Unraveling Clogging of Solid-State Nanopores by Selective Polymer Coating: Surface Potential Measurements and Sensing of Long Single Stranded DNA

Abstract

Solid-state nanopores have emerged as powerful tools for single-molecule analysis, with applications ranging from genomics to diagnostics. However, challenges such as surface interactions and clogging have limited their applicability, and a better characterization of the nanopore wall surfaces and control of the surface coating would provide valuable information to tackle these problems. Here, employing a platform capable of high-pressure streaming current measurements in the picoampere range, we characterize the surface potential of solid-state nanopores and perform selective surface coating to elucidate the mechanism for molecular clogging. By examining different operating conditions, such as pore diameter, salt concentration, and pH, we discuss optimizations for precise streaming current measurements. We validate the performance of the setup by studying both bare SiN and polymer-coated nanopores fabricated by the controlled breakdown method. To address the issue of nanopore clogging, we investigate two distinct coating strategies, which involve functionalizing the surface either prior to or after pore formation, and thus targeting only the membrane outer surface, or also the pore interior, respectively. Our results allow us to establish that outer membrane coating is sufficient to provide antifouling properties during translocation of long single-stranded DNA, and provide insight into the leading causes of nanopore clogging: sticking of polymers on the membrane outside the pore, where the electric field is often too weak to break the biomolecules free. These findings highlight the importance of surface characterization and chemical modification in enhancing nanopore performance for single-molecule detection.