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bioRxiv · 10.1101/2025.07.21.665473

Mechanically Tunable DNA Hydrogel Microparticles for 3D Cellular Systems

Walther, T.·Dalaka, E.·Fläschner, G.·Platzman, I.·Emmert, M.·Roca-Cusachs, P.·Trepat, X.·Göpfrich, K.
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Abstract

Hydrogel microparticles (HMPs) are powerful tools to study and manipulate cellular behavior in 3D cell culture systems and animal models. Here, fully DNA-based HMPs are presented, whose material properties can be precisely tuned by sequence-programmable design of self-assembling DNA nanostructures. These DNA-HMPs offer control over size, stiffness, viscoelasticity and ligand presentation. They are formed by microfluidic encapsulation of two types of orthogonal DNA nanostars and a sequence-complementary DNA linker in water-in-oil droplets. By varying the valency of the DNA nanostar designs, tunable mechanical properties are achieved - spanning three orders of magnitude in Youngs modulus from 30 Pa to 6.5 kPa with distinct viscoelastic behavior. Click-chemistry based functionalization with the small fibronectin-derived peptide cyclic-RGD (c[RGD]) enables integration into fibroblast spheroids. DNA-HMPs are stably retained within the spheroids for several days and undergo design- and stiffness-dependent remodeling, indicating active interactions between the cells and the DNA-HMPs. Combining tunable material properties and inherent biocompatibility of DNA with straightforward functionalization and stimuli-responsiveness, these DNA-HMPs represent a versatile tool to probe and manipulate tissue behaviors in 3D cell cultures and in vivo models. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/665473v2_ufig1.gif" ALT="Figure 1000"> View larger version (51K): org.highwire.dtl.DTLVardef@c226ceorg.highwire.dtl.DTLVardef@81c3b3org.highwire.dtl.DTLVardef@1573ee1org.highwire.dtl.DTLVardef@e1518c_HPS_FORMAT_FIGEXP M_FIG DNA hydrogel microparticles are designed to exhibit controllable viscoelasticity and stiffness across three orders of magnitude from 30 Pa to 6.5 kPa. They are uptaken into fibroblast spheroids where they are actively remodeled by cellular forces depending on their mechanical properties. C_FIG

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Walther, T., Dalaka, E., Fläschner, G., Platzman, I., Emmert, M., Roca-Cusachs, P., Trepat, X., Göpfrich, K.. 2025-07-24. Mechanically Tunable DNA Hydrogel Microparticles for 3D Cellular Systems. https://doi.org/10.1101/2025.07.21.665473

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