Nanopore sequencing technology: nanopore preparations

Trends in Biotechnology

Volumn 25, Issue 4, 2007, Pages 174-181

  Rhee, Minsoung ^a   Burns, Mark A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NANOPORE PREPARATIONS; NANOPORE SEQUENCING TECHNOLOGY; ORGANIC NANOPORES; SYNTHETIC NANOPORES;

DNA; ELECTRON BEAMS; MACROMOLECULES; NANOTECHNOLOGY; NUCLEIC ACID SEQUENCES;

NANOPORES;

ALPHA HEMOLYSIN; HEMOLYSIN; UNCLASSIFIED DRUG;

DNA SEQUENCE; ELECTRON BEAM; NANOPORE; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; REVIEW;

BASE SEQUENCE; DNA; ELECTROCHEMISTRY; ESCHERICHIA COLI PROTEINS; HEMOLYSIN PROTEINS; MEMBRANES, ARTIFICIAL; MOLECULAR SEQUENCE DATA; NANOSTRUCTURES; NANOTECHNOLOGY; POROSITY; SEQUENCE ANALYSIS, DNA;

EID: 33947105421     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2007.02.008     Document Type: Review

References (71)

1. Nakane J.J., et al. Nanopore sensors for nucleic acid analysis. J. Phys. Condens. Matter 15 (2003) R1365-R1393
2. Rhee M., and Burns M.A. Nanopore sequencing technology: research trends and applications. Trends Biotechnol. 24 (2006) 580-586
3. Schmidt J. Stochastic sensors. J. Mater. Chem. 15 (2005) 831-840
4. Bezrukov S.M. Ion channels as molecular Coulters to probe metabolite transport. J. Membr. Biol. 174 (2000) 1-13
5. Bayley H., and Cremer P.S. Stochastic sensors inspired by biology. Nature 413 (2001) 226-230
6. Song L., et al. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 274 (1996) 1859-1865
7. DeBlois R.W., and Bean C.P. Counting and sizing of submicron particles by resistive pulse technique. Rev. Sci. Instrum. 41 (1970) 909-916
8. Kasianowicz J.J., et al. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 13770-13773
9. Winters-Hilt S. Nanopore detector-based analysis of single-molecule conformational kinetics and binding interactions. BMC Bioinformatics 7 Suppl. 2 (2006) S21
10. Szabo I., et al. Double-stranded DNA can be translocated across a planar membrane containing purified mitochondrial porin. FASEB J 12 (1998) 495-502
11. Szabo I., et al. DNA translocation across planar bilayers containing Bacillus subtilis ion channels. J. Biol. Chem. 272 (1997) 25275-25282
12. Rostovtseva T.K., et al. Partitioning of differently sized poly(ethylene glycol)s into OmpF porin. Biophys. J. 82 (2002) 160-169
13. Nestorovich E.M., et al. Residue ionization and ion transport through OmpF channels. Biophys. J. 85 (2003) 3718-3729
14. Li J., et al. DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2 (2003) 611-615
15. Wang H., and Branton D. Nanopores with a spark for single-molecule detection. Nat. Biotechnol. 19 (2001) 622-623
16. Heng J.B., et al. Sizing DNA using a nanometer-diameter pore. Biophys. J. 87 (2004) 2905-2911
17. Chen P., et al. Probing single DNA molecule transport using fabricated nanopores. Nano Lett. 4 (2004) 2293-2298
18. Schenkel T., et al. Formation of a few nanometer-wide holes in membranes with a dual-beam focused ion beam system. J. Vac. Sci. Technol. B 21 (2003) 2720-2723
19. Akeson M., et al. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77 (1999) 3227-3233
20. Mayer M., et al. Functional analysis of ion channels: planar patch clamp and impedance spectroscopy of tethered lipid membranes. Biosensors - A Practical Approach. 2nd edn (2003), Oxford University Press
21. Mayer M., et al. Microfabricated teflon membranes for low-noise recordings of ion channels in planar lipid bilayers. Biophys. J. 85 (2003) 2684-2695
22. Rostovtseva T.K., et al. Dynamics of nucleotides in VDAC channels: structure-specific noise generation. Biophys. J. 82 (2002) 193-205
23. Song J., et al. The topology of VDAC as probed by biotin modification. J. Biol. Chem. 273 (1998) 24406-24413
24. Danelon C., et al. Channel-forming membrane proteins as molecular sensors. IEEE Trans. Nanobioscience 3 (2004) 46-48
25. Hanss B., et al. Identification and characterization of a cell membrane nucleic acid channel. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 1921-1926
26. Leal-Pinto E., et al. Presence of the nucleic acid channel in renal brush-border membranes: allosteric modulation by extracellular calcium. Am. J. Physiol. Renal Physiol. 289 (2005) F97-F106
27. Wright-Lucas S., and Harding M.M. Detection of DNA via an ion channel switch biosensor. Anal. Biochem. 282 (2000) 70-79
28. Deamer D.W., and Branton D. Characterization of nucleic acids by nanopore analysis. Acc. Chem. Res. 35 (2002) 817-825
29. Chen P., et al. Atomic layer deposition to fine tune the surface properties and diameters of fabricated nanopores. Nano Lett. 4 (2004) 1333-1337
30. Li J., et al. Ion-beam sculpting at nanometer length scales. Nature 412 (2001) 166-169
31. Stein D., et al. Feedback-controlled ion beam sculpting apparatus. Rev. Sci. Instrum. 75 (2004) 900-905
