Noise and bandwidth of current recordings from submicrometer pores and nanopores

ACS Nano

Volumn 2, Issue 5, 2008, Pages 857-872

  Uram, Jeffrey D ^a   Ke, Kevin ^a   Mayer, Michael L ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Coulter counter; Current recording; Nanopores; Noise bandwidth; Resistive pulse sensing; Signal bandwidth; Submicromter pores

Indexed keywords

ACOUSTIC EMISSIONS; BANDWIDTH; BIOMOLECULES; CHEMICAL REACTIONS; ELECTRIC POTENTIAL; EXPERIMENTS; FLUIDICS; GLASS; GRAFTING (CHEMICAL); MICROFLUIDICS; NANOPORES; NUCLEIC ACIDS; OPTICAL RECEIVERS; POSITRON ANNIHILATION SPECTROSCOPY; POSITRON EMISSION TOMOGRAPHY; SYNTHESIS (CHEMICAL); THERMOPLASTICS;

(E ,2E) THEORY; APPLIED VOLTAGES; CURRENT TRACES; ELECTRICAL CURRENT; EXPERIMENTAL RESULTS; EXPERIMENTAL STUDIES; IONIC CURRENTS; NANO PORES; POLYETHYLENE TEREPHTHALATE (PET); SENSITIVE MEASUREMENTS; SIGNAL BANDWIDTHS; SINGLE MOLECULE (SM); SOURCE OF NOISE; SPECTRA (CO); SUB MICROMETERS; SUBSTRATE MATERIALS;

NANOSTRUCTURED MATERIALS;

NANOMATERIAL;

ARTICLE; ARTIFICIAL MEMBRANE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ELECTRIC CONDUCTIVITY; ELECTROMAGNETIC FIELD; METHODOLOGY; NANOTECHNOLOGY; PARTICLE SIZE; POROSITY; ULTRASTRUCTURE;

COMPUTER SIMULATION; ELECTRIC CONDUCTIVITY; ELECTROMAGNETIC FIELDS; MEMBRANES, ARTIFICIAL; MODELS, CHEMICAL; NANOSTRUCTURES; NANOTECHNOLOGY; PARTICLE SIZE; POROSITY;

EID: 45749095863     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn700322m     Document Type: Article

References (168)

1. Choi, Y.; Baker, L. A.; Hillebrenner, H.; Martin, C. R. Biosensing with Conically Shaped Nanopores and Nanotubes. Phys. Chem. Chem. Phys. 2006, 8, 4976-4988.
2. Henriquez, R. R., Ito, T.; Sun, L.; Crooks, R. M. The Resurgence of Coulter Counting for Analyzing Nanoscale Objects. Analyst 2004, 129, 478-482.
3. Bayley, H.; Martin, C. R. Resistive-Pulse Sensing - from Microbes to Molecules. Chem. Rev. 2000, 100, 2575-2594.
4. Deamer, D. W.; Branton, D. Characterization of Nucleic Acids by Nanopore Analysis. Acc. Chem. Res. 2002, 35, 817-825.
5. Seidel, R.; Dekker, C. Single-Molecule Studies of Nucleic Acid Motors. Curr. Opin. Struct. Biol. 2007, 17, 80-86.
6. Bayley, H. Sequencing Single Molecules of DNA. Curr. Opin. Chem. Biol. 2006, 10, 628-637.
7. Blake, S.; Mayer, T.; Mayer, M.; Yang, J. Monitoring Chemical Reactions by Using Ion Channel-Forming Peptides. ChemBioChem 2006, 7, 433-435.
8. Capone, R., Blake, S.; Restrepo, M. R.; Yang, J.; Mayer, M. Designing Nanosensors Based on Charged Derivatives of Gramicidin A. J. Am. Chem. Soc. 2007, 129, 9737-9745.
9. Mayer, M.; Semetey, V.; Gitlin, I., Yang, J.; Whitesides, G. M. Using Ion Channel-Forming Peptides to Quantify Protein-Ligand Interactions. J. Am. Chem. Soc. 2008, 130, 1453-1465.
10. Benndorf, K. Low-Noise Recording In Single-Channel Recording, 2nd ed.; Sakmann, B., Neher, E., Eds., Plenum Press: New York, 1995; pp 129-153.
11. Sherman-Gold, R. The Axon Guide; Axon Instruments, Inc.: 1993.
12. Mayer, M.; Kriebel, J. K.; Tosteson, M. T.; Whitesides, G. M. Microfabricated Teflon Membranes for Low-Noise Recordings of Ion Channels in Planar Lipid Bilayers. Biophys. J. 2003, 85, 2684-2695.
13. Levis, R. A., Rae, J. L. Low-Noise Patch-Clamp Techniques. Methods Enzymol. 1998, 293, 218-266.
14. Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Characterization of Individual Polynucleoticle Molecules Using a Membrane Channel. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773.
15. Gu, L.; Braha, O.; Conlan, S.; Cheley, S.; Bayley, H. Stochastic Sensing of Organic Analytes by a Pore-Forming Protein Containing a Molecular Adapter. Nature 1999, 398, 686-690.
