Solid-state nanopores for biosensing with submolecular resolution

Biochemical Society Transactions

Volumn 40, Issue 4, 2012, Pages 624-628

  Bahrami, Azadeh ^a   Doǧan, Fatma ^a   Japrung, Deanpen ^a,b   Albrecht, Tim ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

Author keywords

Biosensing; DNA sequencing; Graphene; Nanopore; Protein DNA interaction; Protein protein interaction

Indexed keywords

GRAPHENE;

CONFERENCE PAPER; DNA SEQUENCE; GENETIC PROCEDURES; NANOPORE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; SENSOR; SOLID STATE; SOLID STATE NANOPORE;

BIOSENSING TECHNIQUES; DNA; NANOPORES; NANOTECHNOLOGY; PROTEINS; RNA;

EID: 84864388269     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120121     Document Type: Conference Paper

References (45)

1. Neher, E. and Sakmann, B. (1976) Single-channel currents recorded from membrane of denervated frog muscle fibres. Nature 260, 799-802
2. Bezrukov, S.M. and Vodyanoy, I. (1993) Probing alamethicin channels with water-soluble polymers: effects on conductance of channel states. Biophys. J. 64, 16-25
3. Deamer, D.W. and Akeson, M. (2000) Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol. 18, 147-151 (Pubitemid 30171332)
4. Kasianowicz, J.J., Brandin, E., Branton, D. and Deamer, D.W. (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 93, 13770-13773 (Pubitemid 26424195)
5. Li, J., Gershow, M., Stein, D., Brandin, E. and Golovchenko, J.A. (2003) DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2, 611-615
6. Schoch, R.B., Han, J. and Renaud, P. (2008) Transport phenomena in nanofluidics. Rev. Mod. Phys. 80, 839-883
7. Smeets, R.M.M., Keyser, U.F., Krapf, D., Wu, M.Y., Dekker, N.H. and Dekker, C. (2006) Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 6, 89-95 (Pubitemid 43166107)
8. Li, J., Stein, D., McMullan, C., Branton, D., Aziz, M.J. and Golovchenko, J.A. (2001) Ion-beam sculpting at nanometre length scales. Nature 412, 166-169 (Pubitemid 32674708)
9. Storm, A.J., Chen, J.H., Zandbergen, H.W. and Dekker, C. (2005) Translocation of double-strand DNA through a silicon oxide nanopore. Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 71, 051903
10. Fologea, D., Brandin, E., Uplinger, J., Branton, D. and Li, J. (2007) DNA conformation and base number simultaneously determined in a nanopore. Electrophoresis 28, 3186-3192 (Pubitemid 47506447)
11. Akeson, M., Branton, D., Kasianowicz, J.J., Brandin, E. and Deamer, D.W. (1999) Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77, 3227-3233
12. Meller, A., Nivon, L., Brandin, E., Golovchenko, J. and Branton, D. (2000) Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. U.S.A. 97, 1079-1084 (Pubitemid 30080815)
13. Kowalczyk, S.W., Tuijtel, M.W., Donkers, S.P. and Dekker, C. (2010) Unraveling single-stranded DNA in a solid-state nanopore. Nano Lett. 10, 1414-1420
14. van den Hout, M., Skinner, G.M., Klijnhout, S., Krudde, V. and Dekker, N.H. (2011) The passage of homopolymeric RNA through small solid-state nanopores. Small 7, 2217-2224
15. Zhao, Q., Comer, J., Dimitrov, V., Yemenicioglu, S., Aksimentiev, A. and Timp, G. (2008) Stretching and unzipping nucleic acid hairpins using a synthetic nanopore. Nucleic Acids Res. 36, 1532-1541 (Pubitemid 351426106)
16. McNally, B., Singer, A., Yu, Z.L., Sun, Y.J., Weng, Z.P. and Meller, A. (2010) Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett. 10, 2237-2244
17. Fologea, D., Ledden, B., McNabb, D.S. and Li, J. (2007) Electrical characterization of protein molecules by a solid-state nanopore. Appl. Phys. Lett. 91, 053901
18. Talaga, D.S. and Li, J. (2009) Single-molecule protein unfolding in solid state nanopores. J. Am. Chem. Soc. 131, 9287-9297
19. Oukhaled, A., Cressiot, B., Bacri, L., Pastoriza-Gallego, M., Betton, J.-M., Bourhis, E., Jede, R., Gierak, J., Auvray, L. and Pelta, J. (2011) Dynamics of completely unfolded and native proteins through solid-state nanopores as a function of electric driving force. ACS Nano 5, 3628-3638
20. Freedman, K.J., Juürgens, M., Prabhu, A., Ahn, C.W., Jemth, P., Edel, J.B. and Kim, M.J. (2011) Chemical, thermal, and electric field induced unfolding of single protein molecules studied using nanopores. Anal. Chem. 83, 5137-5144
21. Ayub, M., Ivanov, A., Hong, J., Kuhn, P., Instuli, E., Edel, J.B. and Albrecht, T. (2010) Precise electrochemical fabrication of sub-20 nm solid-state nanopores for single-molecule biosensing. J. Phys.: Condensed Matter 22, 454128
22. Ayub, M., Ivanov, A., Instuli, E., Cecchini, M., Chansin, G., McGilvery, C., Hong, J.G., Baldwin, G., McComb, D., Edel, J.B. and Albrecht, T. (2010) Nanopore/electrode structures for single-molecule biosensing. Electrochim. Acta 55, 8237-8243
23. Wei, R., Gatterdam, V., Wieneke, R., Tampé, R. and Rant, U. (2012) Stochastic sensing of proteins with receptor-modified solid-state nanopores. Nat. Nanotechnol. 7, 257-263
24. Howorka, S. and Siwy, Z. (2009) Nanopore analytics: sensing of single molecules. Chem. Soc. Rev. 38, 2360-2384
25. Zwolak, M. and Di Ventra, M. (2005) Electronic signature of DNA nucleotides via transverse transport. Nano Lett. 5, 421-424 (Pubitemid 40449709)
26. Tsutsui, M., Taniguchi, M., Yokota, K. and Kawai, T. (2010) Identifying single nucleotides by tunnelling current. Nat. Nanotechnol. 5, 286-290
27. Tsutsui, M., Rahong, S., Iizumi, Y., Okazaki, T., Taniguchi, M. and Kawai, T. (2011) Single-molecule sensing electrode embedded in-plane nanopore. Sci. Rep. 1, 46
28. Huang, S., He, J., Chang, S., Zhang, P., Liang, F., Li, S., Tuchband, M., Fuhrmann, A., Ros, R. and Lindsay, S. (2010) Identifying single bases in a DNA oligomer with electron tunnelling. Nat. Nanotechnol. 5, 868-873
29. Chang, S., Huang, S., He, J., Liang, F. and Zhang, P. (2010) Electronic signatures of all four DNA nucleosides in a tunneling gap. Nano Lett. 10, 1070-1075
30. He, J., Lin, L., Zhang, P. and Lindsay, S. (2007) Identification of DNA basepairing via tunnel-current decay. Nano Lett. 7, 3854-3858
31. Nojima, Y., Tanaka, H., Yoshida, Y. and Kawai, T. (2004) High-resolution scanning tunneling microscopy and spectroscopy studies of deoxyribonucleic acid and fluorescein isothiocyanate. Jpn. J. Appl. Phys., Part 1 43, 5526-5527
32. Ivanov, A.P., Instuli, E., McGilvery, C.M., Baldwin, G., McComb, D.W., Albrecht, T. and Edel, J.B. (2011) DNA tunneling detector embedded in a nanopore. Nano Lett. 11, 279-285
33. Merchant, C.A., Healy, K., Wanunu, M., Ray, V., Peterman, N., Bartel, J., Fischbein, M.D., Venta, K., Luo, Z.T., Johnson, A.T.C. and Drndić, M. (2010) DNA translocation through graphene nanopores. Nano Lett. 10, 2915-2921
34. Postma, H.W.C. (2010) Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett. 10, 420-425
35. Garaj, S., Hubbard, W., Reina, A., Kong, J., Branton, D. and Golovchenko, J.A. (2010) Graphene as a subnanometre trans-electrode membrane. Nature 467, 190-193
36. Schneider, G.F., Kowalczyk, S.W., Calado, V.E., Pandraud, G., Zandbergen, H.W., Vandersypen, L.M.K. and Dekker, C. (2010) DNA translocation through graphene nanopores. Nano Lett. 10, 3163-3167
37. Saha, K.K., Drndić, M. and Nikolić, B.K. (2012) DNA base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore. Nano Lett. 12, 50-55
38. Han, A., Creus, M., Schuürmann, G., Linder, V., Ward, T.R., de Rooij, N.F. and Staufer, U. (2008) Label-free detection of single protein molecules and protein-protein interactions using synthetic nanopores. Anal. Chem. 80, 4651-4658 (Pubitemid 351842344)
39. Kowalczyk, S.W., Hall, A.R. and Dekker, C. (2009) Detection of local protein structures along DNA using solid-state nanopores. Nano Lett. 10, 324-328
40. Hall, A.R., van Dorp, S., Lemay, S.G. and Dekker, C. (2009) Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore. Nano Lett. 9, 4441-4445
41. Zhao, Q., Sigalov, G., Dimitrov, V., Dorvel, B., Mirsaidov, U., Sligar, S., Aksimentiev, A. and Timp, G. (2007) Detecting SNPs using a synthetic nanopore. Nano Lett. 7, 1680-1685 (Pubitemid 47140444)
42. Dorvel, B., Sigalov, G., Zhao, Q., Comer, J., Dimitrov, V., Mirsaidov, U., Aksimentiev, A. and Timp, G. (2009) Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore. Nucleic Acids Res. 37, 4170-4179
43. Soni, G.V., Singer, A., Yu, Z.L., Sun, Y.J., McNally, B. and Meller, A. (2010) Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores. Rev. Sci. Instrum. 81, 014301
44. Singer, A., Wanunu, M., Morrison, W., Kuhn, H., Frank-Kamenetskii, M. and Meller, A. (2010) Nanopore based sequence specific detection of duplex DNA for genomic profiling. Nano Lett. 10, 738-742
45. Yusko, E.C., Johnson, J.M., Majd, S., Prangkio, P., Rollings, R.C., Li, J., Yang, J. and Mayer, M. (2011) Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat. Nanotechnol. 6, 253-260