Detecting and characterizing individual molecules with single nanopores

Methods in Molecular Biology

Volumn 870, Issue , 2012, Pages 3-20

  Kasianowicz, John J ^a   Reiner, Joseph E ^a   Robertson, Joseph W F ^a   Henrickson, Sarah E ^a   Rodrigues, Claudio ^b   Krasilnikov, Oleg V ^b  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^b FEDERAL UNIVERSITY OF PERNAMBUCO   (Brazil)

Author keywords

Biosensing; DNA; DNA sequencing; Electrophysiology; Nanopore; Polymer analysis; Single molecule detection

Indexed keywords

BACTERIAL PROTEIN; BIOPOLYMER; HEMOLYSIN;

ALGORITHM; ARTICLE; ARTIFICIAL MEMBRANE; CHEMICAL ANALYSIS; CHEMISTRY; DNA SEQUENCE; ELECTROCHEMISTRY; IMPEDANCE; INSTRUMENTATION; METHODOLOGY; NANOPORE; PARTICLE SIZE; STANDARD;

ALGORITHMS; BACTERIAL PROTEINS; BIOPOLYMERS; CHEMISTRY TECHNIQUES, ANALYTICAL; ELECTRIC IMPEDANCE; ELECTROCHEMISTRY; HEMOLYSIN PROTEINS; MEMBRANES, ARTIFICIAL; NANOPORES; PARTICLE SIZE; SEQUENCE ANALYSIS, DNA; WEIGHTS AND MEASURES;

EID: 84860525872     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-773-6_1     Document Type: Article

References (79)