16. Fertig, N.; Tilke, A.; Blick, R. H.; Kotthaus, J. P.; Behrends, J. C.; Bruggencate, G. Stable Integration of Isolated Cell Membrane Patches in a Nanomachined Aperture. Appl. Phys. Lett. 2000, 77, 1218-1220.
17. Saleh, O. A.; Sohn, L. L. Quantitative Sensing of Nanoscale Colloids Using a Microchip Coulter Counter. Rev. Sci. Instrum. 2001, 72, 4449-4451.
18. Apel, P. Y.; Korchev, Y. E.; Siwy, Z.; Spohr, R.; Yoshida, M. Diode-Like Single-Ion Track Membrane Prepared by Electro-Stopping. Nucl. Instrum. Methods Phys. Res., Sect. B 2001, 184, 337-346.
19. Li, J.; Stein, D.; McMullan, C.; Branton, D.; Aziz, M. J.; Golovchenko, J. A. Ion-Beam Sculpting at Nanometre Length Scales. Nature 2001, 412, 166-169.
20. Harrell, C. C.; Lee, S. B.; Martin, C. R. Synthetic Single-Nanopore and Nanotube Membranes. Anal. Chem. 2003, 75, 6861-6867.
21. Storm, A. J., Chen, J. H.; Ling, X. S.; Zandbergen, H. W.; Dekker, C. Fabrication of Solid-State Nanopores with Single-Nanometre Precision. Nat. Mater. 2003, 2, 537-540.
22. Ito, T.; Sun, L.; Crooks, R. M. Simultaneous Determination of the Size and Surface Charge of Individual Nanoparticles Using a Carbon Nanotube-Based Coulter Counter. Anal. Chem. 2003, 75, 2399-2406.
23. Saleh, O. A.; Sohn, L. L. Direct Detection of Antibody-Antigen Binding Using an on-Chip Artificial Pore. Proc. Natl. Acad Sci. U.S.A. 2003, 100, 820-824.
24. Chang, H.; Kosari, F.; Andreadakis, G., Alam, M. A.; Vasmatzis, G.; Bashir, R. DNA-Mediated Fluctuations in Ionic Current through Silicon Oxide Nanopore Channels. Nano Lett. 2004, 4, 1551-1556.
25. Heng, J. B.; Ho, C.; Kim, T.; Timp, R.; Aksimentiev, A.; Grinkova, Y. V.; Sligar, S.; Schulten, K.; Timp, G. Sizing DNA Using a Nanometer-Diameter Pore. Biophys. J. 2004, 87, 2905-2911.
26. Berkane, E.; Orlik, F.; Charbit, A.; Danelon, C.; Fournier, D.; Benz, R., Winterhalter, M. Nanopores: Maltoporin Channel as a Sensor for Maltodextrin and Lamda-Phage. J. Nanobiotechnol 2005, 3:3.
27. Uram, J. D.; Ke, K., Hunt, A. J.; Mayer, M. Label-Free Affinity Assays by Rapid Detection of Immune Complexes in Submicrometer Pores. Angew. Chem., Int. Ed. 2006, 45, 2281-2285.
28. Wu, M. Y.; Krapf, D.; Zandbergen, M.; Zandbergen, H. W.; Batson, P. E. Formation of Nanopores in Sin/Sio2 Membrane with an Electron Beam. Appl. Phys. Lett. 2005, 87, 113106.
29. Chang, H.; Iqbal, S. M.; Stach, E. A.; King, A. H.; Zaluzec, N.J., Bashir, R. Fabrication and Characterization of Solid-State Nanopores Using a Field Emission Scanning Electron Microscope. Appl. Phys. Lett. 2006, 88, 103109.
30. Harrell, C. C.; Siwy, Z. S.; Martin, C. R. Conical Nanopore Membranes: Controlling the Nanopore Shape. Small 2006, 2, 194-198.
31. Wei, C.; Bard, A. J.; Feldberg, S. W. Current Rectification at Quartz Nanopipet Electrodes. Anal. Chem. 1997, 69, 4627-4633.
32. Karhanek, M.; Kemp, J. T.; Pourmand, N.; Davis, R. W.; Webb, C. D. Single DNA Molecule Detection Using Nanopipettes and Nanoparticles. Nano Lett. 2005, 5, 403-407.
33. Benndorf, K. Properties of Single Cardiac Na Channels at 35 Degrees C. J. Gen. Physiol. 1994, 104, 801-820.
34. Danelon, C.; Santschi, C.; Brugger, J.; Vogel, H. Fabrication and Functionalization of Nanochannels by Electron-Beam-Induced Silicon Oxide Deposition. Langmuir 2006, 22, 10711-10715.
35. Wu, S.; Park, S. R.; Ling, X. S. Lithography-Free Formation of Nanopores in Plastic Membranes Using Laser Heating. Nano Lett. 2006, 6, 2571-2576.
