DNA unzipping and protein unfolding using nanopores

Methods in Molecular Biology

Volumn 870, Issue , 2012, Pages 55-75

  Merstorf, Céline ^a   Cressiot, Benjamin ^a   Pastoriza Gallego, Manuela ^b   Oukhaled, Abdel Ghani ^b   Bacri, Laurent ^a   Gierak, Jacques ^c   Pelta, Juan ^a   Auvray, Loïc ^d   Mathé, Jérôme ^a  

^a UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^b UNIVERSITÉ DE CERGY PONTOISE   (France)

^c UNIV PARIS SUD   (France)

^d UNIVERSITÉ PARIS DIDEROT   (France)

Author keywords

DNA; Force; Nanopore; Protein; Unfolding

Indexed keywords

BACTERIAL PROTEIN; HEMOLYSIN; MALTOSE BINDING PROTEIN;

ALGORITHM; ARTIFICIAL MEMBRANE; CHEMISTRY; DNA DENATURATION; ELECTROOSMOSIS; NANOPORE; PROTEIN UNFOLDING; REVIEW; TRANSPORT AT THE CELLULAR LEVEL;

ALGORITHMS; BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; ELECTROOSMOSIS; HEMOLYSIN PROTEINS; MALTOSE-BINDING PROTEINS; MEMBRANES, ARTIFICIAL; NANOPORES; NUCLEIC ACID DENATURATION; PROTEIN UNFOLDING;

EID: 84860502314     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-773-6_4     Document Type: Review

References (61)