1. Krasilnikov OV, Sabirov RZ, Ternovsky VI, Merzliak PG, Muratkhodjaev JN (1992) A simple method for the determination of the pore radius of ion channels in planar lipid bilayer membranes. FEMS Microbiol Immunol 105:93-100
2. Krasilnikov OV (2002) Sizing channels with nonelectrolyte polymers. NATO Advanced Research Workshop. In: Kasianowicz JJ, Kellermayer M, Deamer DW (eds) Structure and dynamics of confi ned polymers. Kluwer, Dordrecht, pp 97-115
3. Nablo BJ, Halverson KM, Robertson JWF, Nguyen TL, Bavari S, Panchal RG, Gussio R, Krasilnikov OV, Kasianowicz JJ (2008) Probing the Bacillus anthracis PA 63 channel with nonelectrolyte polymers. Biophys J 95:1157-1164
4. Henrickson SE, Misakian M, Robertson B, Kasianowicz JJ (2000) Driven asymmetric DNA transport in a nanometer-scale pore. Phys Rev Lett 85:3057-3060
5. Henrickson SE, DiMarzio EA, Wang Q, Stanford VM, Kasianowicz JJ (2010) Probing single nanometer-scale pores with polymeric molecular rulers. J Chem Phys 132:135101
6. Purnell RF, Schmidt JJ (2009) Discrimination of single base substitutions in a DNA strand immobilized in a biological nanopore. ACS Nano 3:2533-2538
7. Kasianowicz JJ, Henrickson SE, Weetall HH, Robertson B (2001) Simultaneous multianalyte detection with a nanopore. Anal Chem 73: 2268-2272
8. Kasianowicz JJ, Robertson JWF, Chan ER, Reiner JE, Stanford VM (2008) Nanoscopic porous sensors. Annu Rev Anal Chem 1: 737-766
9. Coulter WH (1953) US Patent 2,656,508
10. DeBlois RW, Bean CP (1970) Counting and sizing of submicron particles by resistive pulse technique. Rev Sci Instrum 41:909-916
11. Ito T, Sun L, Crooks RM (2003) Simultaneous determination of the size and surface charge of individual nanoparticles using a carbon nanotube-based Coulter counter. Anal Chem 75: 2399-2406 (Pubitemid 36582825)
12. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93:13770-13773 (Pubitemid 26424195)
13. Krasilnikov OV, Ternovsky VI, Tashmukhamedov BA (1981) Properties of alpha-staphylotoxininduced conductivity channels in bilayer phospholipid- membranes. Biofi zika 26:271-276
14. Menestrina G (1986) Ionic channels formed by Staphylococcus aureus a-toxin: voltage dependent inhibition by divalent and trivalent cations. J Membr Biol 90:177-190 (Pubitemid 16075063)
15. Bhakdi S, Füssle R, Tranum-Jensen J (1981) Staphylococcal a-toxin: oligomerization of hydrophilic monomers to form amphiphilic hexamers induced through contact with deoxycholate detergent micelles. Proc Natl Acad Sci USA 78:5475-5479 (Pubitemid 12248609)
16. Bhakdi S, Tranum-Jensen J (1991) a-toxin of Staphylococcus aureus . Microbiol Rev 55:733-751
17. Bezrukov SM, Kasianowicz JJ (1993) Current noise reveals protonation kinetics and number of ionizable sites in an open protein ion channel. Phys Rev Lett 70:2352-2355
18. Kasianowicz JJ, Bezrukov SM (1995) Protonation dynamics of the a-toxin ion channel from spectral analysis of pH dependent current fl uctuations. Biophys J 69:94-105
19. Braha O, Walker B, Cheley S, Kasianowicz JJ, Hobaugh MR, Song L, Gouaux JE, Bayley H (1997) Structure-based design of a heteromeric transmembrane pore. Chem Biol 4:497-505
20. Kasianowicz JJ, Burden DL, Han LC, Cheley S, Bayley H (1999) Genetically engineered metal ion binding sites on the outside of a channel's transmembrane b-barrel. Biophys J 76:837-845 (Pubitemid 29264563)
21. Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW (1999) Microsecond time-scale discrimination between polycytidylic acid and polyadenylic acid segments within single RNA molecules. Biophys J 77:3227-3233
22. Robertson JWF, Rodrigues CG, Stanford VM, Rubinson K, Krasilnikov OV, Kasianowicz JJ (2007) Single molecule mass spectrometry in solution using solitary nanopores. Proc Natl Acad Sci USA 104:8207-8211 (Pubitemid 47175466)
23. Rodrigues CG, Machado DC, Chevtchenko SF, Krasilnikov OV (2008) Mechanism of KCl enhancement in detection of nonionic polymers by nanopore sensors. Biophys J 95: 5186-5192
24. Reiner JE, Kasianowicz JJ, Nablo BJ, Robertson JWF (2010) Theory for polymer analysis using nanopore-based single-molecule mass spectrometry. Proc Natl Acad Sci USA 107:12080-12085
25. Oukhaled G, Mathe J, Biance AL, Bacri L, Betton JM, Lairez D, Pelta J, Auvray L (2007) Unfolding of proteins and long transient conformations detected by single nanopore recording. Phys Rev Lett 98:158101
26. Bezrukov SM, Kullman L, Winterhalter M (2000) Probing sugar translocation through maltoporin at the single channel level. FEBS Lett 476:224-238
