Engineering Surfaces of Solid-State Nanopores for Biomolecule Sensing

Shiyu Li
Abstract & Cover

Nanopores have emerged as a special class of single-molecule analytical tool that offers immense potential for sensing and characterizing biomolecules such as nucleic acids and proteins. As an alternative to biological nanopores, solid-state nanopores present remarkable versatility due to their wide-range tunability in pore geometry and dimension as well as their excellent mechanical robustness and stability. However, being intrinsically incompatible with biomolecules, surfaces of inorganic solids need be modified to provide desired functionalities for real-life sensing purposes. In this thesis, we presented an exploration of various surface engineering strategies and an examination of several surface associated phenomena pertaining specifically to solid-state nanopores. Based on the parallel sensing concept using arrayed pores, optical readout is mainly employed throughout the whole study.
For the surface engineering aspect, a list of approaches was explored. A versatile surface patterning strategy for immobilization of biomolecules was developed based on selective poly(vinylphosphonic acid) passivation and electron beam induced deposition technique. This scheme was then implemented on nanopore arrays for nanoparticle localization. In addition, vesicle rupture-based lipid bilayer coating was adapted to truncated-pyramidal nanopores, which was shown to be effective for the minimizing DNA-pore interaction. Further, HfO2 coating by means of atomic layer deposition was employed to prevent the erosion of Si-based pores and to shrink the pore diameter, which enabled reliable investigations of DNA clogging and DNA polymerase docking.
For the surface associated phenomena, several findings were made. The lipid bilayer formation on truncated pyramidal nanopores via instantaneous rupture of individual vesicles was quantified based on combined ionic current monitoring and optical observation.  The probability of pore clogging appeared to linearly increase with the length of DNA strands and applied bias voltage, which could be attributed a higher probability of knotting and/or folding of longer DNA strands and more frequent translocation events at higher voltage. A free-energy based analytical model was proposed to evaluate the DNA-pore interaction and to interpret observed clogging behavior. Finally, docking of DNA polymerase on nanopore arrays was demonstrated using label-free optical method based on Ca2+ indicator dyes, which may open the avenue to sequencing-by-synthesis enabled by the docked polymerase.

Uppsala University
(Uppsala, Sweden)
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