Single molecule sensing using solid-state nanopores has sparked tremendous interest within the last decade, whether it be electrical or optical detection of biomolecules, their complexes or binding kinetics. Therefore, the main focus of this thesis was on developing a nanopore biosensor integrated into a microfluidic channel for in-flow electrochemical detection of DNA at single molecule level. By constituting such a compact planar device, nanopores can potentially be turned into future lab-on-chip biosensors with a capability of in-flow single molecule detection.
Two different types of nanopore materials were initially fabricated; a novel ultra thin PI membrane and SiN, and characterized in terms of nanopore conductance and electric noise. An alternative approach to locally and gradually thin SiN nanopores using Reactive Ion Etch technique was also presented with detailed fabrication, optimization and characterization steps. DNA translocation using polymer and thinned SiN nanopores was shown at the end of each fabrication chapter.
On account of their compatibility with microfluidic integration, SiN nanopore chip was compacted into a PDMS microfluidic channel for the purpose of creating potential single molecule detection capabilities under continuous flow conditions. The introduction of flow to the nanopore system is important, because it would ideally bring the benefit of simultaneous electrochemical detection of biological entities in flow, where the idea of lab-on-chip biosensing devices is built upon. To characterize the rheological properties of DNA and flow characteristics, optical experiments were carried out using Confocal Microscopy and Fluorescence Correlation Spectroscopy. The effect of flow rate on the basics of nanopore detection (e.g. nanopore conductance and noise) was discussed, and investigated experimentally. Last, DNA translocation in the absence and the presence of flow was studied as a proof-of-principle. The investigation of detection capability of the integrated device using the chosen flow rates sets the basics for the future applications of nanopore-integrated microfluidic systems (e.g. on-nanopore chip capillary electrophoresis).