27. Kullman L, Winterhalter M, Bezrukov SM (2002) Transport of maltodextrins through maltoporin: a single-channel study. Biophys J 82:803-812 (Pubitemid 34111221)
28. Nestorovich EM, Danelon C, Winterhalter M, Bezrukov SM (2002) Designed to penetrate: time-resolved interaction of single antibiotic molecules with bacterial pores. Proc Natl Acad Sci USA 99:9789-9794 (Pubitemid 34831126)
29. Panchal RG, Halverson KM, Ribot W, Kenny T, Lane D, Abshire TG, Ezzell JW, Powell B, Kasianowicz JJ, Bavari S (2005) Purifi ed anthrax lethal toxin complex exhibits functional and biological activity. J Biol Chem 280:10834-10839
30. Halverson KM, Panchal RG, Nguyen TL, Gussio R, Little SF, Misakian M, Bavari S, Kasianowicz JJ (2005) Asymmetric blockade of anthrax protective antigen ion channel by lethal factor: anthrax therapeutic sensor. J Biol Chem 280:34056-34062 (Pubitemid 41443128)
31. Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA (2001) Ion-beam sculpting at nanometer length scales. Nature 422: 166-169 (Pubitemid 32674708)
32. Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C (2003) Fabrication of solidstate nanopores with single-nanometer precision. Nat Mater 2:537-540
33. Kim MJ, Wanunu M, Bell DC, Meller A (2006) Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA analysis. Adv Mater 18:3149-3153 (Pubitemid 46080209)
34. Fologea D, Gershow M, Ledden B, McNabb DS, Golovchenko JA, Li JL (2005) Detecting single-stranded DNA with a solid-state nanopore. Nano Lett 5:1905-1909 (Pubitemid 41548439)
35. Singer A, Wanunu M, Morrison W, Kuhn H, Frank-Kamenetskii M, Meller M (2010) Nanopore based sequence specifi c detection of duplex DNA for genomic profi ling. Nano Lett 10:738-742
36. Luan B, Peng H, Polonsky S, Rossnagel S, Stolovitzky G, Martyna G (2010) Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Phys Rev Lett 104:238103
37. Schneider GF, Kowalczyk SW, Calado VE, Pandraud G, Zandbergen HW, Vandersypen LMK, Dekker C (2010) DNA translocation through graphene nanopores. Nano Lett 10:3163-3167
38. Garaj S, Hubbard W, Reina A, Kong J, Branton D, Golovchenko JA (2010) Graphene as a subnanometre trans-electrode membrane. Nature 467:190-193
39. Zhao Q, Sigalov G, Dimitrov V, Dorvel B, Mirsaidov U, Sligar S, Aksimentiev A, Timp G (2007) Detecting SNPs using a synthetic nanopore. Nano Lett 7:1680-1685 (Pubitemid 47140444)
40. Clarke J, Wu H-C, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identifi cation for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265-270
41. Berg HC, Purcell EM (1977) Physics of chemoreception. Biophys J 20:193-219 (Pubitemid 8220672)
42. Montal M, Mueller P (1972) Formation of bimolecular membranes from lipid monolayers and a study of their electrical properties. Proc Natl Acad Sci USA 12:3561-3566
43. Mueller P, Rudin DO, Tien H, Wescott WC (1962) Reconstitution of cell membrane structure in vitro and its transformation into an excitable system. Nature 194:979-980
44. Song LZ, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouaux JE (1996) Structure of staphylococcal a-hemolysin, a heptameric transmembrane pore. Science 274:1859-1866 (Pubitemid 26424757)
45. Krasilnikov OV, Sabirov RZ (1989) Iontransport through channels formed in lipid bilayers by Staphylococcus aureus alpha-toxin. Gen Physiol Biophys 8:213-222
46. Kasianowicz JJ, Henrickson SE, Misakian M, Weetall HH, Robertson B, Stanford V (2002) Physics of DNA threading through a nanometer pore and applications to simultaneous multianalyte sensing. NATO Advanced Research Workshop. In: Kasianowicz JJ, Kellermayer M, Deamer DW (eds) Structure and dynamics of confi ned polymers. Kluwer, Dordrecht, pp 141-163
47. Uram JD, Ke K, Mayer M (2008) Noise and bandwidth of current recordings from submicrometer pores and nanopores. ACS Nano 2:857-872
48. Pedone D, Firnkes M, Rant U (2009) Data analysis of translocation events in nanopore experiments. Anal Chem 81:9689-9694
49. Robertson JWF, Kasianowicz JJ, Reiner JE (2010) Ion channel geometry can be resolved to sub-angstrom resolution through single molecule mass spectrometry. J Phys Condens Matter 22:454108
50. Krantz BA, Finkelstein A, Collier RJ (2006) Protein translocation through the anthrax toxin transmembrane pore is driven by a proton gradient. J Mol Biol 355:968-979 (Pubitemid 43012140)
