Simulation guided intramolecular orthogonal reporters for dissecting cellular oxidative stress and response

Cellular oxidative stress from effects of reactive oxygen species (ROS) and its induced molecular response play an important role in the pathogenesis of various diseases and important biological processes. Nanostructure-based fluorescent probes can simultaneously map the localization and abundance of ROS and its induced molecules in living cells. However, proximity-induced fluorophore interaction leads to low sensitivity and poor specificity. Here, we engineered intramolecular Orthogonal Reporters (iOR) based on DNA nanostructure scaffolds. Fluorescence reporters in iOR were precisely located with appropriate distance by simulation eliminating the undesired interaction of fluorophores. iOR functionalized with nuclear localization signal peptide is capable of imaging ROS and its related DNA repair enzyme (APE1) in the nucleus and cytoplasm with high sensitivity and specificity. iOR discloses the strong positive relation of ROS and APE1 as well as their synergistic regulation in living cells and tumor-bearing mice. This fact is first presented by direct fluorescence imaging. This work reported a new procedure for developing nanostructure-based molecular probes and would find broad applications in cellular biology and nanotechnology.