36. Quist, A. P.; Chand, A.; Ramachandran, S.; Daraio, C.; Jin, S.; Lai, R. Atomic Force Microscopy Imaging and Electrical Recording of Lipid Bilayers Supported over Microfabricated Silicon Chip Nanopores: Lab-on-a-Chip System for Lipid Membranes and Ion Channels. Langmuir 2007, 23, 1375-1380.
37. Harrell, C. C.; Choi, Y.; Horne, L. P., Baker, L. A.; Siwy, Z. S. Martin, C. R. Resistive-Pulse DNA Detection with a Conical Nanopore Sensor. Langmuir 2006, 22, 10837-10843.
38. Kim, M. J.; Wanunu, M.; Bell, D. C.; Meller, A. Rapid Fabrication of Uniformly Sized Nanopores and Nanopore Arrays for Parallel DNA Analysis. Adv. Mater. 2006, 18, 3149-3153.
39. Park, S. R.; Peng, H.; Ling, X. S. Fabrication of Nanopores in Silicon Chips Using Feedback Chemical Etching. Small 2007, 3, 116-119.
40. Siwy, Z.; Apel, P.; Baur, D.; Dobrev, D. D.; Korchev, Y. E.; Neumann, R.; Spohr, R.; Trautmann, C.; Voss, K. Preparation of Synthetic Nanopores with Transport Properties Analogous to Biological Channels. Surf. Sci. 2003, 532-535, 1061-1066.
41. Schmidt, C.; Mayer, M.; Vogel, H. A Chip-Based Biosensor for the Functional Analysis of Single Ion Channels. Angew. Chem. Int. Ed. 2000, 39, 3137-3140.
42. Cai, Q.; Ledden, B.; Krueger, E.; Golovchenko, J. A.; Li, J. Nanopore Sculpting with Noble Gas Ions. J. Appl. Phys. 2006, 100, 024914.
43. Mitsui, T.; Stein, D.; Kim, Y. R.; Hoogerheide, D.; Golovchenko, J. A. Nanoscale Volcanoes: Accretion of Matter at Ion-Sculpted Nanopores. Phys. Rev. Lett. 2006, 96, 036102.
44. Sun, L.; Crooks, R. M. Single Carbon Nanotube Membranes: A Well-Defined Model for Studying Mass Transport through Nanoporous Materials. J. Am. Chem. Soc. 2000, 122, 12340-12345.
45. Kovarik M. L.; Jacobson, S. C. Attoliter-Scale Dispensing in Nanofluidic Channels. Anal. Chem. 2007, 79, 1655-1660.
46. Wharton, J. E.; Jin, P.; Sexton, L. T., Horne, L. P.; Sherrill, S. A., Mino, W. K.; Martin, C. R. A Method for Reproducibly Preparing Synthetic Nanopores for Resistive-Pulse Biosensors. Small 2007, 3, 1424-1430.
47. von Schulthess, G. K.; Benedek, G. B.; DeBlois, R. W. Measurement of the Cluster Size Distributions for High Functionality Antigens Cross-Linked by Antibody. Macromolecules 1980, 13, 939-945.
48. von Schulthess, G. K.; Benedek G. B.; DeBlois, R. W. Experimental Measurements of the Temporal Evolution of Cluster Size Distributions for High-Functionality Antigens Cross-Linked by Antibody. Macromolecules 1983, 16, 434-440.
49. Uram, J. D.; Ke, K.; Hunt, A. J.; Mayer, M. Submicrometer Pore-Based Characterization and Quantification of Antibody-Virus Interactions. Small 2006, 2, 967-972.
50. Siwy, Z. S. Ion-Current Rectification in Nanopores and Nanotubes with Broken Symmetry. Adv. Funct. Mater. 2006, 16, 735-746.
51. Siwy, Z. S.; Heins, E.; Harrell, C. C.; Kohli, P.; Martin, C. R. Conical-Nanotube Ion-Current Rectifiers: The Role of Surface Charge. J. Am. Chem. Soc. 2004, 126, 10850-10851.
52. Siwy, Z. S.; Powell, M. R.; Kalman, E.; Astumian, R. D., Eisenberg, R. S. Negative Incremental Resistance Induced by Calcium in Asymmetric Nanopores. Nano Lett. 2006, 6, 473-477.
53. Siwy, Z. S.; Powell, M. R.; Petrov, A.; Kalman, E.; Trautmann, C.; Eisenberg, R. S. Calcium-Induced Voltage Gating in Single Conical Nanopores. Nano Lett. 2006, 6, 1729-1734.
54. Siwy, Z.; Fulinski, A. Fabrication of a Synthetic Nanopore Ion-Pump. Phys. Rev. Lett. 2002, 89, 198103.
55. Siwy, Z. S.; Fulinski, A. 1/F Noise in Ion Transport through Nanopores: Origins and Mechanism. AIP Conf. Proc. 2003, 665, 273-282.
56. Luchian, T.; Shin, S. H.; Bayley, H. Kinetics of a Three-Step Reaction Observed at the Single-Molecule Level. Angew. Chem., Int. Ed. 2003, 42, 1926-1929.
