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Erschienen in:
Solid-State Nanopore Sensors for Nucleic Acid Analysis Kapitel lesen Erstes Kapitel lesen

2011 | OriginalPaper | Buchkapitel

5. Solid State Nanopores for Selective Sensing of DNA

verfasst von : Waseem Asghar, Joseph A. Billo, Samir M. Iqbal

Erschienen in: Nanopores

Verlag: Springer US

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Abstract

This chapter focuses on the functionalized solid state nanopores for the purpose of rapidly and accurately sensing specific sequence of DNA. Fabrication processes are described, consisting of standard photolithography followed by using either a transmission electron microscope or a plasma polymer film to create and shrink the nanopore. The molecular dynamics of DNA-nanopore interactions are also discussed. Smaller pore diameter results in slower translocation of DNA through the nanopore, but increases van der waals force on the DNA and decreases the ionic current. Increase in applied voltage decreases the van der Waals force while increasing the ionic current and translocation velocity. Chemical functionalization of nanopores is then discussed. This allows a nanopore to be selective with translocating specific DNA sequence. This is done by modifying the surface in an attempt to control its surface charges and hydrophobicity. Probe DNA is used to functionalize the pore and achieve selectivity. In terms of sensing, perfect complementary DNA translocates faster than single-base-mismatch DNA. The flux can be measured from the current pulses when the translocating DNA blocks the nanopore under applied voltage.

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Vorheriges Kapitel Membrane-Embedded Channel of Bacteriophage Phi29 DNA-Packaging Motor for Translocation and Sensing of Double-Stranded DNA
Nächstes Kapitel Sensing Single Protein Molecules with Solid-State Nanopores
Literatur
1.
Iqbal, S.M., D. Akin, and R. Bashir, Solid-state nanopore channels with DNA selectivity. nature nanotechnology, 2007. 2(4): p. 243–248.
2.
Li, J., et al., Ion-beam sculpting at nanometre length scales. Nature, 2001. 412(6843): p. 166–169.CrossRef
3.
Stein, D., J. Li, and J.A. Golovchenko, Ion-beam sculpting time scales. Physical review letters, 2002. 89(27): p. 276106.CrossRef
4.
Storm, A.J., et al., Fabrication of solid-state nanopores with single-nanometre precision. Nature materials, 2003. 2(8): p. 537–540.CrossRef
5.
Wu, S., S.R. Park, and X.S. Ling, Lithography-free formation of nanopores in plastic membranes using laser heating. Nano Lett, 2006. 6(11): p. 2571–2576.CrossRef
6.
Park, S.R., H. Peng, and X.S. Ling, Fabrication of nanopores in silicon chips using feedback chemical etching. Small, 2007. 3(1): p. 116.CrossRef
7.
Chang, H., et al., Fabrication and characterization of solid-state nanopores using a field emission scanning electron microscope. Applied Physics Letters, 2006. 88: p. 103109.CrossRef
8.
Sato, K., et al., Anisotropic etching rates of single-crystal silicon for TMAH water solution as a function of crystallographic orientation. Sensors & Actuators: A. Physical, 1999. 73(1–2): p. 131–137.CrossRef
9.
Sundaram, K.B., A. Vijayakumar, and G. Subramanian, Smooth etching of silicon using TMAH and isopropyl alcohol for MEMS applications. Microelectronic Engineering, 2005. 77(3–4): p. 230–241.CrossRef
10.
Biance, A.L., et al., Focused ion beam sculpted membranes for nanoscience tooling. Microelectronic Engineering, 2006. 83(4–9): p. 1474–1477.CrossRef
11.
Gierak, J., et al., Sub-5 nm FIB direct patterning of nanodevices. Microelectronic Engineering, 2007. 84(5–8): p. 779–783.CrossRef
12.
Gadgil, V.J., et al., Fabrication of nano structures in thin membranes with focused ion beam technology. Surface & Coatings Technology, 2009. 203(17–18): p. 2436–2441.CrossRef
13.
Danelon, C., et al., Fabrication and functionalization of nanochannels by electron-beam-induced silicon oxide deposition. Nano Lett, 2005. 5: p. 403–407.CrossRef
14.
Nilsson, J., et al., Localized functionalization of single nanopores. Advanced Materials, 2006. 18(4): p. 427–431.CrossRef
15.
Harrell, C.C., et al., DNA-nanotube artificial ion channels. Journal of the American Chemical Society, 2004. 126(48): p. 15646.CrossRef
16.
Chen, P., et al., Atomic layer deposition to fine-tune the surface properties and diameters of fabricated nanopores. Nano Letters, 2004. 4(7): p. 1333–1337.CrossRef
17.
Heng, J.B., et al., Stretching DNA using the electric field in a synthetic nanopore. Nano letters, 2005. 5(10): p. 1883.CrossRef
18.
Kim, M.J., et al., Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA analysis. Adv. Mater, 2006. 18(23): p. 3149–3153.CrossRef
19.
Kim, M.J., et al., Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope. Nanotechnology, 2007. 18: p. 205302.CrossRef
20.
Chapman, C.L., et al., Plasma polymer thin film depositions to regulate gas permeability through nanoporous track etched membranes. Journal of Membrane Science, 2008. 318(1–2): p. 137–144.CrossRef
21.
Timmons, R.B. and A.J. Griggs, Pulsed plasma polymerizations. Plasma Polymer Films: p. 217–245.
22.
Han, L.M. and R.B. Timmons, Pulsed-plasma polymerization of 1-vinyl-2-pyrrolidone: Synthesis of a linear polymer. Journal of Polymer Science Part A Polymer Chemistry, 1998. 36: p. 3121–3129.CrossRef
23.
Zhang, J., et al., Investigation of the plasma polymer deposited from pyrrole. Thin solid films, 1997. 307(1–2): p. 14–20.CrossRef
24.
Rinsch, C.L., et al., Pulsed radio frequency plasma polymerization of allyl alcohol: Controlled deposition of surface hydroxyl groups. Langmuir, 1996. 12(12): p. 2995–3002.CrossRef
25.
Cross, J.D., E.A. Strychalski, and H.G. Craighead, Size-dependent DNA mobility in nanochannels. Journal of Applied Physics, 2007. 102: p. 024701.CrossRef
26.
Fyta, M.G., et al., Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore. Arxiv preprint physics/0701029, 2007.
27.
Ramachandran, A., et al., Characterization of DNA-Nanopore Interactions by Molecular Dynamics. American Journal of Biomedical Sciences, 2009. 1(4): p. 344–351.CrossRef
28.
Kalé, L., et al., NAMD2: Greater Scalability for Parallel Molecular Dynamics* 1. Journal of Computational Physics, 1999. 151(1): p. 283–312.MATHCrossRef
29.
MacKerell Jr, A.D., et al., All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B-Condensed Phase, 1998. 102(18): p. 3586–3616.
30.
Aksimentiev, A., et al., Microscopic kinetics of DNA translocation through synthetic nanopores. Biophysical journal, 2004. 87(3): p. 2086–2097.CrossRef
31.
Meller, A., et al., Rapid nanopore discrimination between single polynucleotide molecules. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(3): p. 1079.CrossRef
32.
Xiao, K.P., et al., A chloride ion-selective solvent polymeric membrane electrode based on a hydrogen bond forming ionophore. Anal. Chem, 1997. 69(6): p. 1038–1044.CrossRef
33.
Minami, H., et al., AN EVALUATION OF SIGNAL AMPLIFICATION BY THE ION CHANNEL SEBSIR BASED ON A GLUTAMATE RECEPTOR ION CHANNEL PROTEIN. Analytical Sciences, 1991. 7(Supple): p. 1675–1676.
34.
Kuramitz, H., et al., Electrochemical immunoassay at a 17-estradiol self-assembled monolayer electrode using a redox marker. The Analyst, 2003. 128(2): p. 182–186.CrossRef
35.
Aoki, H. and Y. Umezawa, Trace analysis of an oligonucleotide with a specific sequence using PNA-based ion-channel sensors. The Analyst, 2003. 128(6): p. 681–685.CrossRef
