Nanopore unzipping of individual DNA hairpin molecules

Biophysical Journal

Volumn 87, Issue 5, 2004, Pages 3205-3212

  Mathé, Jérôme ^a   Visram, Hasina ^a   Viasnoff, Virgile ^a   Rabin, Yitzhak ^b   Meller, Amit ^a  

^a HARVARD UNIVERSITY   (United States)

^b BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HEMOLYSIN; POLYNUCLEOTIDE; ESCHERICHIA COLI PROTEIN; HLYA PROTEIN, E COLI;

ARTICLE; CHANNEL GATING; ELECTRIC POTENTIAL; ENERGY; FORCE; KINETICS; MEASUREMENT; MEMBRANE CHANNEL; NANOTECHNOLOGY; CHEMISTRY; CONFORMATION; ELECTROMAGNETIC FIELD; ELECTROPORATION; METHODOLOGY; POROSITY; RADIATION EXPOSURE; RADIATION RESPONSE;

DNA; DOSE-RESPONSE RELATIONSHIP, RADIATION; ELECTROMAGNETIC FIELDS; ELECTROPORATION; ESCHERICHIA COLI PROTEINS; HEMOLYSIN PROTEINS; KINETICS; NUCLEIC ACID CONFORMATION; POROSITY;

EID: 14844318136     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.047274     Document Type: Article

References (26)

1. Akeson, M., D. Branton, J. Kasianowicz, E. Brandin, and D. Deamer. 1999. Microsecond timescale discrimination among polycytidylic acid, poly-adenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77:3227-3233.
2. Alberts, B., D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson. 1994. Molecular Biology of the Cell. Garland Publishing, New York.
3. Bates, M., M. Burns, and A. Meller. 2003. Dynamics of DNA molecules in a membrane channel probed by active control techniques. Biophys. J. 84:2366-2372.
4. Bell, G. I. 1978. Models for the specific adhesion of cells to cells. Science. 200:618-627.
5. Bockelmann, U., B. Essevaz-Roulet, and F. Heslot. 1997. Molecular stick-slip motion revealed by opening DNA with piconewton forces. Phys. Rev. Lett. 79:4489-492.
6. Bockelmann, U., P. Thomen, B. Essevaz-Roulet, V. Viasnoff, and F. Heslot. 2002. Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys. J. 82:1537-1553.
7. Bustamante, C., S. B. Smith, J. Liphart, and D. Smith. 2000. Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol. 10:279-285.
8. Cocco, S., R. Monasson, and J. F. Marko. 2001. Force and kinetic barriers to unzipping of the DNA double helix. Proc. Natl. Acad. Sci. USA. 98:8608-8613.
9. Evans, E. 2001. Probing the relation between force-lifetime and chemistry in single molecule bonds. Annu. Rev. Biophys. Biomol. Struct. 30:105-128.
10. Evans, E., and K. Ritchie. 1999. Strength of a weak bond connecting flexible polymer chains. Biophys. J. 76:2439-2447.
11. Evans, E., and P. Williams. 2002. Dynamic force spectroscopy. In Physics of Biomolecules and Cells. H. Flyvberg, F. Julicher, P. Ormos, and F. David, editors. Ecole des Mouches d'Ete, LXXV. EDP Sciences, Springer-Verlag, Berlin. 145-185.
12. Howorka, S., L. Movileanu, O. Braha, and H. Bayley. 2001. Kinetics of duplex formation for individual DNA strands within a single protein nanopore. Proc. Natl. Acad. Sci. USA. 98:12996-13001.
13. Kasianowicz, J., E. Brandin, D. Branton, and D. Deamer. 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA. 93:13770-13773.
14. Liphart, J., B. Onoa, S. B. Smith, I. Tinoco, Jr., and C. Bustamante. 2001. Reversible Unfolding of Single RNA Molecules by Mechanical Force. Science. 292:733-737.
15. Lubensky, D. K., and D. R. Nelson. 2002. Single molecule statistics and the polynucleotide unzipping transition. Phys. Rev. E. 65:031917-1.
16. Meller, A., and D. Branton. 2002. Single molecule measurements of DNA transport through a nanopore. Electrophoresis. 23:2583-2591.
17. Meller, A., L. Nivon, E. Brandin, J. Golovchenko, and D. Branton. 2000. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. USA. 97:1079-1084.
18. Meller, A., L. Nivon, and D. Branton. 2001. Voltage-Driven DNA Translocations through a Nanopore. Phys. Rev. Lett. 86:3435-3438.
19. Nakane, J., M. Wiggin, and A. Marziali. 2004. A nanosensor for trans-membrane capture and identification of single nucleic acid molecules. Biophys. J. 87:615-621.
20. Rief, M., H. Clausen-Schaumann, and H. E. Gaub. 1999. Sequence-dependent mechanics of single DNA molecule. Nat. Struct. Biol. 6:346-349.
21. SantaLucia, J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.
22. Sauer-Budge, A. F., J. A. Nyamwanda, D. K. Lubensky, and D. Branton. 2003. Unzipping kinetics of double-stranded DNA in a nanopore. Phys. Rev. Lett. 90:238101.
23. Song, L., M. R. Hobaugh, C. Shustak, S. Cheley, H. Bayley, and J. E. Gouax. 1996. Structure of staphylococcal α-hemolysin a heptameric transmembrane pore. Science. 274:1859-1865.
24. Strunz, T., K. Oroszlan, R. Schäfer, and H.-J. Güntherodt. 1999. Dynamic force spectroscopy of single DNA molecules. Proc. Natl. Acad. Sci. USA. 96:11277-11282.
25. Vercoutere, W. A., S. Winters-Hilt, H. Olsen, D. Deamer, D. Haussler, and M. Akeson. 2001. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat. Biotechnol. 19:248-252.
26. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.