Molecular Programming of Steric Tags for Controlled Nanopore Translocation toward Precision Clinical Diagnostic Assistance

Using this strategy, we achieve a six-order-of-magnitude dynamic range (0.001–1000 ng/mL) for matrix metalloproteinases (MMP-1, -2, and -9). In a cohort of 231 clinical urine samples, the nanopore-derived MMP activity profiles showed excellent agreement with ELISA-derived measurements and, when integrated with a machine-learning classifier, enabled classification of urothelial carcinoma with 96.2% accuracy. As a proof-of-concept extension, the modular probe design was further adapted for PSA/KLK3 activity analysis in clinical serum samples, supporting the feasibility of extending the approach to an additional protease target.

This work establishes a general chemical framework for programming molecular behavior in confined nanoscale environments, bridging molecular design principles with functional nanopore sensing.