36.
Gadzekpo, V.P.Y., et al., Development of an ion-channel sensor for heparin detection. Analytica Chimica Acta, 2000. 411(1–2): p. 163–173.CrossRef
37.
Ali, M., et al., Chemical modification of track-etched single conical nanopores inducing inversed inner wall polarity. GSI Annu. Rep. 2006, 2007. 1: p. 323.
38.
Lee, S.B., et al., Antibody-based bio-nanotube membranes for enantiomeric drug separations. Science, 2002. 296(5576): p. 2198.CrossRef
39.
Siwy, Z., et al., Conical-nanotube ion-current rectifiers: the role of surface charge. Journal of the American Chemical Society, 2004. 126(35): p. 10850.CrossRef
40.
Siwy, Z., et al., Protein biosensors based on biofunctionalized conical gold nanotubes. Journal of the American Chemical Society, 2005. 127(14): p. 5000.CrossRef
41.
Manning, M., et al., A versatile multi-platform biochip surface attachment chemistry. Materials Science & Engineering C, 2003. 23(3): p. 347–351.CrossRef
42.
Chen, P., et al., Probing single DNA molecule transport using fabricated nanopores. Nano Letters, 2004. 4(11): p. 2293–2298.CrossRef
43.
Meller, A., L. Nivon, and D. Branton, Voltage-driven DNA translocations through a nanopore. Physical Review Letters, 2001. 86(15): p. 3435–3438.CrossRef
44.
Fologea, D., et al., Slowing DNA translocation in a solid-state nanopore. Nano Lett., 2005. 5: p. 1734–1737.CrossRef
45.
Kim, Y.R., et al., Nanopore sensor for fast label-free detection of short double-stranded DNAs. Biosensors and Bioelectronics, 2007. 22(12): p. 2926–2931.CrossRef
46.
Guo, Z., et al., Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Research, 1994. 22(24): p. 5456.CrossRef
47.
Balladur, V., A. Theretz, and B. Mandrand, Determination of the main forces driving DNA oligonucleotide adsorption onto aminated silica wafers. Journal of colloid and interface science, 1997. 194(2): p. 408–418.CrossRef
48.
Fang, Y. and J.H. Hoh, Early intermediates in spermidine-induced DNA condensation on the surface of mica. J. Am. Chem. Soc, 1998. 120(35): p. 8903–8909.CrossRef
49.
Umehara, S., et al., Current rectification with poly- l -lysine-coated quartz nanopipettes. Nano Lett, 2006. 6(11): p. 2486–2492.CrossRef
50.
Wang, G., et al., Electrostatic-gated transport in chemically modified glass nanopore electrodes. J. Am. Chem. Soc, 2006. 128(23): p. 7679–7686.CrossRef
51.
Wanunu, M. and A. Meller, Chemically modified solid-state nanopores. Nano Letters, 2007. 7(6): p. 1580–1585.CrossRef
52.
Jang, L.S. and H.K. Keng, Modified fabrication process of protein chips using a short-chain self-assembled monolayer. Biomedical Microdevices, 2008. 10(2): p. 203–211.CrossRef
53.
Gyurcsányi, R.E., T. Vigassy, and E. Pretsch, Biorecognition-modulated ion fluxes through functionalized gold nanotubules as a novel label-free biosensing approach. Chemical Communications, 2003. 2003(20): p. 2560–2561.CrossRef
54.
Zhao, Q., et al., Detecting SNPs using a synthetic nanopore. Nano letters, 2007. 7(6): p. 1680.CrossRef
55.
Kohli, P., et al., DNA-functionalized nanotube membranes with single-base mismatch selectivity. Science, 2004. 305(5686): p. 984.CrossRef
56.
Vlassiouk, I., P. Takmakov, and S. Smirnov, Sensing DNA hybridization via ionic conductance through a nanoporous electrode. Langmuir, 2005. 21(11): p. 4776–4778.CrossRef
57.
Pretsch, E., The new wave of ion-selective electrodes. Trends in Analytical Chemistry, 2007. 26(1): p. 46–51.CrossRef
58.
Howorka, S., S. Cheley, and H. Bayley, Sequence-specific detection of individual DNA strands using engineered nanopores. Nature biotechnology, 2001. 19(7): p. 636–639.CrossRef
59.
Berezhkovskii, A.M. and S.M. Bezrukov, Optimizing transport of metabolites through large channels: molecular sieves with and without binding. Biophysical journal, 2005. 88(3): p. 17–19.CrossRef
60.
Bauer, W.R. and W. Nadler, Molecular transport through channels and pores: Effects of in-channel interactions and blocking. Proceedings of the National Academy of Sciences, 2006. 103(31): p. 11446.CrossRef
61.
Chaara, M. and R.D. Noble, Effect of convective flow across a film on facilitated transport. Separation Science and Technology, 1989. 24(11): p. 893–903.CrossRef
62.
Noble, R.D., Generalized microscopic mechanism of facilitated transport in fixed site carrier membranes. Journal of membrane science, 1992. 75(1–2): p. 121–129.CrossRef
63.
Liu, Y. and S.M. Iqbal, A mesoscale model of DNA interaction with functionalized nanopore. Applied Physics Letters, 2009. 95: p. 223701.CrossRef
64.
Brogan, K.L., et al., Direct oriented immobilization of F (ab) antibody fragments on gold. Analytica Chimica Acta, 2003. 496(1–2): p. 73–80.CrossRef
65.
Kim, B.Y., et al., Direct Immobilization of Fabin Nanocapillaries for Manipulating Mass-Limited Samples. J. Am. Chem. Soc, 2007. 129(24): p. 7620–7626.CrossRef
66.
Benson, D.E., et al., Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins. Science, 2001. 293(5535): p. 1641.CrossRef
67.
Tripathi, A., et al., Nanobiosensor Design Utilizing a Periplasmic E. coli Receptor Protein Immobilized within Au/Polycarbonate Nanopores. Biosens. Bioelectron, 2003. 19: p. 249–259.CrossRefMathSciNet
68.
Uram, J.D., et al., Submicrometer pore-based characterization and quantification of antibody-virus interactions. Small (Weinheim an der Bergstrasse, Germany), 2006. 2(8–9): p. 967.
Metadaten
Titel
Solid State Nanopores for Selective Sensing of DNA
verfasst von
Waseem Asghar
Joseph A. Billo
Samir M. Iqbal
Copyright-Jahr
2011
Verlag
Springer US
Buch
Nanopores

Print ISBN: 978-1-4419-8251-3

Electronic ISBN: 978-1-4419-8252-0

Copyright-Jahr: 2011

DOI
https://doi.org/10.1007/978-1-4419-8252-0_5

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