57. Shin, S. H.; Bayley, H. Stepwise Growth of a Single Polymer Chain. J. Am. Chem. Soc. 2005, 127, 10462-10463.
58. Uram, J. D.; Mayer, M. Estimation of Solid Phase Affinity Constants Using Resistive-Pulses from Functionalized Nanoparticles. Biosens. Bioelectron. 2007, 22, 1556-1560.
59. Siwy, Z.; Trofin, L; Kohli, P.; Baker, L. A.; Trautmann, C.; Martin, C. R. Protein Biosensors Based on Biofunctionalized Conical Gold Nanotubes. J. Am. Chem. Soc. 2005, 127, 5000-5001.
60. Howorka, S.; Nam, J.; Bayley, H.; Kahne, D. Stochastic Detection of Monovalent and Bivalent Protein-Ligand Interactions. Angew. Chem., Int. Ed. 2004, 43, 842-846.
61. Keyser, U. F.; Krapf, D.; Koeleman, B. N.; Smeets, R. M. M.; Dekker, N. H.; Dekker, C. Nanopore Tomography of a Laser Focus. Nano Lett. 2005, 5, 2253-2256.
62. Smeets, R. M. M.; Keyser, U. F.; Wu, M. Y.; Dekker, N. H.; Dekker, C. Nanobubbles in Solid-State Nanopores. Phys. Rev. Lett. 2006, 97, 088101.
63. 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.
64. Shin, S. H.; Luchian, T.; Cheley, S., Braha, O.; Bayley, H. Kinetics of a Reversible Covalent-Bond-Forming Reaction Observed at the Single-Molecule Level. Angew. Chem., Int. Ed. 2002, 41, 3707-3709.
65. Luchian, T.; Shin, S. H.; Bayley, H. Single-Molecule Covalent Chemistry with Spatially Separated Reactants. Angew. Chem., Int. Ed. 2003, 42, 3766-3771.
66. Kamik, R.; Duan, C.; Castelino, K; Daiguji, H.; Majumdar, A. Rectification of Ionic Current in a Nanofluidic Diode. Nano Lett. 2007, 7, 547-551.
67. Vlassiouk, I.; Siwy, Z. S. Nanofluidic Diode. Nano Lett. 2007, 7, 552-556.
68. Howorka, S.; Cheley, S.; Bayley, H. Sequence-Specific Detection of Individual DNA Strands Using Engineered Nanopores. Nat. Biotechnol. 2001, 19, 636-639.
69. Saleh, O. A.; Sohn, L. L. An Artificial Nanopore for Molecular Sensing. Nano Lett. 2003, 3, 37-38.
70. Bezrukov, S. M.; Kasianowicz, J. J. Dynamic Partitioning of Neutral Polymers into a Single Ion Channel In Structure and Dynamics of Confined Polymers; Kasianowicz, J. J., Kellermayer, M. S. Z., Deamer, D. W., Eds; Kluwer Academic Publishers: Norwell, MA, 2002; pp 117-130.
71. Bezrukov, S. M.; Vodyanoy, I.; Parsegian, V. A. Counting Polymers Moving through a Single Ion Channel. Nature 1994, 370, 279-281.
72. Li, J.; Gershow, M.; Stein, D.; Brandin, E., Golovchenko, J. A. DNA Molecules and Configurations in a Solid State Nanopore Microscope. Nat. Mater. 2003, 2, 611-615.
73. DeBlois, R. W.; Bean, C. P. Counting and Sizing of Submicron Particles by the Resistive Pulse Technique. Rev. Sci. Instrum. 1970, 41, 909-916.
74. Anderson, J. L.; Quinn, J. A. The Relationship between Particle Size and Signal in Coulter-Type Counters. Rev. Sci. Instrum. 1971, 42, 1257-1258.
75. DeBlois, R. W.; Bean, C. P.; Wesley, R. K. A. Electrokinetic Measurements with Submicron Particles and Pores by the Resistive Pulse Technique. J. Colloid Interface Sci. 1977, 61, 323-335.
76. Ito, T.; Sun, L.; Bevan, M. A.; Crooks, R. M. Comparison of Nanoparticle Size and Electrophoretic Mobility Measurements Using a Carbon-Nanotube-Based Coulter Counter, Dynamic Light Scattering, Transmission Electron Microscopy, and Phase Analysis Light Scattering. Langmuir 2004, 20, 6940-6945.
77. Lee, S.; Zhang, Y.; White, H. S.; Harrell, C. C., Martin, C. R. Electrophoretic Capture and Detection of Nanoparticles at the Opening of a Membrane Pore Using Scanning Electrochemical Microscopy. Anal. Chem. 2004, 76, 6108-6115.
78. Ouali, L.; Stoll, S.; Pefferkorn, E., Elaissari, A.; Lanet, V.; Pichot, C.; Mandrand, B. Coagulation of Antibody-Sensitized Latexes in the Presence of Antigen. Poly. Adv. Technol. 1995, 6, 541-546.
79. Pefferkorn, E., Varoqui, R. Dynamics of Latex Aggregation - Modes of Cluster Growth. J. Chem. Phys. 1989, 91, 5679-5686.
