Progress towards single-molecule DNA sequencing: A one color demonstration

Journal of Biotechnology

Volumn 102, Issue 1, 2003, Pages 1-14

  Werner, James H ^a   Cai, Hong ^a   Jett, James H ^a   Reha Krantz, Linda ^b   Keller, Richard A ^a   Goodwin, Peter M ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

DNA sequencing; Fluorescence; Single molecule detection

Indexed keywords

CYTOLOGY; FLUORESCENCE; LASER APPLICATIONS; MOLECULES;

SINGLE MOLECULES;

DNA SEQUENCES;

DNA FRAGMENT; EXONUCLEASE; FLUORESCENT DYE; ISOENZYME; MICROSPHERE; RHODAMINE; SINGLE STRANDED DNA; URIDINE DERIVATIVE;

ARTICLE; DNA BINDING; DNA CLEAVAGE; DNA SEQUENCE; ENZYME BINDING; FLOW CYTOMETRY; MEDICAL INSTRUMENTATION; PRIORITY JOURNAL;

EID: 0037430847     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-1656(03)00006-3     Document Type: Article

References (39)

1. Affleck R.L., Ambrose W.P., Demas J.N., Goodwin P.M., Schecker J.A., Wu M., Keller R.A. Reduction of luminescent background in ultrasensitive fluorescence detection by photobleaching. Anal. Chem. 68:1996;2270-2276.
2. Ambrose W.P., Goodwin P.M., Jett J.H., Johnson M.E., Martin J.C., Marrone B.L., Schecker J.A., Wilkerson C.W., Keller R.A., Haces A., Shih P.-J., Harding J.D. Application of single molecule detection to DNA sequencing and sizing. Ber. Bunsenges. Phys. Chem. 97:1993;1535-1542.
3. Augustin M.A., Ankenbauer W. Progress towards single-molecule sequencing: enzymatic synthesis of nucleotide-specifically labeled DNA. J. Biotechnol. 86:2001;289-301.
4. Blackwell T.W. Estimating Consensus DNA Sequences. 1993;Department of Statistics, Harvard, Cambridge.
5. 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. 261:1986;7136-7143.
6. Dapprich J. Single-molecule DNA digestion by lambda-exonuclease. Cytometry. 36:1999;163-168.
7. Dapprich J., Nicklaus N. Attachment to optically trapped beads in microstructures monitored by bead displacement. Bioimaging. 6:1998;25-32.
8. Dörre K., Brakmann S., Brinkmeier M., Han K.-T., Riebeseel K., Schwille P., Stephan J., Wetzel T., Lapczyna M., Stuke M., Bader R., Hinz M., Seliger H., Holm J., Eigen M., Rigler R. Techniques for single molecule sequencing. Bioimaging. 5:1997;139-152.
9. Dörre K., Stephan J., Lapczyna M., Stuke M., Dunkel H., Eigen M. Highly efficient single molecule detection in microstructures. J. Biotechnol. 86:2001;225-236.
10. Eggeling C., Berger S., Brand L., Fries J.R., Schaffer J., Volkmer A., Seidel C.A.M. Data registration and selective single-molecule analysis using multi-parameter fluorescence detection. J. Biotechnol. 86:2001;163-180.
11. Eigen M., Rigler R. Sorting single molecules: applications to diagnostics and evolutionary biotechnology. Proc. Natl. Acad. Sci. USA. 91:1994;5740-5747.
12. Földes-Papp Z., Angerer B., Ankenbauer W., Rigler R. Fluorescent high-density labeling of DNA: error-free substitution for a normal nucleotide. J. Biotechnol. 86:2001;237-253.
13. Földes-Papp Z., Angerer B., Thyberg P., Hintz M., Wennmalm S., Ankenbauer W., Seliger H., Holmgren A., Rigler R. Fluorescently labeled model DNA sequences for exonucleolytic sequencing. J. Biotechnol. 86:2001;203-224.
14. Goodwin P.M., Wilkerson C.W. Jr, Ambrose W.P., Keller R.A. Ultrasensitive detection of single molecules in flowing sample streams by laser-induced fluorescence. Proc. SPIE. 1895:1993;79-89.
15. Goodwin P.M., Affleck R.L., Ambrose W.P., Demas J.N., Jett J.H., Martin J.C., Reha-Krantz L.J., Semin D.J., Schecker J.A., Wu M., Keller R.A. Progress toward DNA sequencing at the single molecule level. Exp. Tech. Phys. 41:1995;279-294.
16. Goodwin P.M., Affleck R.L., Ambrose W.P., Jett J.H., Johnson M.E., Martin J.C., Petty J.T., Schecker J.A., Wu M., Keller R.A. Brown S.D. