Controlling DNA translocation through gate modulation of nanopore wall surface charges

ACS Nano

Volumn 5, Issue 7, 2011, Pages 5509-5518

  He, Yuhui ^a   Tsutsui, Makusu ^a   Fan, Chun ^b   Taniguchi, Masateru ^a   Kawai, Tomoji ^a  

^a OSAKA UNIVERSITY   (Japan)

^b PEKING UNIVERSITY   (China)

Author keywords

gate control; nanopore sequencing; wall surface charges

Indexed keywords

CAPTURE RATE; COUNTERIONS; DNA MOLECULES; DNA SEQUENCING; DNA TRANSLOCATION; DRAGGING FORCES; ELECTRICAL TUNING; ELECTROOSMOTIC; FEEDBACK DEVICE; GATE BIAS; GATE CONTROL; IONIC CURRENT; POSITIVE GATE BIAS; WALL SURFACE CHARGES; WALL SURFACES;

CHARGED PARTICLES; DNA; DNA SEQUENCES; ELECTRIC FIELDS; NANOPORES; SURFACE CHARGE;

GENE ENCODING;

DNA;

ARTICLE; CHEMISTRY; ELECTRICITY; METHODOLOGY; NANOPORE; NANOTECHNOLOGY; SURFACE PROPERTY;

DNA; ELECTRICITY; NANOPORES; NANOTECHNOLOGY; SURFACE PROPERTIES;

EID: 79961044530     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn201883b     Document Type: Conference Paper

References (38)

1. Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Characterization of Individual Polynucleotide Molecules Using a Membrane Channel Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773 (Pubitemid 26424195)
2. Meller, A.; Nivon, L.; Brandin, E.; Golovchenko, J.; Branton, D. Rapid Nanopore Discrimination between Single Polynucleotide Molecules Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 1079-1084 (Pubitemid 30080815)
3. Dekker, C. Solid-State Nanopores Nat. Nanotechnol. 2007, 2, 209-215 (Pubitemid 46739810)
4. Branton, D.; Deamer, D. W.; Marziali, A.; Bayley, H.; Benner, S. A.; Butler, T.; Di Ventra, M.; Garaj, S.; Hibbs, A.; Huang, X. et al. The Potential and Challenges of Nanopore Sequencing Nat. Biotechnol. 2008, 26, 1146-1153
5. Zwolak, M.; Di Ventra, M. Colloquium: Physical Approaches to DNA Sequencing and Detection Rev. Mod. Phys. 2008, 80, 141-165
6. Kang, X.; Gu, L.-Q.; Cheley, S.; Bayley, H. Single Protein Pores Containing Molecular Adapters at High Temperatures Angew. Chem., Int. Ed. 2005, 117, 1519-1523
7. Akeson, M.; Branton, D.; Kasianowicz, J. J.; Brandin, E.; Deamer, D. W. Microsecond Time-Scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments within Single RNA Molecules Biophys. J. 1999, 77, 3227-3233
8. Meller, A.; Nivon, L.; Branton, D. Voltage-Driven DNA Translocations through a Nanopore Phys. Rev. Lett. 2001, 86, 3435-3438 (Pubitemid 32380654)
9. Zwolak, M.; Di Ventra, M. Electronic Signature of DNA Nucleotides via Transverse Transport Nano Lett. 2005, 5, 421-424 (Pubitemid 40449709)
10. Lagerqvist, J.; Zwolak, M.; Di Ventra, M. Fast DNA Sequencing via Transverse Electronic Transport Nano Lett. 2006, 6, 779-782
11. Tsutsui, M.; Taniguchi, M.; Yokota, K.; Kawai, T. Identifying Single Nucleotides by Tunnelling Current Nat. Nanotechnol. 2010, 5, 286-290
12. Huang, S.; He, J.; Chang, S.; Zhang, P.; Liang, F.; Li, S.; Tuchband, M.; Fuhrmann, A.; Ros, R.; Lindsay, S. Identifying Single Bases in a DNA Oligomer with Electron Tunnelling Nat. Nanotechnol. 2010, 5, 868-873
13. Muthukumar, M. Mechanism of DNA Transport through Pores Annu. Rev. Biophys. Biomed. 2007, 36, 435-450 (Pubitemid 46998127)
14. Li, J.; Talaga, D. S. The Distribution of DNA Translocation Times in Solid-State Nanopores J. Phys.: Condens. Matter 2010, 22, 454129
15. Fologea, D.; Uplinger, J.; Thomas, B.; McNabb, D. S.; Li, J. Slowing DNA Translocation in a Solid-State Nanopore Nano Lett. 2005, 5, 1734-1737 (Pubitemid 41396156)
16. Ghosal, S. Effect of Salt Concentration on the Electrophoretic Speed of a Polyelectrolyte through a Nanopore Phys. Rev. Lett. 2007, 98, 238104
17. Trepagnier, E. H.; Radenovic, A.; Sivak, D.; Geissler, P.; Liphardt, J. Controlling DNA Capture and Propagation through Artificial Nanopores Nano Lett. 2007, 7, 2824-2830 (Pubitemid 47522445)
18. Keyser, U. F.; Koeleman, B. N.; van Dorp, S.; Ralph M. M. Smeets, D. K.; Lemay, S. G.; Dekker, N. H.; Dekker, C. Direct Force Measurements on DNA in a Solid-State Nanopore Nat. Phys. 2006, 2, 473-477 (Pubitemid 44022563)
19. He, H.; Scheicher, R. H.; Pandey, R.; Rocha, A. R.; Sanvito, S.; Grigoriev, A.; Ahuja, R.; Karna, S. P. Functionalized Nanopore-Embedded Electrodes for Rapid DNA Sequencing J. Phys. Chem. C 2008, 112, 3456-3459
20. Nam, S.-W.; Rooks, M. J.; Kim, K.-B.; Rossnagel, S. M. Ionic Field Effect Transistors with Sub-10 nm Multiple Nanopores Nano Lett. 2009, 9, 2044-2048
21. Nam, S.-W.; Lee, M.-H.; Lee, S.-H.; Lee, D.-J.; Rossnagel, S. M.; Kim, K.-B. Sub-10-nm Nanochannels by Self-Sealing and Self-Limiting Atomic Layer Deposition Nano Lett. 2010, 10, 3324-3329
22. Wong, C. T. A.; Muthukumar, M. Polymer Capture by Electro-osmotic Flow of Oppositely Charged Nanopores J. Chem. Phys. 2007, 126, 164903
23. Muthukumar, M. Theory of Capture Rate in Polymer Translocation J. Chem. Phys. 2010, 132, 195101
24. Storm, A. J.; Storm, C.; Chen, J.; Zandbergen, H.; Joanny, J.-F.; Dekker, C. Fast DNA Translocation through a Solid-State Nanopore Nano Lett. 2005, 5, 1193-1197 (Pubitemid 41084390)
25. Smeets, R. M. M.; Keyser, U. F.; Krapf, D.; Wu, M.-Y.; Dekker, N. H.; Dekker, C. Salt Dependence of Ion Transport and DNA Translocation through Solid-State Nanopores Nano Lett. 2006, 6, 89-95 (Pubitemid 43166107)
26. Behrens, S. H.; Grier, D. G. The Charge of Glass and Silica Surfaces J. Chem. Phys. 2001, 115, 6716-6721 (Pubitemid 33046645)
27. Stein, D.; Kruithof, M.; Dekker, C. Surface-Charge-Governed Ion Transport in Nanofluidic Channels Phys. Rev. Lett. 2004, 93, 035901
28. van Dorp, S.; Keyser, U. F.; Dekker, N. H.; Dekker, C.; Lemay, S. G. Origin of the Electrophoretic Force on DNA in Solid-State Nanopores Nat. Phys. 2009, 5, 347-351
29. Manning, G. S. The Molecular Theory of Polyelectrolyte Solutions with Applications to the Electrostatic Properties of Polynucleotides Q. Rev. Biophys. 1978, 11, 179-246 (Pubitemid 8373665)
30. Chang, H.; Kosari, F.; G., A.; Alam, M. A.; Vasmatzis, G.; Bashir, R. DNA-Mediated Fluctuations in Ionic Current through Silicon Oxide Nanopore Channels Nano Lett. 2004, 4, 1551-1556 (Pubitemid 39186347)
31. Kowalczyk, S. W.; Tuijtel, M. W.; Donkers, S. P.; Dekker, C. Unraveling Single-Stranded DNA in a Solid-State Nanopore Nano Lett. 2010, 10, 1414-1420
32. Skinner, G. M.; van den Hout, M.; Broekmans, O.; Dekker, C. D. N. H. Distinguishing Single- and Double-Stranded Nucleic Acid Molecules Using Solid-State Nanopores Nano Lett. 2009, 9, 2953-2960
33. Chen, P.; Mitsui, T.; Farmer, D. B.; Golovchenko, J.; Gordon, R. G.; Branton, D. Atomic Layer Deposition to Fine-Tune the Surface Properties and Diameters of Fabricated Nanopores Nano Lett. 2004, 4, 1333-1337 (Pubitemid 39092181)
34. Venkatesan, B. M.; Dorvel, B.; Yemenicioglu, S.; Watkins, N.; Petrov, I.; Bashir, R. Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis Adv. Mater. 2009, 21, 2771
35. 3 Nanopore Sensors Adv. Funct. Mater. 2010, 20, 1266-1275
36. Mirsaidov, U.; Comer, J.; Dimitrov, V.; Aksimentiev, A.; Timp, G. Slowing the Translocation of Double-Stranded DNA Using a Nanopore Smaller Than the Double Helix Nanotechnology 2010, 21, 395501
37. Deamer, D. W.; Branton, D. Characterization of Nucleic Acids by Nanopore Analysis Acc. Chem. Res. 2002, 35, 817-825
38. Ai, Y.; Liu, J.; Zhang, B.; Qian, S. Field Effect Regulation of DNA Translocation through a Nanopore Anal. Chem. 2010, 82, 8217-8225