Biology subjects

Paffen, L. J. M. M.

Publications and source records attributed to Paffen, L. J. M. M..

3 recordsLinked to original sources

bioRxiv2025

Enzyme-powered DNA origami nanostructures for enhanced mucosal diffusion

Crossing mucosal barriers is a central challenge for oral drug delivery, where nanoparticle design must balance stability with mobility in complex fluids. Here, we demonstrate DNA origami as a programmable platform to investigate these processes. Using FRET analysis, we show that DNA nanostructures retain their structural integrity for extended periods in porcine intestinal fluid and mucus, establishing their suitability for biologically relevant environments. Building on this, we used single-particle tracking to assess enzyme-powered propulsion within mucus. Both urease and catalase enhanced diffusion only when anchored to the DNA origami structure, with propulsion persisting for tens of minutes. Importantly, enzyme spatial organization dictated performance: symmetric urease placement improved mobility via uniform local pH shifts, while asymmetric catalase placement enabled efficient bubble-driven propulsion. These results highlight DNA origami as a uniquely versatile tool to dissect structure-function relationships in mucus transport and provide design principles for next-generation, enzyme-powered oral delivery systems.

bioengineering↗

bioRxiv2025

Topology Determines DNA Origami Diffusion in Intestinal Mucus

Efficient nanomedicine delivery across mucosal barriers remains a challenge, due to the complex and poorly understood relationship between nanoparticle design and mucus transport. Here, we present DNA origami as a platform to investigate how nanoparticle shape and ligand patterning influence diffusivity in mucus. By decoupling these parameters while maintaining identical material composition, we systematically evaluated the diffusion of rod, icosahedral, and rectangular nanostructures using high-resolution single-particle tracking. Our results reveal that diffusivity in mucus is not solely determined by shape or functionalization alone, but by their interplay: while unmodified rods diffused poorly, their mobility increased significantly upon antibody functionalization, reaching a maximum at an intermediate ligand density. In contrast, rods and icosahedra exhibited less pronounced and non-optimal responses to surface modification. These findings highlight the importance of topology-specific optimization in nanoparticle design and demonstrate the utility of DNA nanotechnology to uncover design rules for next generation mucus-penetrating drug delivery systems.

bioengineering↗

bioRxiv2024

Unveiling DNA Origami Interaction Dynamics on Living Cell Surfaces by Single Particle Tracking

Due to the unique spatial addressability of DNA origami, targeting ligands (e.g. aptamers or antibodies) can be specifically positioned onto the surface of the nanostructure, constituting an essential tool for studying ligand-receptor interactions at the cell surface. While the design and ligand incorporation into DNA origami nanostructures are well-established, the study of cell surface interaction dynamics is still in the explorative phase, where in depth fundamental understanding on the molecular interactions remains underexplored. This study uniquely captures real-time encounters between DNA origami and cells in-situ using single particle tracking (SPT). Here, we functionalized DNA nanorods (NRs) with antibodies or aptamers specific to the epidermal growth factor receptor (EGFR) and used them to target EGFR-overexpressing cancer cells. SPT data revealed that ligand coated NRs selectively bound to the receptors expressed in target cancer cells, while non-functionalized NRs only display negligible cell interactions. Furthermore, we explored the effect of ligand density on the DNA origami, which revealed that aptamer-decorated NRs exhibit non-linear binding characteristics, whereas this effect in antibody-decorated NRs was less pronounced. This study provides new mechanistic insights into the fundamental understanding of DNA origami behaviour at the cell interface, with unprecedented spatiotemporal resolution, aiding the rational design of ligand-targeted DNA origami for biomedical applications.

bioengineering↗