80. DeBlois, R. W., Wesley, R. K. A. Sizes and Concentrations of Several Type C Oncornaviruses and Bacteriophage T2 by the Resistive-Pulse Technique. J. Virol. 1977, 23, 227-233.
81. DeBlois, R. W.; Uzgiris, E. E.; Cluxton, D. H.; Mazzone, H. M. Comparative Measurements of Size and Polydispersity of Several Insect Viruses. Anal. Biochem. 1978, 90, 273-288.
82. Feuer, B. I.; Uzgiris, E. E.; Deblois, R. W.; Cluxton, D. H.; Lenard, J. Length of Glycoprotein Spikes of Vesicular Stomatitis Virus and Sindbis Virus, Measured in Situ Using Quasi Elastic Light Scattering and a Resisitve-Pulse Technique. Virology 1978, 90, 156-161.
83. Sauer-Budge, A. F.; Nyamwanda, J. A.; Lubensky, D. K.; Branton, D. Unzipping Kinetics of Double-Stranded DNA in a Nanopore. Phys. Rev. Lett. 2003, 90, 238101.
84. Aksimentiev, A., Heng, J. B.; Timp, G.; Schulten, K. Microscopic Kinetics of DNA Translocations through Synthetic Nanopores. Biophys. J. 2004, 87, 2086-2097.
85. Mara, A.; Siwy, Z.; Trautmann, C.; Wan, J., Kamme, F. An Asymmetric Polymer Nanopore for Single Molecule Detection. Nano Lett 2004, 4, 497-501.
86. Chen, P.; Gu, J.; Brandin, E., Kim, Y.; Wang, Q.; Branton, D. Probing Single DNA Molecule Transport Using Fabricated Nanopores. Nano Lett. 2004, 4, 2293-2298.
87. Storm, A. J.; Chen, J. H.; Zandbergen, H. W.; Dekker, C. Translocation of Double-Strand DNA through a Silicon Oxide Nanopore. Phys. Rev. E 2005, 71, 051903.
88. Storm, A. J.; Storm, C.; Chen, J.; Xandbergen, H.; Joanny, J.; Dekker, C. Fast DNA Translocation through a Solid-State Nanopore. Nano Lett. 2005, 5, 1193-1197.
89. Smeets, R. M. M.; Keyser, U. F.; Krapf, D.; Wu, M.; Dekker, N. H.; Dekker, C. Salt Dependence of Ion Transport and DNA Translocation through Solid-State Nanopores. Nano Lett. 2006, 6, 89-95.
90. Fan, R.; Karnik, R.; Yue, M.; Li, D.; Majumdar, A.; Yang, P. DNA Translocation in Inorganic Nanotubes. Nano Lett. 2005, 5, 1633-1637.
91. Meller, A.; Nivon, L; Branton, D. Voltage-Driven DNA Translocations through a Nanopore. Phys. Rev. Lett. 2001, 86, 3435-3438.
92. 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.
93. Meller, A.; Branton, D. Single Molecule Measurements of DNA Transport through a Nanopore. Electrophoresis 2002, 23, 2583-2591.
94. Bates, M., Burns, M.; Meller, A. Dynamics of DNA Molecules In a Membrane Channel Probed by Active Control Techniques. Biophys. J. 2003, 84, 2366-2372.
95. Mathe, J.; Visram, H., Viasnoff, V., Rabin, Y.; Meller, A. Nanopore Unzipping of Individual DNA Hairpin Molecules. Biophys. J. 2004, 87, 3205-3212.
96. Keyser, U. F.; Koeleman, B. N.; Van Dorp, S.; Krapf, D.; Smeets, R. M. M.; Lemay, S. G.; Dekker, N. H.; Dekker, C. Direct Force Measurements on DNA in a Solid-State Nanopore. Nat. Phys. 2006, 2, 473-477.
97. Chang, H.; B. M. V.; Iqbal, S. M., Andreadakis, G.; Kosari, F.; Vasmatzis, G. D. P.; Bashir, R. DNA Counterion Current and Saturation Examined by a Mems-Based Solid State Nanopore Sensor. Biomed. Microdevices 2006, 8, 263-269.
98. 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.
99. Sánchez-Quesada, J.; Saghatelian, A.; Cheley, S.; Bayley, H.; Ghadiri, M. R. Single DNA Rotaxanes of a Transmembrane Protein. Angew. Chem., Int. Ed. 2004, 43, 3063-3067.
100. Butler, T. Z.; Gundlach, J. H.; Troll, M. A. Determination of RNA Orientation During Translocation through a Biological Nanopore. Biophys. J. 2006, 90, 190-199.
101. Keyser, U. F.; van der Does, J.; Dekker, C.; Dekker, N. H. Optical Tweezers for Force Measurements on DNA in Nanopores. Rev. Sci. Instrum. 2006, 77, 105105.
102. Meller, A. Dynamics of Polynucleotlcle Transport through Nanometre-Scale Pores. J. Phys.: Condens. Matter 2003, 15, R581-R607.
