Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore (original) (raw)

References

  1. Deamer, D. W. & Branton, D. Characterization of nucleic acids by nanopore analysis. Acc. Chem. Res. 35, 817–825 (2002).
    Article CAS Google Scholar
  2. Dekker, C. Solid-state nanopores. Nature Nanotechnol. 2, 209–215 (2007).
    Article CAS Google Scholar
  3. Siwy, Z. et al. Protein biosensors based on biofunctionalized conical gold nanotubes. J. Am. Chem. Soc. 127, 5000–5001 (2005).
    Article CAS Google Scholar
  4. Hornblower, B. et al. Single-molecule analysis of DNA–protein complexes using nanopores. Nature Methods 4, 315–317 (2007).
    Article CAS Google Scholar
  5. Zhao, Q. et al. Detecting SNPs using a synthetic nanopore. Nano Lett. 7, 1680–1685 (2007).
    Article CAS Google Scholar
  6. Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl Acad. Sci. USA 93, 13770–13773 (1996).
    Article CAS Google Scholar
  7. Song, L. Z. et al. Structure of Staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 274, 1859–1866 (1996).
    Article CAS Google Scholar
  8. Vercoutere, W. et al. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nature Biotechnol. 19, 248–252 (2001).
    Article CAS Google Scholar
  9. Vercoutere, W. A. et al. Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules. Nucleic Acids Res. 31, 1311–1318 (2003).
    Article CAS Google Scholar
  10. Akeson, M., Branton, D., Kasianowicz, J. J., Brandin, E. & Deamer, D. W. 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 (1999).
    Article CAS Google Scholar
  11. Ashkenasy, N., Sanchez-Quesada, J., Bayley, H. & Ghadiri, M. R. Recognizing a single base in an individual DNA strand: A step toward DNA sequencing in nanopores. Angew. Chem. Int. Edn 44, 1401–1404 (2005).
    Article CAS Google Scholar
  12. Howorka, S., Cheley, S. & Bayley, H. Sequence-specific detection of individual DNA strands using engineered nanopores. Nature Biotechnol. 19, 636–639 (2001).
    Article CAS Google Scholar
  13. Butler, T. Z., Gundlach, J. H. & Troll, M. A. Determination of RNA orientation during translocation through a biological nanopore. Biophys. J. 90, 190–199 (2006).
    Article CAS Google Scholar
  14. Sauer-Budge, A. F., Nyamwanda, J. A., Lubensky, D. K. & Branton, D. Unzipping kinetics of double-stranded DNA in a nanopore. Phys. Rev. Lett. 90, 23801 (2003).
    Article Google Scholar
  15. Storm, A. J. et al. Fast DNA translocation through a solid-state nanopore. Nano Lett. 5, 1193–1197 (2005).
    Article CAS Google Scholar
  16. Nakane, J., Akeson, M. & Marziali, A. Evaluation of nanopores as candidates for electronic analyte detection. Electrophoresis 23, 2592–2601 (2002).
    Article CAS Google Scholar
  17. Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 (2001).
    Article CAS Google Scholar
  18. Gu, L.-Q., Cheley, S. & Bayley, H. Capture of a single molecule in a nanocavity Science 291, 636–640 (2001).
    Article CAS Google Scholar
  19. Iqbal, S. M., Akin, D. & Bashir, R. Solid-state nanopore channels with DNA selectivity. Nature Nanotechnol. 2, 243–248 (2007).
    Article CAS Google Scholar
  20. Joyce, C. M. & Steitz, T. A. Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63, 777–822 (1994).
    Article CAS Google Scholar
  21. Joyce, C. M. & Benkovic, S. J. DNA polymerase fidelity: Kinetics, structure, and checkpoints. Biochemistry 43, 14317–14324 (2004).
    Article CAS Google Scholar
  22. Beese, L. S., Derbyshire, V. & Steitz, T. A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260, 352–355 (1993).
    Article CAS Google Scholar
  23. Li, Y., Korolev, S. & Waksman, G. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation. EMBO J. 17, 7514–7525 (1998).
    Article CAS Google Scholar
  24. Johnson, S. J., Taylor, J. S. & Beese, L. S. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc. Natl Acad. Sci. USA 100, 3895–3900 (2003).
    Article CAS Google Scholar
  25. Purohit, V., Grindley, N. D. F. & Joyce, C. M. Use of 2-aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment). Biochemistry 42, 10200–10211 (2003).
    Article CAS Google Scholar
  26. Sanger, F., Nicklen, S. & Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463–5467 (1977).
    Article CAS Google Scholar
  27. Steitz, T. A., Smerdon, S. J., Jager, J. & Joyce, C. M. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science 266, 2022–2025 (1994).
    Article CAS Google Scholar
  28. Bates, M., Burns, M. & Meller, A. Dynamics of DNA molecules in a membrane channel probed by active control techniques. Biophys. J. 84, 2366–2372 (2003).
    Article CAS Google Scholar
  29. Winters-Hilt, S. et al. Highly accurate classification of Watson–Crick basepairs on termini of single DNA molecules. Biophys. J. 84, 967–976 (2003).
    Article CAS Google Scholar
  30. Gill, A. Introduction to the Theory of Finite-State Machines (McGraw-Hill, 1962).
  31. Trimberger, S. M. Field-Programmable Gate Array Technology (Springer, 1994).
  32. Smeets, R. M. M. et al. Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 6, 89–95 (2006).
    Article CAS Google Scholar

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