Continuous base identification for single-molecule nanopore DNA sequencing

Nature Nanotechnology

Volumn 4, Issue 4, 2009, Pages 265-270

  Clarke, James ^a   Wu, Hai Chen ^b   Jayasinghe, Lakmal ^a,b   Patel, Alpesh ^a   Reid, Stuart ^a   Bayley, Hagan ^b  

^a Oxford Nanopore Technologies Ltd   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA SEQUENCES; NANOPORES; NUCLEIC ACIDS; NUCLEOTIDES;

ADAPTER MOLECULES; DETECTION SYSTEM; EPIGENETIC MODIFICATION; HIGH PROBABILITY; HIGHLY ACCURATE; OPERATING CONDITION; SINGLE MOLECULE; SINGLE-MOLECULE METHODS;

GENE ENCODING;

DNA; EXONUCLEASE; HEMOLYSIN; SINGLE STRANDED DNA;

ARTICLE; BIOSENSOR; COVALENT BOND; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; DNA STRAND; ELECTRIC POTENTIAL; ENZYME ACTIVITY; EPIGENETICS; FLUORESCENCE ANALYSIS; MUTAGENESIS; NANOPORE; PRIORITY JOURNAL;

EID: 64449088698     PISSN: 17483387     EISSN: 17483395     Source Type: Journal    
DOI: 10.1038/nnano.2009.12     Document Type: Article

References (32)

1. Bayley, H. Sequencing single molecules of DNA. Curr. Opin. Chem. Biol, l0, 628-637(2006).
2. Branton, D. et al. The potential and challenges of nanopore sequencing. Nature Biotechnol. 26, 1146-1153 (2008).
3. 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).
4. Deamer, D. W. & Branton, D. Characterization of nucleic acids by nanopore analysis. Acc. Chem. Res. 35, 817-825 (2002).
5. 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. Ed. Engl. 44, 1401-1404 (2005).
6. Mitchell, N. & Howorka, S. Chemical tags facilitate the sensing of individual DNA strands with nanopores. Angew Chem. Int. Ed. Engl. 47, 5565-5568 (2008).
7. Astier, Y., Kainov, D. E., Bayley, H., Tuma, R. & Howorka, S. Stochastic detection of motor protein-RNA complexes by single-channel current recording. Chem. Phys. Chem. 8, 2189-2194 (2007).
8. Hornblower, B. et al. Single-molecule analysis of DNA - protein complexes using nanopores. Nature Methods 4, 315-317 (2007).
9. Cockroft, S. L., Chu, J., Amorin, M. & Ghadiri, M. R. A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. J. Am. Chem. Soc. 130, 818-820 (2008).
10. Maglia, G., Restrepo, M. R., Mikhailova, E. & Bayley, H. Enhanced translocation of single DNA molecules through alpha-hemolysin nanopores by manipulation of internal charge. Proc. Natl Acad. Sci. USA 105, 19720-19725 (2008).
11. Jett, J. H. et al. High-speed DNA sequencing: an approach based upon fluorescence detection of single molecules. J. Biomol. Struct. Dyn. 7, 301 -309 (1989).
12. Sauer, M. et al. Single molecule DNA sequencing in submicrometer channels: state of the art and future prospects. J. Biotechnol. 86, 181-201 (2001).
13. Stephan, J. et al. Towards a general procedure for sequencing single DNA molecules. J. Biotechnol. 86, 255-267 (2001).
14. Werner, J. H. et al. Progress towards single-molecule DNA sequencing: a one color demonstration. J. Biotechnol. 102, 1-14 (2003).
15. Werner, J. H., Cai, H., Keller, R. A. & Goodwin, P. M. Exonuclease I hydrolyzes DNA with a distribution of rates. Biophys. J. 88, 1403-1412 (2005).
16. Bayley, H. & Cremer, P. S. Stochastic sensors inspired by biology. Nature 413, 226-230 (2001).
17. Cheley, S., Gu, L. Q. & Bayley, H. Stochastic sensing of nanomolar inositol 1,4,5- trisphosphate with an engineered pore. Chem. Biol. 9, 829-838 (2002).
18. Shin, S. H., Luchian, T., Cheley, S., Braha, O. & Bayley, H. Kinetics of a reversible covalent-bond-forming reaction observed at the single-molecule level. Angew Chem. Int. Ed. Engl. 41, 3707-3709, 3523 (2002).
19. Gu, L. Q., Braha, O., Conlan, S., Cheley, S. & Bayley, H. Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter. Nature 398, 686-690 (1999).
20. Astier, Y., Braha, O. & Bayley, H. 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, 1705-1710 (2006).
21. Brody, R. S., Doherty, K. G. & Zimmerman, P. D. Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides. J. Biol. Chem. 261, 7136-7143 (1986).
22. Enderlein, J. Nucleotide specificity versus complex heterogeneity in exonuclease activity measurements. Biophys. J. 92, 1556-1558 (2007).
23. Cheley, S., Braha, O., Lu, X., Conlan, S. & Bayley, H. A functional protein pore with a 'retro' transmembrane domain. Protein Sci. 8, 1257-1267 (1999).
24. Song, L. et al. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 274, 1859-1866 (1996).
25. Gu, L. Q., Cheley, S. & Bayley, H. Capture of a single molecule in a nanocavity Science 291, 636-640 (2001).
26. Wu, H. C, Astier, Y., Maglia, G., Mikhailova, E. & Bayley, H. Protein nanopores with covalently attached molecular adapters. J. Am. Chem. Soc. 129, 16142-16148 (2007).
27. Sanchez-Quesada, J., Ghadiri, M. R., Bayley, H. & Braha, O. Cyclic peptides as molecular adapters for a pore-forming protein. J. Am. Chem. Soc. 122, 11757-11766 (2000).
28. Brena, R. M., Huang, T. H. & Plass, C. Toward a human epigenome. Nature Genet. 38, 1359-1360 (2006).
29. Schaefer, C. B., Ooi, S. K., Bestor, T. H. & Bourc'his, D. Epigenetic decisions in mammalian germ cells. Science 316, 398-399 (2007).
30. Ooi, S. K. & Bestor, T. H. The colorful history of active DNA demethylation. Cell133, 1145-1148(2008).
31. Hayatsu, H. The bisulfite genomic sequencing used in the analysis of epigenetic states, a technique in the emerging environmental genotoxicology research. Mutat. Res. 659, 77-82 (2008).
32. Howorka, S., Cheley, S. & Bayley, H. Sequence-specific detection of individual DNA strands using engineered nanopores. Nature Biotechnol. 19, 636-639 (2001).