University of Illinois Urbana-Champaign

2D materials based nanopore structures as single molecule sensors

Banerjee, Shouvik

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BANERJEE-DISSERTATION-2016.pdf

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https://hdl.handle.net/2142/90944

Description

Title
2D materials based nanopore structures as single molecule sensors
Author(s)
Banerjee, Shouvik
Issue Date
2016-04-22
Director of Research (if dissertation) or Advisor (if thesis)
Bashir, Rashid
Doctoral Committee Chair(s)
Zuo, Jian-Min
Committee Member(s)
  • Braun, Paul V.
  • Kilian, Kristopher A.
Department of Study
Materials Science & Engineerng
Discipline
Materials Science & Engr
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Date of Ingest
2016-07-07T21:17:58Z
Keyword(s)
  • Nanopores
  • 2D Materials
  • DNA sensors
Abstract
Nanopores are impedance based bio-sensors. The principle of nanopore sensors is analogous to that of a Coulter counter. A nanoscale aperture (the nanopore) is formed in an insulating membrane separating two chambers filled with conductive electrolyte. Charged molecules are driven through the pore under an applied electric voltage (a process known as electrophoresis), thereby modulating the ionic current through the nanopore. The temporary modulation of ionic current due to translocation of the molecule provides useful information about the structure, length, orientation and sequence. This versatile approach permits the label-free, amplification-free analysis of charged biopolymers. The major challenges facing nanopore based techniques for practical sequencing applications are the limitations on temporal and spatial resolution. The finite thickness of membranes limit the spatial resolution of the measurement as multiple nucleotides occupy the pore at a given instant, reducing the sensitivity of the signal making single nucleotide resolution difficult to achieve. Graphene and MoS¬2 as a single layer material of the same order of thickness as the nucleotide separation in a DNA strand presents an exciting alternative to commercial Silicon nitride membranes. These materials also provide potential for exploration of field effect mechanisms which can be an alternative mechanism detect the individual nucleotides in the DNA strand. The possibility and feasibility of using the unique electrical properties of embedded active layers of graphene and MoS2 in stacked membranes has been explored here. The embedded graphene layers presented unique insights into the electrochemical properties of graphene edges in an embedded nanopore structure. The lack of a bad gap in graphene (unless extremely narrow constrictions are fabricated, which is very challenging) makes MoS2 (monolayers have a direct band gap of 1.85 eV) the more favorable material for charge based detection. The electrical properties of both graphene and MoS2 channels are reported here. Additionally we also studied the DNA transport through nanopores in freely suspended MoS2 membranes as well as integration of MoS2 in our stacked architecture. The other major challenge is to control/slow down DNA transport to within bandwidth limitation of commercial instruments to ensure reliable nucleotide separation in the blockade signal. The application of graphene-DNA hydrophobic attractions as a method to reduce DNA translocation speed is reported. A final device with integrated graphene, MoS2 and dielectric layers could provide the required structure to achieve DNA sequencing. In addition atomic layer thin membranes could also improve the diagnostic capabilities of nanopore detection. The atomic layer thickness of these membranes could enable spatial mapping of size differences of an individual molecule. We report the ability of MoS2 membrane to distinguish free DNA from DNA-protein complex molecules. The ability to detect the presence of methyl binding domain proteins on methylated sites of DNA is valuable to the field of cancer diagnostics and such thin membranes could provide a pathway for spatial mapping of individual methylated sites.
Graduation Semester
2016-05
Type of Resource
text
Permalink
http://hdl.handle.net/2142/90944
Copyright and License Information
Copyright 2016 Shouvik Banerjee

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