss in image quality. We also show their superiority already for short imaging times commonly used for classical D-DNA tension probes. We showcase the potential of these resilient probes to image minute movements, and for generating long term force maps of single cells and for the first time, of collectively migrating cell populations.

biophysics↗