Tunable DNA Origami Nanosensors for Detection of Multiscale Spatial Ion Concentration Gradients

Ion gradients play a vital role in cellular signaling, mechanobiology, and organ-level homeostasis. Despite their importance, accurately mapping these spatial gradients at biologically relevant length scales remains a challenge due to the limited tunability and spatial resolution of conventional fluorescent sensors. Here, we present a DNA origami-based sensor (NanoDyn) with tunable sensitivity that enables the detection of Na⁺-ion gradients across micron to millimeter scales. The sensor design leverages programmable DNA base-pairing interactions to control both the detection range and sensitivity of the sensor. Using fluorescence spectroscopy, we show that NanoDyn can exhibit programmable sensing ranges spanning ∼100-1675 mM Na⁺. To validate the ability to quantify ion gradients and investigate their spatial resolution, we use a custom microfluidic gradient generator, showing that NanoDyn can resolve changes in ion gradients across multiple scales and over distances as little as ∼6 μm, which, here, is limited by the resolution of the microfluidic device. By highlighting the potential of DNA nanodevices as multiscale, tunable ion-gradient sensors, together with their biocompatibility, high temporal resolution, and potential for multiplexed functionalization, this work expands on the role that DNA nanodevices can play in spatial sensing to study ion-mediated processes in microenvironments. Overall, this work advances DNA nanotechnology as a versatile foundation for biosensing with capabilities to probe ion-mediated signaling in health and disease.