1. Citovsky V, Zambryski P (1993) Transport of nucleic-acids through membrane channels-snaking through small holes. Annu Rev Microbiol 47:167-197 (Pubitemid 23302932)
2. Matlack K, Mothes W, Rapoport T (1998) Protein translocation: tunnel vision. Cell 92: 381-390 (Pubitemid 28093015)
3. Berrier C, Bonhivers M, Letellier L, Ghazi A (2000) High-conductance channel induced by the interaction of phage lambda with its receptor maltoporin. FEBS Lett 476:129-133 (Pubitemid 30410803)
4. Lambert O, Letellier L, Gelbart W, Rigaud J (2000) DNA delivery by phage as a strategy for encapsulating toroidal condensates of arbitrary size into liposomes. Proc Natl Acad Sci USA 97:7248-7253 (Pubitemid 30431449)
5. Guillot G, Léger L, Rondelez R (1987) Polymers that slip away. Recherche 18: 1126-1128
6. Lal J, Sinha S, Auvray L (1997) Structure of polymer chains confi ned in Vycor. J Phys 7:1597-1615 (Pubitemid 127806171)
7. Gilbert E, Auvray L, Lal J (2001) Structure of polyelectrolyte chains confi ned in nanoporous glass. Macromolecules 34:4942-4948 (Pubitemid 34217355)
8. 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
9. Church G, Deamer D, Branton D, Baldarelli R, Kasianowicz, J (1998) US Patent 5795782 Characterization of individual polymer molecules based on monomer-interface interactions
10. Coulter WH (1953) US Patent 2656508 means for counting particles suspended in uid
11. Sakmann B, Neher E (eds) (1995) Single-channel recording. 2nd edn. Springer, New York
12. Hille B (2001) Ion channels of excitable membranes. 3rd edn. Sinauer Associates, Sunderland, MA
13. Mueller P, Rudin D, Tien H, Wescott W (1962) Reconstitution of cell membrane structure in vitro and its transformation into excitable system. Nature 194:979
14. Mueller P, Wescott W, Rudin D, Tien H (1963) Methods for formation of single biomolecular lipid membranes in aqueous solution. J Phys Chem 67:534
15. Lubensky DK, Nelson DR (1999) Driven polymer translocation through a narrow pore. Biophys J 77:1824-1838 (Pubitemid 29463147)
16. Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW (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
17. Bates M, Burns M, Meller A (2003) Dynamics of DNA molecules in a membrane channel probed by active control techniques. Biophys J 84:2366-2372 (Pubitemid 36373559)
18. Howorka S, Nam J, Bayley H, Kahne D (2004) Stochastic detection of monovalent and bivalent protein-ligand interactions. Angew Chem Int Ed Engl 43:842-846 (Pubitemid 39256210)
19. Movileanu L, Cheley S, Bayley H (2003) Partitioning of individual fl exible polymers into a nanoscopic protein pore. Biophys J 85:897-910 (Pubitemid 36909654)
20. Szabo I, Bathori G, Tombola F, Brini M, Coppola A, Zoratti M (1997) DNA translocation across planar bilayers containing Bacillus subtilis ion channels. J Biol Chem 272:25275-25282 (Pubitemid 27415717)
21. Bacri L, Benkhaled A, Guegan P, Auvray L (2005) Ionic channel behavior of modifi ed cyclodextrins inserted in lipid membranes. Langmuir 21:5842-5846 (Pubitemid 40925830)
22. Sun L, Crooks R (2000) Single carbon nanotube membranes: a well-defi ned model for studying mass transport through nanoporous materials. J Am Chem Soc 122:12340-12345 (Pubitemid 32062272)
23. Mara A, Siwy Z, Trautmann C, Wan J, Kamme F (2004) An asymmetric polymer nanopore for single molecule detection. Nano Lett 4: 497-501 (Pubitemid 38402640)
24. Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA (2001) Ion-beam sculpting at nanometre length scales. Nature 412:166-169 (Pubitemid 32674708)
25. Biance A, Gierak J, Bourhis E, Madouri A, Lafosse X, Patriarche G, Oukhaled G, Ulysse C, Galas J, Chen Y, Auvray L (2006) Focused ion beam sculpted membranes for nanoscience tooling. Microelectron Eng 83:1474-1477, 31st International Conference on Micro-and Nano-Engineering, Vienna, Austria, Sep 19-22, 2005
26. Storm AJ, Chen JH, Ling XS, Zandbergen H, Dekker C (2005) Electron-beam-induced deformations of SiO[sub 2] nanostructures. J Appl Phys 98:014307
27. Dekker C (2007) Solid-state nanopores. Nat Nanotechnol 2:209-215 (Pubitemid 46739810)
28. Schoch RB, Han J, Renaud P (2008) Transport phenomena in nanofl uidics. Rev Mod Phys 80:839-883
29. Kasianowicz JJ, Robertson J, Chan E, Reiner J, Stanford V (2008) Nanoscopic porous sensors. Annu Rev Anal Chem 1:737-766
30. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Ventra MD, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, Meller A, Oliver JS, Pershin YV, Ramsey JM, Riehn R, Soni GV, Tabard-Cossa V, Wanunu M, Wiggin M, Schloss JA (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26:1146-1153
31. Howorka S, Siwy Z (2009) Nanopore analytics: sensing of single molecules. Chem Soc Rev 38:2360-2384
32. Majd S, Yusko EC, Billeh YN, Macrae MX, Yang J, Mayer M (2010) Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Curr Opin Biotechnol 21: 439-476
