Long dwell-time passage of DNA through nanometer-scale pores: Kinetics and sequence dependence of motion

Biophysical Journal

Volumn 100, Issue 12, 2011, Pages 2974-2980

  Jetha, Nahid N ^a   Feehan, Christopher ^a   Wiggin, Matthew ^b   Tabard Cossa, Vincent ^c   Marziali, Andre ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^c UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79960292997     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.05.007     Document Type: Article

References (25)

1. Branton, D., D. W. Deamer, ..., J. A. Schloss. 2008. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26:1146-1153.
2. Bayley, H. 2006. Sequencing single molecules of DNA. Curr. Opin. Chem. Biol. 10:628-637. (Pubitemid 44821904)
3. de Zoysa, R. S. S., D. A. Jayawardhana, ..., X. Guan. 2009. Slowing DNA translocation through nanopores using a solution containing organic salts. J. Phys. Chem. B. 113:13332-13336.
4. Fologea, D., J. Uplinger, ..., J. Li. 2005. Slowing DNA translocation in a solid-state nanopore. Nano Lett. 5:1734-1737. (Pubitemid 41396156)
5. Tabard-Cossa, V., D. Trivedi, ..., A. Marziali. 2007. Noise analysis and reduction in solid-state nanopores. Nanotechnology. 18:305505.
6. Benner, S., R. J. A. Chen, ..., M. Akeson. 2007. Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore. Nat. Nanotechnol. 2:718-724. (Pubitemid 350071065)
7. Cockroft, S. L., J. Chu, ..., M. R. Ghadiri. 2008. A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. J. Am. Chem. Soc. 130:818-820.
8. Wiggin, M., C. Tropini, ..., A. Marziali. 2008. Nonexponential kinetics of DNA escape from α-hemolysin nanopores. Biophys. J. 95:5317- 5323.
9. Wanunu, M., J. Sutin, ..., A. Meller. 2008. DNA translocation governed by interactions with solid-state nanopores. Biophys. J. 95:4716-4725.
10. 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. (Pubitemid 36373559)
11. Wanunu, M., B. Chakrabarti, ..., A. Meller. 2008. Orientation-dependent interactions of DNA with an α-hemolysin channel. Phys. Rev. E. 77:031904.
12. Tropini, C., and A. Marziali. 2007. Multi-nanopore force spectroscopy for DNA analysis. Biophys. J. 92:1632-1637. (Pubitemid 46393474)
13. Wallace, E. V. B., D. Stoddart, ..., H. Bayley. 2010. Identification of epigenetic DNA modifications with a protein nanopore. Chem. Commun. (Camb.). 46:8195-8197.
14. Clarke, J., H. C. Wu, ..., H. Bayley. 2009. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4:265-270.
15. Akeson, M., D. Branton, ..., D. W. Deamer. 1999. Microsecond timescale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77:3227-3233.
16. Jetha, N. N., M. Wiggin, and A. Marziali. 2009. Forming an α-hemolysin nanopore for single molecule analysis. In Micro and Nano Technologies in Bioanalysis. J. W. Lee and R. S. Foote, editors. Humana Press, Totowa, NJ. 113-127.
17. Jetha, N. N., M. Wiggin, and A. Marziali. 2009. Nanopore force spectroscopy on DNA duplexes. In Micro and Nano Technologies in Bioanalysis. J.W. Lee and R. S. Foote, editors. Humana Press, Totowa, NJ. 129-150.
18. Tabard-Cossa, V., M. Wiggin, ..., A. Marziali. 2009. Single-molecule bonds characterized by solid-state nanopore force spectroscopy. ACS Nano. 3:3009-3014.
19. Song, L., M. R. Hobaugh, ..., J. E. Gouaux. 1996. Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore. Science. 274:1859-1866. (Pubitemid 26424757)
20. Liebovitch, L. S., and T. I. Toth. 1991. Distributions of activation energy barriers that produce stretched exponential probability distributions for the time spent in each state of the two state reaction A ↔ B. Bull. Math. Biol. 53:443-455.
21. Austin, R. H., K. W. Beeson, ..., I. C. Gunsalus. 1975. Dynamics of ligand binding to myoglobin. Biochemistry. 14:5355-5373.
22. Bruskov, V. 1978. Specificity of interaction of nucleic acid bases with hydrogen bond forming amino acids. Stud. Biophys. (Berlin). 67S:43-44. (Pubitemid 8240948)
23. Meller, A., and D. Branton. 2002. Single molecule measurements of DNA transport through a nanopore. Electrophoresis. 23:2583-2591. (Pubitemid 35023698)
24. Meller, A., L. Nivon, ..., D. Branton. 2000. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. USA. 97:1079-1084. (Pubitemid 30080815)
25. Henrickson, S. E., M. Misakian, ..., J. J. Kasianowicz. 2000. Driven DNA transport into an asymmetric nanometer-scale pore. Phys. Rev. Lett. 85:3057-3060.