Sequencing single molecules of DNA

Current Opinion in Chemical Biology

Volumn 10, Issue 6, 2006, Pages 628-637

  Bayley, Hagan ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; DNA POLYMERASE; EXONUCLEASE; GENOMIC DNA; MEMBRANE PROTEIN; POLYMER; SINGLE STRANDED DNA;

DNA EXTRACTION; DNA SEQUENCE; DNA TRANSFER; ELECTRON MICROSCOPY; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE AMPLIFICATION; GENE MAPPING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HYBRIDIZATION; LIPID BILAYER; MEMBRANE POTENTIAL; MOLECULAR CLONING; MOLECULAR RECOGNITION; NANOTECHNOLOGY; NONHUMAN; POLYMERASE CHAIN REACTION; POROSITY; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA; NANOTECHNOLOGY; SEQUENCE ANALYSIS, DNA;

EID: 33751414735     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.10.040     Document Type: Review

References (37)

1. Shendure J., Mitra R.D., Varma C., and Church G.M. Advanced sequencing technologies: methods and goals. Nat Rev Genet 5 (2004) 335-344
2. Blazej R.G., Kumaresan P., and Mathies R.A. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing. Proc Natl Acad Sci USA 103 (2006) 7240-7245. Pushing the limits of Sanger sequencing. Amplifying, purifying and sequencing DNA in a single laboratory-on-a-chip device.
3. Zhang K., Martiny A.C., Reppas N.B., Barry K.W., Malek J., Chisholm S.W., and Church G.M. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24 (2006) 680-686. Sequencing of bacterial genomes after multiple displacement amplification (MDA) of chromosomal DNA from single cells with φ{symbol}29 DNA polymerase.
4. ••], this work represents efforts at the leading edge of non-electrophoretic sequence determination after massively parallel amplification of genomic DNA. Both groups amplified DNA by emulsion PCR and bead capture. Shendure et al. carried out sequencing by automated cycles of hybridization and ligation of fluorescent probes. Margulies et al. used a pyrosequencing protocol.
5. ••].
6. Dressman D., Yan H., Traverso G., Kinzler K.W., and Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci USA 100 (2003) 8817-8822
7. Ramanathan A., Pape L., and Schwartz D.C. High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Anal Biochem 337 (2005) 1-11
8. Lacenere C., Garg M.K., Stoltz B.M., and Quake S.R. Effects of a modified dye-labeled nucleotide spacer arm on incorporation by thermophilic DNA polymerases. Nucleosides Nucleotides Nucleic Acids 25 (2006) 9-15
9. Seo T.S., Li Z., Ruparel H., and Ju J. Click chemistry to construct fluorescent oligonucleotides for DNA sequencing. J Org Chem 68 (2003) 609-612
10. Meng Q., Kim D.H., Bai X., Bi L., Turro N.J., and Ju J. Design and synthesis of a photocleavable fluorescent nucleotide 3′-O-allyl-dGTP-PC-Bodipy-FL-510 as a reversible terminator for DNA sequencing by synthesis. J Org Chem 71 (2006) 3248-3252
11. Bi L., Kim D.H., and Ju J. Design and synthesis of a chemically cleavable fluorescent nucleotide, 3′-O-allyl-dGTP-allyl-bodipy-FL-510, as a reversible terminator for DNA sequencing by synthesis. J Am Chem Soc 128 (2006) 2542-2543
12. Sakata T., and Miyahara Y. DNA sequencing based on intrinsic molecular charges. Angew Chem Int Ed Engl 45 (2006) 2225-2228. Enzymatic DNA extension detected when templates are immobilized on the surface of a field-effect transistor, based on the additional negative charge of the extended strand, rather than fluorescence. It is unclear how long reads will be achieved.
13. Drmanac R., Drmanac S., Chui G., Diaz R., Hou A., Jin H., Jin P., Kwon S., Lacy S., Moeur B., et al. Sequencing by hybridization (SBH): advantages, achievements, and opportunities. Adv Biochem Eng Biotechnol 77 (2002) 75-101
14. Edwards J.R., Ruparel H., and Ju J. Mass-spectrometry DNA sequencing. Mutat Res 573 (2005) 3-12
15. Stephan J., Dorre K., Brakmann S., Winkler T., Wetzel T., Lapczyna M., Stuke M., Angerer B., Ankenbauer W., Foldes-Papp Z., et al. Towards a general procedure for sequencing single DNA molecules. J Biotechnol 86 (2001) 255-267
16. Braslavsky I., Hebert B., Kartalov E., and Quake S.R. Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci USA 100 (2003) 3960-3964