33. Nakane J, Wiggin M, Marziali A (2004) A nanosensor for transmembrane capture and identifi cation of single nucleic acid molecules. Biophys J 87:615-621 (Pubitemid 38880113)
34. Mathé J, Visram H, Viasnoff V, Rabin Y, Meller A (2004) Nanopore unzipping of individual DNA hairpin molecules. Biophys J 87:3205-3212 (Pubitemid 40468577)
35. McNally B, Wanunu M, Meller A (2008) Electromechanical unzipping of individual DNA molecules using synthetic sub-2 nm pores. Nano Lett 8:3418-3422
36. Tabard-Cossa V, Wiggin M, Trivedi D, Jetha NN, Dwyer JR, Marziali A (2009) Single-molecule bonds characterized by solid-state nanopore force spectroscopy. ACS Nano 3:3009-3014
37. Keyser UF, Koeleman BN, Van Dorp S, Krapf D, Smeets RMM, Lemay SG, Dekker NH, Dekker C (2006) Direct force measurements on DNA in a solid-state nanopore. Nat Phys 2:473-477 (Pubitemid 44022563)
38. Daoud M, de Gennes P (1977) Statistics of macromolecular solutions trapped in small pores. J Phys 38:85-93
39. De Gennes P-G (1980) Scaling concepts in polymer physics. 1st edn. Cornell University Press, New York
40. 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)
41. Biance A-L, Oukhaled G, Auvray L (2010) Electrical characterization and dynamics of transport. In: Nanoscience, nanobiotechnology and nanobiology. Springer, London. Translation from the French language edition, "Les Nanosciences-3. Nanobiotechnologies et Nanobiologie" (2007) Editions Belin, France
42. Brochard-Wyart F, de Gennes P-G (1977) Dynamics of confi ned polymer chains. J Chem Phys 67:52
43. Lee N, Obukhov S (1996) Diffusion of a polymer chain through a thin membrane. J Phys 6:195-204 (Pubitemid 126793595)
44. van Dorp S, Keyser UF, Dekker NH, Dekker C, Lemay SG (2009) Origin of the electrophoretic force on DNA in solid-state nanopores. Nat Phys 5:347-351
45. Ghosal S (2007) Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore. Phys Rev Lett 98:238104
46. Dudko OK, Mathe J, Szabo A, Meller A, Hummer G (2007) Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophys J 92:4188-4195 (Pubitemid 46910535)
47. Dudko OK, Mathe J, Meller A (2010) Nanopore force spectroscopy tools for analyzing single biomolecular complexes. Methods Enzymol 475:565-589
48. Viasnoff V, Chiaruttini N, Bockelmann U (2009) Probing DNA base pairing energy profi les using a nanopore. Eur Biophys J 38:263-269
49. Makarov DE (2009) Computer simulations and theory of protein translocation. Acc Chem Res 42:281-289
50. Chinappi M, Cecconi F, Casciola CM (2011) Computational analysis of maltose binding protein translocation. Philos Mag 91:2034-2048
51. Tsitrin Y, Morton CJ, el-Bez C, Paumard P, Velluz MC, Adrian M, Dubochet J, Parker MW, Lanzavecchia S, van der Goot FG (2002) Conversion of a transmembrane to a water-soluble protein complex by a single point mutation. Nat Struct Biol 9:729-733
52. Betton J-M, Hofnung M (1996) Folding of a mutant maltose-binding protein of Escherichia coli which forms inclusion bodies. J Biol Chem 271:8046-8052 (Pubitemid 26108625)
53. Raffy S, Sassoon N, Hofnung M, Betton J-M (1998) Tertiary structure-dependence of misfolding substitutions in loops of the maltosebinding protein. Protein Sci 7:2136-2142 (Pubitemid 28495800)
54. Schiedt B, Auvray L, Bacri L, Oukhaled G, Madouri A, Bourhis E, Patriarche G, Pelta J, Jede R, Gierak J (2010) Direct FIB fabrication and integration of "single nanopore devices" for the manipulation of macromolecules. Microelectronic Engineering 87:1300-1303, 35th International Conference on Micro-and Nano-Engineering, Ghent, Belgium, Sep 28-Oct 01, 2009
55. Bacri L, Oukhaled AG, Schiedt B, Patriarche G, Bourhis E, Gierak J, Pelta J, Auvray L (2011) Dynamics of colloids in single solidstate nanopores. J Phys Chem B 115(12): 2890-2898
56. Oukhaled G, Mathé J, Biance A-L, Bacri L, Betton J-M, Lairez D, Pelta J, Auvray L (2007) Unfolding of proteins and long transient conformations detected by single nanopore recording. Phys Rev Lett 98:158101
57. Pastoriza-Gallego M, Rabah L, Gibrat G, Thiebot B, van der Goot FG, Auvray L, Betton J-M, Pelta J (2011) Dynamics of unfolded protein transport through an aerolysin pore. J Am Chem Soc 133:2923-2931
58. Oukhaled A, Cressiot B, Bacri L, Pastoriza-Gallego M, Betton J-M, Bourhis E, Jede R, Gierak J, Auvray L, Pelta J (2011) Dynamics of completely unfolded and native proteins through solid-state nanopores as a function of electric driving force. ACS Nano 5(5): 3628-3638
59. Talaga DS, Li J (2009) Single-molecule protein unfolding in solid state nanopores. J Am Chem Soc 131:9287-9297
60. Pedone D, Firnkes M, Rant U (2009) Data analysis of translocation events in nanopore experiments. Anal Chem 81:9689-9694
61. Muzard J, Martinho M, Mathé J, Bockelmann U, Viasnoff V (2010) DNA translocation and unzipping through a nanopore: some geometrical effects. Biophys J 98:2170-2178