DNA Characterization with Solid-State Nanopores and Combined Carbon Nanotube across Solid-State Nanopore Sensors

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DNA Characterization with Solid-State Nanopores and Combined Carbon Nanotube across Solid-State Nanopore Sensors

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Title: DNA Characterization with Solid-State Nanopores and Combined Carbon Nanotube across Solid-State Nanopore Sensors
Author: Vlassarev, Dimitar
Citation: Vlassarev, Dimitar. 2012. DNA Characterization with Solid-State Nanopores and Combined Carbon Nanotube across Solid-State Nanopore Sensors. Doctoral dissertation, Harvard University.
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Abstract: A DNA molecule passing through a nanopore in a liner and sequential fashion allows for unprecedented interrogation of the polymer. Adding transverse electrodes that are comparable in size and sensitive to the DNA molecule, can further the attempts to rapidly sequence DNA. Carbon nanotubes are comparable in size and interact strongly with the DNA molecule. This makes them an excellent choice for integration with nanopores. Only the section of the carbon nanotube in immediate proximity to the nanopore should be sensitive to the DNA molecules. Atomic layer deposition of metal-oxides passivates the sections of the carbon nanotube that are not to interact with the DNA molecule. The coating also protects the thin film interconnects leading to the carbon nanotube. Hafnium oxide is superior to aluminum oxide in chemical resistance and electrical insulation but leads to a high failure rate of the carbon nanotube across nanopore devices. Aluminum oxide, combined with gold thin film interconnects to the carbon nanotube, produced the first functioning devices in electrolyte. These devices had concurrently functioning ionic (current across the nanopore) and transverse (current through the carbon nanotube) channels. No concurrent DNA translocation signal was recorded on the ionic and nanotube current traces. Analyzing the translocation events recorded on the ionic channel indicated that double-stranded DNA (dsDNA) passed through the carbon nanotube articulated nanopore an order of magnitude slower than it would have through a comparable unarticulated nanopore. The slower translocation observed is a necessary condition for sequencing. Investigating dsDNA translocation under various experimental conditions led to the discovery of a new interaction between the molecule and small nanopores. A dsDNA molecule is trapped when the electric field near the nanopore attracts and immobilizes a non-end segment of the molecule at the nanopore orifice without inducing folded translocation. In this work, the expression “trapped dsDNA” will exclusively refer to the immobilization of a dsDNA molecule at the orifice of the nanopore. The ionic current through the nanopore decreases when the dsDNA molecule is trapped by the nanopore. By contrast, a translocating dsDNA molecule under the same conditions causes an ionic current increase. Finite element modeling results predict this behavior for the conditions of the experiment.
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10288439
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