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DNA translocation through an array of kinked nanopores

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Please use this identifier to cite or link to this item: http://hdl.handle.net/1928/11091

DNA translocation through an array of kinked nanopores

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Title: DNA translocation through an array of kinked nanopores
Author: Chen, Zhu
Advisor(s): Brinker, C. Jeffrey
Committee Member(s): Brinker, C. Jeffrey
Ward, Tim
Keller, David
Thomas, James
Dunphy, Darren
Department: University of New Mexico. Dept. of Chemical and Nuclear Engineering
Subject(s): sol-gel
nanopore fabrication
DNA detection
self-assembly
LC Subject(s): Nanostructured materials
Biosensors
Translocation (genetics)
Degree Level: Doctoral
Abstract: Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA, and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these behaviors in more robust synthetic materials that are more readily integrated into practical devices. To date, the guided etching of polymer films, focused ion beam sculpting, and electron-beam lithography and tuning of silicon nitride membranes have emerged as three promising approaches to define synthetic solid-state pores with sub-nanometer resolution. These procedures have in common the formation of nominally cylindrical or conical pores aligned normal to the membrane surface. Here we report the formation of ‘kinked’ silica nanopores, using evaporation induced self-assembly, and their further tuning and chemical derivatization using atomic layer deposition. Compared to ‘straight-through’ proteinaceous nanopores of comparable dimensions, kinked nanopores exhibit a factor of up to 5x reduction in translocation velocity, which has been identified as one of the critical issues in DNA sequencing. Additionally we demonstrate an efficient two-step approach to create a nanopore array exhibiting nearly perfect selectivity for ssDNA over dsDNA. We show that a coarse-grained drift-diffusion theory with a sawtooth like potential can reasonably describe the velocity and translocation time of DNA through the pore. By control of pore size, length, and shape, we capture the major functional behaviors of protein pores in our solid-state nanopore system.
Graduation Date: July 2010
URI: http://hdl.handle.net/1928/11091

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