Mimicking the Cell Signaling Environment with Spatially-Encoded DNA Hydrogels

Extracellular matrix (ECM) biochemical and biophysical cues play a key role in cellular processes, including cellular proliferation, differentiation, migration, and apoptosis. Yet understanding the specific role among the hundreds of biochemical cues is incredibly complex. Synthetic hydrogels offer a route to recapitulate the ECM through incorporation of user-defined biochemical cues in biologically relevant physical environments. Patterning biomolecules in hydrogels offers a route to visualizing and measuring the role of how spatially organized cue presentation can modulate cell behavior. However, the number of orthogonal bioconjugation chemistries limits the ability to probe the role of many biochemical cues at once. To this end, we have developed a technique for spatially encoding PEG hydrogels with oligonucleotides using thiol-yne photochemistry, where the sequence specificity of DNA enables chemical control over individual patterned domains. Herein we demonstrate that these hydrogels can be rapidly photo-patterned using mask-free digital photolithography with high resolution DNA features (1.5 mm) over centimeter-scale areas, with control over DNA density and feature depth. Moreover, we exploit the sequence dependent properties of DNA to reversibly tether DNA strands, localize protein-DNA conjugates, and bind unmodified proteins with DNA aptamers. Importantly, we observe that localized cell signaling protein-DNA conjugates can selectively activate cells on patterned domains. This work highlights that this approach is capable of isolating biochemical cues allowing one to observe spatially confined cell signaling processes, which may lead to a better understanding, and control, over the complex signaling environments that determine cell fate.