51. Mathe J, Aksimentiev A, Nelson DR, Schulten K, Meller A (2005) Orientation discrimination of single-stranded DNA inside the a-hemolysin membrane channel. Proc Natl Acad Sci USA 102:12377-12382 (Pubitemid 41266367)
52. Zwolak M, Di Ventra M (2005) Electronic signature of DNA nucleotides via transverse transport. Nano Lett 5:421-424 (Pubitemid 40449709)
53. Zwolak M, DiVentra M (2008) Physical approaches to DNA sequencing and detection. Rev Mod Phys 80:141-165
54. Gracheva ME, Aksimentiev A, Leburton JP (2006) Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor. Nanotechnology 17:3160-3165 (Pubitemid 44149642)
55. Gracheva ME, Xiong AL, Aksimentiev A, Schulten K, Timp G, Leburton JP (2006) Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor. Nanotechnology 17:622-633 (Pubitemid 43121666)
56. Saenger W (1984) Principles of nucleic acid structure. Springer, New York
57. Kawano R, Schibel AEP, Cauley C, White HS (2009) Controlling the translocation of singlestranded DNA through a-hemolysin ion channels using viscosity. Langmuir 25:1233-1237
58. Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M (2010) Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J Am Chem Soc 132: 17961-17972
59. Ying YL, Li DW, Lee JS, Long YT (2011) Enhanced translocation of poly(dT) 45 through an a-hemolysin nanopore by binding with antibody. Chem Commun (Camb) 47: 5690-5692
60. De Gennes PG (1979) Scaling concepts in polymer physics. Cornell University Press, Ithaca, NY
61. Bezrukov SM, Vodyanoy I, Brutyan RA, Kasianowicz JJ (1996) Dynamics and free energy of polymers partitioning into a nanoscale pore. Macromolecules 29:8517-8522
62. Bezrukov SM, Kasianowicz JJ (2002) Dynamic partitioning of polymers into a channel. NATO Advanced Research Workshop. In: Kasianowicz JJ, Kellermayer M, Deamer DW (eds) Structure and dynamics of confi ned polymers. Kluwer, Dordrecht, pp 117-130
63. Movileanu L, Bayley H (2001) Partitioning of a polymer into a nanoscopic protein pore obeys a simple scaling law. Proc Natl Acad Sci USA 98:10137-10141 (Pubitemid 32802987)
64. Krasilnikov OV, Rodrigues CG, Bezrukov SM (2006) Single polymer molecules in a protein nanopore in the limit of a strong polymer-pore attraction. Phys Rev Lett 97:018301
65. Mooney M (1951) The viscosity of a concentrated suspension of spherical particles. J Coll Sci 6:162-170
66. Bezrukov SM, Kasianowicz JJ (1997) Charge state of an ion channel controls neutral polymer entry into its pore. Eur Biophys J 26: 471-476 (Pubitemid 27509263)
67. Aksimentiev A, Schulten K (2005) Imaging a-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys J 88: 3745-3761 (Pubitemid 40991090)
68. Merzlyak P, Capistrano M-FP, Valeva A, Kasianowicz JJ, Krasilnikov OV (2005) Conductance and ion selectivity of a mesoscopic protein nanopore probed with cysteine scanning mutagenesis. Biophys J 89: 3059-3070 (Pubitemid 41636062)
69. Sung W, Park PJ (1996) Polymer translocation through a pore in a membrane. Phys Rev Lett 77:783-786
70. Ambjörnsson T, Apell SP, Konkoli Z, DiMarzio E, Kasianowicz JJ (2002) Charged polymer membrane translocation. J Chem Phys 117:4063-4073 (Pubitemid 34992690)
71. Lubensky DK, Nelson DR (1999) Driven polymer translocation through a narrow pore. Biophys J 77:1824-1838 (Pubitemid 29463147)
72. Muthukumar M (1999) Polymer translocation through a hole. J Chem Phys 111: 10371-10374 (Pubitemid 129590277)
73. Muthukumar M (2002) Theory of sequence effects on DNA translocation through proteins and nanopores. Electrophoresis 23:1417-1420 (Pubitemid 34649570)
74. Barcilon V (1992) Ion fl ow through narrow membrane channels. Part 1. SIAM J Appl Math 52:1391-1404 (Pubitemid 23589680)
75. Barcilon V, Chen DP, Eisenberg RS (1992) Ion fl ow through narrow membrane channels. Part 2 SIAM J Appl Math 52:1405-1425 (Pubitemid 23589679)
76. Graf P, Kurnikova MG, Coalson RD, Nitzan A (2004) Comparison of dynamic lattice Monte Carlo simulations and the dielectric self-energy Poisson-Nernst-Planck continuum theory for model ion channels. J Phys Chem B 108: 2006-2015
77. Hall JE (1975) Access resistance of a small circular pore. J Gen Physiol 66:531-532
78. Merchant CA, Healy K, Wanunu M, Ray V, Peterman N, Bartel J, Fischbein MD, Venta K, Luo Z, Johnson ATC, Drndic M (2010) DNA translocation through graphene nanopores. Nano Lett 10:2915-2921
79. Polonsky S, Rossnagel S, Stolovitzky G (2007) Nanopore in metal-dielectric sandwich for DNA position control. Appl Phys Lett 91:153103