Mapping 3D cellular mechanical activity with matrix-embedded DNA force-history probes

Cells continuously integrate mechanical cues from the surrounding extracellular matrix to control fundamental biological processes such as proliferation and migration. Yet, studying the mechanical activity of cells in 3D over time is challenging, low-throughput, and requires specialized equipment. Here, we introduce DNA-based force-history probes, which convert transient pico-Newton forces into cumulative fluorescent signals within a mechanically adjustable DNA-crosslinked cell culture matrix. The probes provide control over signal lifetimes, allowing stress patterns to be recorded over minutes to days with tunable temporal memory. We use this system to visualize the mechanical activity of breast cancer spheroids and map the trajectories of migrating cancer cells. By combining different fluorophores and DNA-encoded signal lifetimes, we produce dual-color probes that associate temporal information to mechanical events. Overall, force-history probes provide an endpoint-readable record of mechanical cell-matrix activity, offering new opportunities for studying cell function in physiology and disease.