103. Heng, J. B.; Aksimentiev, A.; Ho, C.; Marks, P.; Grinkova, Y. V.; Sligar, S., Schulten, K.; Timp, G. The Electromechanics of DNA in a Synthetic Nanopore. Biophys. J. 2006, 90, 1098-1106.
104. Heng, J. B.; Aksimentiev, A.; Ho, C.; Marks, P.; Grinkova, Y. V.; Sligar, S.; Schulten, K.; Timp, G. Stretching DNA Using the Electric Field in a Synthetic Nanopore. Nano Lett. 2005, 5, 1883-1888.
105. Howorka, S., Movileanu, L; Braha, O.; Bayley, H. Kinetics of Duplex Formation for Individual DNA Strands within a Single Protein Nanopore. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 12996-13001.
106. Fologea, D.; Gershow, M.; Ledden, B., McNabb, D. S.; Golovchenko, J. A., Li, J. Detecting Single Stranded DNA with a Solid State Nanopore. Nano Lett. 2005, 5, 1905-1909.
107. Hornblower, B.; Coombs, A.; Whitaker, R. D.; Kolomeisky, A.; Picone, S. J.; Meller, A.; Akeson, M. Single-Molecule Analysis of DNA-Protein Complexes Using Nanopores. Nat. Methods 2007, 4, 315-317.
108. Winters-Hilt, S.; Vercoutere, W.; DeGuzman, V. S.; Deamer, D.; Akeson, M.; Haussler, D. Highly Accurate Classification of Watson-Crick Basepairs on Termini of Single DNA Molecules. Biophys. J. 2003, 84, 967-976.
109. Vercoutere, W.; Winters-Hilt, S.; Olsen, H.; Deamer, D.; Haussler, D.; Akeson, M. Rapid Discrimination among Individual DNA Hairpin Molecules at Single-Nucleotide Resolution Using an Ion Channel. Nat. Biorechnol. 2001, 19, 248-252.
110. 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.
111. Kubitschek, H. E. Research (London) 1960, 13, 128.
112. Carbonaro, A.; Sohn, L. L. A Resistive-Pulse Sensor Chip for Multianalyte Immunoassays. Lab Chip 2005, 5, 1155-1160.
113. Kullman, L.; Winterhalter, M.; Bezrukov, S. M. Transport of Maltodextrins through Maltoporin: A Single-Channel Study. Biophys. J. 2002, 82, 803-812.
114. Heins, E. A.; Siwy, Z. S.; Baker, L. A.; Martin, C. R. Detecting Single Porphyrin Molecules in a Conically Shaped Synthetic Nanopore. Nano Lett. 2005, 5, 1824-1829.
115. Danelon, C.; Lindemann, M.; Borin, C.; Fournier, D.; Winterhalter, M. Channel-Forming Membrane Proteins as Molecular Sensors. IEEE Trans. Nonobiosci. 2004, 3, 46-48.
116. Sutherland, T. C.; Long, Y. T.; Stefureac, R. I.; Bediako-Amoa, I.; Kraatz, H. B., Lee, J. S. Structure of Peptides Investigated by Nanopore Analysis. Nano Lett. 2004, 4, 1273-1277.
117. Movileanu, L.; Howorka, S.; Braha, O.; Bayley, H. Detecting Protein Analytes That Modulate Transmembrane Movement of a Polymer Chain within a Single Protein Pore. Nat. Biotechnol. 2000, 18, 1091-1095.
118. Danelon, C.; Nestorovich, E. M.; Winterhalter, M.; Ceccarelli, M., Bezrukov, S. M. Interaction of Zwitterionic Penicillins with the Ompf Channel Facilitates Their Translocation. Biophys. J. 2006, 90, 1617-1627.
119. Iqbal, S. M.; Akin, D.; Bashir, R. Solid-Stage Nanopore Channels with DNA Selectivity. Nat. Nanotechnol. 2007, 2, 243-248.
120. Tabard-Cossa, V.; Trivedi, D.; Wiggin, M.; Jetha, N. N.; Marziali, A. Noise Analysis and Reduction in Solid-State Nanopores. Nanotechnology 2007, 18, 305505.
121. Oukhaled, G.; Mathe, J.; Biance, A. L.; Bacri, L.; Betton, J. M.; Lairez, D.; Pelta, J.; Auvray, L. Unfolding of Proteins and Long Transient Conformations Detected by Single Nanopore Recording. Phys. Rev. Lett. 2007, 98, 158101.
122. Sexton, L.T.; Horne, L. P.; Martin, C. R. Developing Synthetic Conical Nanopores for Biosensing Applications. Mol. Biosyst. 2007, 3, 667-685.
123. Fologea, D.; Ledden, B., McNabb, D. S.; Li, J. Electrical Characterization of Protein Molecules by a Solid-State Nanopore. Appl. Phys. Lett. 2007, 91, 053901.
124. Han, A., Schürmann, G.; Mondin, G4 Bitterli, R. A.; Hegelbach, N. G.; de Rooij, N. F.; Staufer, U. Sensing Protein Molcules Using Nanofabricated Pores. Appl. Phys. Lett. 2006, 88, 093901.
