Engineering Linker-Enhanced OmpG Nanopores for Rapid Single-Molecule Protease Detection

Single-molecule nanopore sensors have enabled real-time detection of enzymatic cleavage events, yet achieving sensitive and specific analysis of protease activity remains an important challenge for diagnostic applications. We engineered OmpG nanopore constructs incorporating thrombin recognition peptides into loop 6 with varied flexible and negatively charged linkers to optimize accessibility and cleavage. SDS-PAGE gel analysis showed that constructs with the recognition peptide placed after residue D225 and incorporating dual linkers achieved cleavage efficiencies up to 95%, whereas constructs without linkers showed limited cleavage. Single-channel recordings revealed that linker integration modulates pore conductance, with extended loops exhibiting intermediate open-state currents near 18 pA compared to 25 pA in wild-type OmpG. Upon thrombin addition, rapid and irreversible current drops confirmed real-time protease activity detection. These results demonstrate the critical role of linker design, particularly flexibility and charge, in optimizing nanopore protease sensors, providing a versatile platform for biomedical applications.