32. Heng J.B., et al. Stretching DNA using the electric field in a synthetic nanopore. Nano Lett. 5 (2005) 1883-1888
33. Stein D., et al. Ion-beam sculpting time scales. Phys. Rev. Lett. 89 (2002) 27-30
34. 2. J. Appl. Phys. 88 (2000) 59-64
35. Fologea D., et al. Detecting single-stranded DNA with a solid state nanopore. Nano Lett. 5 (2005) 1905-1909
36. Mitsui T., et al. Nanoscale volcanoes: accretion of matter at ion-sculpted nanopores. Phys. Rev. Lett. 96 (2006) 036102
37. Lo C.J., et al. Fabrication of symmetric sub-5 nm nanopores using focused ion and electron beams. Nanotechnology 17 (2006) 3264-3267
38. Gordon R.G., et al. A kinetic model for step coverage by atomic layer deposition in narrow holes or trenches. J. Chem. Vap. Deposition 9 (2003) 73-78
39. Hausmann D.M., et al. Atomic layer deposition of hafnium and zirconium oxides using metal amide precursors. Chem. Mater. 14 (2002) 4350-4358
40. Saleh O.A., and Sohn L.L. An artificial nanopore for molecular sensing. Nano Lett. 3 (2003) 37-38
41. Saleh, O.A. and Sohn, L.L. (2004) Biological sensing with an on-chip resistive pulse analyzer. In Proceedings of the 26th Annual International Conference of the IEEE EMBS San Francisco, CA, USA, pp. 2568-2570.
42. Schmid H., and Michel B. Siloxane polymers for high-resolution, high-accuracy soft lithography. Macromolecules 33 (2000) 3042-3049
43. Mara A., et al. An asymmetric polymer nanopore for single molecule detection. Nano Lett. 4 (2004) 497-501
44. Siwy Z., and Fulinski A. Fabrication of a synthetic nanopore ion pump. Phys. Rev. Lett. 89 (2002) 198103
45. Heins E.A., et al. Detecting single porphyrin molecules in a conically shaped synthetic nanopore. Nano Lett. 5 (2005) 1824-1829
46. Harrell C.C., et al. Synthetic single-nanopore and nanotube membranes. Anal. Chem. 75 (2003) 6861-6867
47. Harrell C.C., et al. DNA nanotube artificial ion channels. J. Am. Chem. Soc. 126 (2004) 15646-15647
48. Storm A.J., et al. Fabrication of solid-state nanopores with single-nanometre precision. Nat. Mater. 2 (2003) 537-541
49. Keyser U.F., et al. Nanopore tomography of a laser focus. Nano Lett. 5 (2005) 2253-2256
50. Smeets R.M., et al. Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 6 (2006) 89-95
51. Heng J.B., et al. The electromechanics of DNA in a synthetic nanopore. Biophys. J. 90 (2006) 1098-1106
52. Ho C., et al. Electrolytic transport through a synthetic nanometer-diameter pore. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 10445-10450
53. Chang H., et al. DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels. Nano Lett. 4 (2004) 1551-1556
54. Chang H., et al. Fabrication and characterization of solid-state nanopores using a field emission scanning electron microscope. Appl. Phys. Lett. 88 (2006) 103109
55. 2 membrane with an electron beam. Appl. Phys. Lett. 87 (2005) 113106
56. 2 nanostructures. J. Appl. Phys. 98 (2005) 014307
57. Ito T., et al. A carbon nanotube-based coulter nanoparticle counter. Acc. Chem. Res. 37 (2004) 937-945
58. Ito T., et al. Observation of DNA transport through a single carbon nanotube channel using fluorescence microscopy. Chem. Commun. 12 (2003) 1482-1483
59. Henriquez R.R., et al. The resurgence of Coulter counting for analyzing nanoscale objects. Analyst 129 (2004) 478-482
60. Fan S., et al. Self-oriented regular arrays of carbon nanotubes and their field emission properties. Science 283 (1999) 512-514
61. Sun L., and Crooks R.M. Single carbon nanotube membranes: a well-defined model for studying mass transport through nanoporous materials. J. Am. Chem. Soc. 122 (2000) 12340-12345
62. Fan R., et al. DNA translocation in inorganic nanotubes. Nano Lett. 5 (2005) 1633-1637
63. Burns M.A., et al. An integrated nanoliter DNA analysis device. Science 282 (1998) 484-487
64. Meller A., et al. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 1079-1084
65. Wang H., et al. DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 13472-13477
66. Vercoutere W., et al. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat. Biotechnol. 19 (2001) 248-252
67. Howorka S., et al. Sequence-specific detection of individual DNA strands using engineered nanopores. Nat. Biotechnol. 19 (2001) 636-639
68. Kasianowicz J.J. Nanopores: flossing with DNA. Nat. Mater. 3 (2004) 355-356
69. Sanchez-Quesada J., et al. DNA rotaxanes of a transmembrane pore protein. Angew. Chem. Int. Ed. 43 (2004) 3063-3067
70. Astier Y., et al. Toward single-molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5′-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J. Am. Chem. Soc. 128 (2006) 1705-1710
71. Chang H., et al. DNA counter ion current and saturation examined by a MEMS-based solid state nanopore sensor. Biomed. Microdevices 8 (2006) 263-269