125. Sexton, L. T.; Horne, L P.; Sherrill, S. A.; Bishop, G. W.; Baker, L. A.; Martin, C. R. Resistive-Pulse Studies of Proteins and Protein/ Antibody Complexes Using a Conical Nanotube Sensor. J. Am. Chem. Soc. 2007, 13144-13152.
126. Colquhoun, D.; Sigworth, F. J. Fitting and Statistical Analysis of Single-Channel Records In Single-Channel Recording, 2nd ed.; Sakmann, B., Neher, E., EdS4 Plenum Press: New York 1995; pp 483-587.
127. Kubltschek, H. E. Electronic Counting and Sizing of Bacteria. Nature 1958, 182, 234-235.
128. Liu, H.; Qian, S.; Bau, H. H. The Effect of Translocating Cylindrical Particles on the Ionic Current through a Nanopore. Biophys. J. 2007, 92, 1164-1177.
129. Levis, R. A., Rae, J. L. Constructing a Patch Clamp Setup. Methods Enzymol. 1992, 207, 14-66.
130. Rae, J. L.; Levis, R. A. Glass Technology for Patch Clamp Electrodes. Methods Enzymol. 1992, 207, 66-92.
131. Sigworth, F. J. Electronic Design of the Patch Clamp In Single-Channel Recording, 2nd ed.; Sakmann, B., Neher, E., Eds.; Plenum Press: New York, 1995; pp 95-127.
132. Benndorf, K. Multiple Levels of Native Cardiac Na+ Channels at Elevated Temperature Measured with High-Bandwidth/Low-Noise Patch Clamp. Pflügers Arch. 1993, 422, 506-515.
133. Sigworth, F. J. Open Channel Noise 1. Noise in Acetylcholine Receptor Currents Suggests Conformational Fluctuations. Biophys. J. 1985, 47, 709-720.
134. Verveen, A. A.; DeFelice, L. J. Membrane Noise. Prog. Biophys. Mol. Biol. 1974, 28, 189-265.
135. Wonderlin, W. F.; Finkel, A.; French, R. J. Optimizing Planar Lipid Bilayer Single-Channel Recordings for High Resolution with Rapid Voltage Steps. Biophys. J. 1990, 58, 289-297.
136. c in the equations.
137. Raistrick, I. D.; Franceschetti, D. R.; Macdonald, J. R. Theory In Impedance Spectroscopy, 2nd ed.; Barsoukov, E., Macdonald, J. R., Eds.; John Wiley & Sons, Inc.: Hoboken, NJ, 2005; pp 27-128.
138. Hille, B. Elementary Properties of Pores In Ion Channels of Excitable Membranes, 3rd ed., Sinauer Associates Inc: Sunderland, MA, 2001; pp 347-375.
139. Hall, J. E. Access Resistance of a Small Circular Pore. J. Gen. Physiol. 1975, 66, 531-532.
140. c, could limit the bandwidth of this structure below the values estimated here. We do not think however, that the bandwidth limitation of the pore would be significant compared to the bandwidth limitation of the recording electronics (headstage, amplifier, analog low-pass filter, and digitizer) of ∼52 kHz as discussed in the text.
141. -6 Ohm F), the signal bandwidth will not be limited by the pore structure itself but rather by the recording electronics as discussed in the text.
142. While this relationship was derived for Gaussian filters, (see ref 126) it can also be used to approximate the signal bandwidth of measurements that employ low-pass Bessel filters since a low-pass Bessel filter with a large number of poles approximates the response of a low-pass Gaussian filter (see ref 126).
143. The third mode of this amplifier uses a feedback capacitor instead of a resistor to decrease the noise; however, due to the relatively large currents recorded in most pore-based sensing experiments (hundreds of picoamps to nanoamps), this capacitive feedback mode is often not practical because of the large number of resets required to discharge the feedback capacitor.
144. The manufacturer states that this signal bandwidth is lower than expected for a low-pass Bessel filter with a cutoff frequency of 100 kHz due to the signal bandwidth limitation of the electronics in the headstage of the amplifier (for a discussion of the electronic components used in a patch-clamp amplifier, see refs 129 and 131).
145. Shapovalov, G., Lester, H. A. Gating Transitions in Bacterial Ion Channels Measured at 3 Ms Resolution. J. Gen. Physiol. 2004, 124, 151-161.
146. A more complicated situation would arise if the pore had a signal bandwidth of approximately 20-150 kHz (i.e., a signal bandwidth that would be close to that of the HAFD). In this instance, the overall signal bandwidth of the recording would be set by the filter combination of the HAFD with the pore; a theoretical calculation of the overall signal bandwidth would be difficult to obtain. If the signal bandwidth of the pore would be less than approximately 20 kHz, then its signal bandwidth would then determine (i.e., limit) the overall signal bandwidth of the current recordings (assuming the signal bandwidth of the HAFD would be ∼52 kHz).
