DNA Sensing using Nano-crystalline Surface Enhanced Al(2)O(3) Nanopore Sensors

Advanced Functional Materials (Impact Factor: 11.81). 04/2010; 20(8). DOI: 10.1002/adfm.200902128


A new solid-state, Al2O3 nanopore sensor with enhanced surface properties for the real-time detection and analysis of individual DNA molecules is reported. Nanopore formation using electron-beam-based decomposition transforms the local nanostructure and morphology of the pore from an amorphous, stoichiometric structure (O to Al ratio of 1.5) to a heterophase crystalline network, deficient in O (O to Al ratio of ≈0.6). Direct metallization of the pore region is observed during irradiation, thereby permitting the potential fabrication of nanoscale metallic contacts in the pore region with application to nanopore-based DNA sequencing. Dose-dependent phase transformations to purely γ and/or α-phase nanocrystallites are also observed during pore formation, allowing for surface-charge engineering at the nanopore/fluid interface. DNA transport studies reveal an order-of-magnitude reduction in translocation velocities relative to alternate solid-state architectures, accredited to high surface-charge density and the nucleation of charged nanocrystalline domains. The unique surface properties of Al2O3 nanopore sensors make them ideal for the detection and analysis of single-stranded DNA, double-stranded DNA, RNA secondary structures, and small proteins. These nanoscale sensors may also serve as useful tools in studying the mechanisms driving biological processes including DNA–protein interactions and enzyme activity at the single-molecule level.

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Available from: Jian-Min Zuo, Sep 30, 2015
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    • "Once a protein or DNA contacts the pore wall, Van der Waals interactions between the biomolecule and the pore wall slow down the translocation velocity of biomolecule as reported previously with single-stranded DNA49. Electrostatic polymer-pore interactions are also likely and have been reported to slow DNA in systems where the nanopore surface charge is opposite in polarity to the charge on the translocating biomolecule4250. As our experiments were carried out in pH 8 electrolyte and as the isoelectric points of MBD1x and the SiN pore are 8.85 and ~4 respectively5152, we expect electrostatic interactions between the positively charged protein and the negatively charged nanopore surface. "
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    ABSTRACT: Epigenetic modifications in eukaryotic genomes occur primarily in the form of 5-methylcytosine (5 mC). These modifications are heavily involved in transcriptional repression, gene regulation, development and the progression of diseases including cancer. We report a new single-molecule assay for the detection of DNA methylation using solid-state nanopores. Methylation is detected by selectively labeling methylation sites with MBD1 (MBD-1x) proteins, the complex inducing a 3 fold increase in ionic blockage current relative to unmethylated DNA. Furthermore, the discrimination of methylated and unmethylated DNA is demonstrated in the presence of only a single bound protein, thereby giving a resolution of a single methylated CpG dinucleotide. The extent of methylation of a target molecule could also be coarsely quantified using this novel approach. This nanopore-based methylation sensitive assay circumvents the need for bisulfite conversion, fluorescent labeling, and PCR and could therefore prove very useful in studying the role of epigenetics in human disease.
    Scientific Reports 03/2013; 3:1389. DOI:10.1038/srep01389 · 5.58 Impact Factor
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    • "The use of α-hemolysin protein pores for single and doublestranded DNA translocation have inspired the development of solid-state nanopores for DNA and protein analysis [1] [2] [3] [4] [5] [6] [7] [8] [9] [10]. "
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    ABSTRACT: Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.
    Nanotechnology 06/2011; 22(28):285304. DOI:10.1088/0957-4484/22/28/285304 · 3.82 Impact Factor
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    • "The use of α-hemolysin protein nanopores inspired the fabrication of solid-state nanopores. Solid-state nanopores have emerged as novel biosensors for single molecule analysis of DNA, proteins, etc. [1-7]. Solid-state nanopores are more stable than protein nanopores under various experimental conditions like pH, salinity, and temperature [8-11]. "
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    ABSTRACT: Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A novel and simple technique for solid-state nanopore fabrication is reported here. The process involves direct thermal heating of 100 to 300 nm nanopores, made by focused ion beam (FIB) milling in free-standing membranes. Direct heating results in shrinking of the silicon dioxide nanopores. The free-standing silicon dioxide membrane is softened and adatoms diffuse to a lower surface free energy. The model predicts the dynamics of the shrinking process as validated by experiments. The method described herein, can process many samples at one time. The inbuilt stress in the oxide film is also reduced due to annealing. The surface composition of the pore walls remains the same during the shrinking process. The linear shrinkage rate gives a reproducible way to control the diameter of a pore with nanometer precision.
    Nanoscale Research Letters 05/2011; 6(1):372. DOI:10.1186/1556-276X-6-372 · 2.78 Impact Factor
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