17. Levene M.J., Korlach J., Turner S.W., Foquet M., Craighead H.G., and Webb W.W. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299 (2003) 682-686
18. Church G, Deamer DW, Branton D, Baldarelli R, Kasianowicz J: Characterization of individual polymer molecules based on monomer-interface interactions. US Patent 1998, 5 795 782.
19. Kasianowicz J.J., Brandin E., Branton D., and Deamer D.W. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93 (1996) 13770-13773
20. Akeson M., Branton D., Kasianowicz J.J., Brandin E., and 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 (1999) 3227-3233
21. Ashkenasy N., Sánchez-Quesada J., Bayley H., and Ghadiri M.R. Recognizing a single base in an individual DNA strand: a step toward nanopore DNA sequencing. Angew Chem Int Ed Engl 44 (2005) 1401-1404. An important step towards DNA sequencing by the nanopore approach. Demonstrates both single base resolution and base recognition in an immobilized single-stranded DNA. Must be extended to a moving strand.
22. Astier Y., Braha O., and 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 (2006) 1705-1710. Identification of all four nucleoside monophosphates by single-molecule detection with a protein nanopore. Again demonstrates base recognition, and may be a means for reagent-free base detection in exonuclease sequencing.
23. Shapovalov G., and Lester H.A. Gating transitions in bacterial ion channels measured at 3 microseconds resolution. J Gen Physiol 124 (2004) 151-161
24. King G.M., and Golovchenko J.A. Probing nanotube-nanopore interactions. Phys Rev Lett 95 (2005) 216103
25. Krieger K. Nanopore arrays for DNA sequencing. Anal Chem 78 (2006) 3486
26. Kang X., Gu L.-Q., Cheley S., and Bayley H. Single protein pores containing molecular adapters at high temperatures. Angew Chem Int Ed Engl 44 (2005) 1495-1499. Protein pores are stable at the high temperatures that might be required nanopore sequencing.
27. Shenoy D.K., Barger W.R., Singh A., Panchal R.G., Misakian M., Stanford V.M., and Kasianowicz J.J. Functional reconstitution of protein ion channels into planar polymerizable phospholipid membranes. Nano Lett 6 (2005) 1181-1185. Protein pores can function in polymerized bilayers, which are likely to be more stable than conventional lipid bilayers.
28. Gufler P.C., Pum D., Sleytr U.B., and Schuster B. Highly robust lipid membranes on crystalline S-layer supports investigated by electrochemical impedance spectroscopy. Biochim Biophys Acta 1661 (2004) 154-165
29. Holden M.A., and Bayley H. Direct introduction of single protein channels and pores into lipid bilayers. J Am Chem Soc 127 (2005) 6502-6503
30. Holden M.A., Jayasinghe L., Daltrop O., Mason A., and Bayley H. Direct transfer of membrane proteins from bacteria to planar bilayers for rapid screening by single-channel recording. Nat Chem Biol 2 (2006) 314-318. With [29], demonstrates means for the direct transfer of protein nanopores into lipid bilayers. Potential use for the fabrication of nanopore arrays.
31. Lagerqvist J., Zwolak M., and Di Ventra M. Fast DNA sequencing via transverse electronic transport. Nano Lett 6 (2006) 779-782
32. Gracheva M.E., Xiong A., Aksimentiev A., Schulten K., Timp G., and Leburton J.-P. Simulation of the electric response of DNA translocation through a semiconductor nanpore-capacitor. Nanotechnology 17 (2006) 622-633
33. Mitra R.D., Butty V.L., Shendure J., Williams B.R., Housman D.E., and Church G.M. Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci USA 100 (2003) 5926-5931
34. Henrickson S.E., Misakian M., Robertson B., and Kasianowicz J.J. Driven DNA transport into an asymmetric nanometer-scale pore. Phys Rev Lett 85 (2000) 3057-3060
35. Bates M., Burns M., and Meller A. Dynamics of DNA molecules in a membrane channel probed by active control techniques. Biophys J 84 (2003) 2366-2372
36. Bayley H., and Cremer P.S. Stochastic sensors inspired by biology. Nature 413 (2001) 226-230
37. Howorka S., Cheley S., and Bayley H. Sequence-specific detection of individual DNA strands using engineered nanopores. Nat Biotechnol 19 (2001) 636-639