Biocompatible Microscale DNA Hydrogels with Programmable Swelling and Sequence-Specific Dissolution

Stimulus-responsive DNA hydrogels with swelling capabilities are a promising class of materials for biomedical applications such as drug delivery and biosensing. However, translation of these systems to microscale applications requires fabrication methods that are both biocompatible and material-efficient, while enabling precise control over stimulus-induced swelling and its impact on molecular transport. Here, we present a biocompatible fabrication and characterization platform for microscale DNA-hydrogels (μSDs) with tunable isotropic swelling and dissolving properties. Our approach includes a biocompatible, material-efficient fabrication workflow that conserves valuable DNA reagents by minimizing dead volume and process loss. We then demonstrated modular control over isotropic swelling in μSDs, achieving up to a two-fold size increase through programmable DNA design parameters. We further established a quantitative reaction-diffusion workflow to estimate effective diffusivity and characterize swelling dependent transport of a DNA binding fluorescent probe in spherical μSDs. Finally, we demonstrate the dissolution of μSDs using a DNA strand and find that dissolution kinetics are governed by the rates of coupled strand-displacement reactions and diffusive transport. This platform enables programmable swelling and structural disassembly in μSDs. Swelling-induced network expansion further modulates transport of a DNA binding fluorescent probe within the μSD network, highlighting the potential of programmable structural remodeling for future biosensing, controlled release, and single-cell assay applications.