147. If the pore had signal bandwidth that was comparable to the signal bandwidth of the HAFD combination or the digital filter, then the exact overall signal bandwidth of the current recordings after digital filtering would be difficult to predict theoretically. In this case, the overall signal bandwidth would be smaller than the lowest signal bandwidth of the individual elements (pore, HAFD, digital filter); if a single element would have a signal bandwidth significantly lower than the other elements (by a factor of ∼3), it would determine the overall signal bandwidth of the current recordings.
148. c2 is the cutoff frequency of the digital filter.
149. 3 as the best available approximation for all theoretical rms calculations performed in this report (the characteristics of a low-pass Bessel filter with an increasing number of poles approximates the response of a low-pass Gaussian filter, see reference 126).
150. MacAvoy, T. C.; Halaby, S. A. Substrates for Thin-Film Circuitry. IEEE Trans. Component Parts 1964, 11, 15-22.
151. http://www.goodfellow.com/csp/active/STATIC/A/ Polyethylene_terephthalate.html.
152. We point out that the noise bandwidth of the headstage and amplifier, the dielectric noise of the substrate, and the thermal noise of the pore should even be calculated by using the signal bandwidth of the HAFD combination (or the HAFD-digital filter combination) if the pore has a signal bandwidth that is comparable to or less than the signal bandwidth of the HAFD combination. We make this recommendation because the ability of the pore to limit the signal bandwidth is due to the design of patch-clamp amplifiers and not due to the pore acting like a low-pass filter (see ref 131). Since the pore does not act like a low-pass filter, additional noise but not information is included in current traces when the signal bandwidth of the amplifier is greater than the signal bandwidth of the pore (see ref 11).
153. a = 25 pF). In this case, the maximum error between the measured noise and the theoretical noise was smaller than 30% for both β = 0.1 and for β = 1 (not including the data points marked with an asterisk).
154. 10-90 risetime of a digitally filtered square wave that was coupled in capacitively. To compare theory with experimental results, we subtracted the experimentally measured quantization noise from the data (since the experimental quantization noise was a factor of 16 larger than its theoretical prediction).
155. 10-90 risetime. Another possibility is that the coefficients we used to calculate the noise bandwidth did not perfectly describe the filtering characteristics of the headstage-analog filter combination.
156. 2 and the power spectral density of the dielectric noise is proportional to f). Thus, small inaccuracies in determining the signal bandwidth can have a noticeable effect on the predicted values of the current noise (especially at high signal-bandwidths).
157. Horowitz, P., Hill, W. Precision Circuits and Low-Noise Techniques In The Art of Electronics, 2nd ed.; Cambridge University Press: New York, 1989; pp 391-470.
158. Sigworth, F. J., Urry, D. W.; Prasad, K. U. Open Channel Noise III. High-Resolution Recordings Show Rapid Current Fluctuations in Gramicidin A and Four Chemical Analogues. Biophys. J. 1987, 52, 1055-1064.
159. Heinemann, S. H.; Sigworth, F. J. Open Channel Noise V. Fluctuating Barriers to Ion Entry in Gramicidin A Channels. Biophys. J. 1990, 57, 499-514.
160. Lauger, P. Shot Noise in Ion Channels. Biochim. Biophys. Acta 1975, 413, 1-10.
161. Mak, D. O.; Webb, W. W. Molecular Dynamics of Alamethicin Transmembrane Channels from Open-Channel Current Noise Analysis. Biophys. J. 1995, 69, 2337-2349.
162. Robinson, F. N. H., Noise and Fluctuations in Electronic Devices and Circuits; Oxford University Press: London, England, 1974.
163. Nanopores under certain conditions may contain a potential barrier and can be strongly rectifying (see references 40, 50-52, 66, and 67); these pores may therefore require a shot noise term to predict the noise accurately.
164. Many of the power spectra examined showed trends similar to Figure 8. In some power spectra, however, the noise power had a sigmoidal shape ( i.e., initially the noise power would grow in a linear fashion with decreasing frequency but would eventually reach a steady value at the lowest frequencies).
165. Ke, K.; Hasselbrink, E. F.; Hunt, A. J. Rapidly Prototyped Three-Dimensional Nanofludic Channel Networks in Glass Substrates. Anal. Chem. 2005, 77, 5083-5088.
166. Joglekar, A. P., Liu, H.; Meyhöfer, E.; Mourou, G., Hunt, A. J. Optics at Critical Intensity: Applications to Nanomorphing. Proc. Natl. Acad Sci. U.S.A. 2004, 101, 5856-5861.
167. Joglekar, A. P.; Liu, H., Spooner, G. J., Meyhöfer, E.; Mourou, G.; Hunt, A. J. A Study of the Deterministic Character of Optical Damage by Femtosecond Laser Pulses and Applications to Nanomachining. Appl. Phys. B: Lasers Opt. 2003, 77, 25-30.
168. Ke, K.; Hasselbrink, E.; Hunt, A. J. Nanofabrication with Ultrafast Lasers at Critical Intensity. Proc. Int. Soc. Opt. Eng. 2005, 5714, 53-62.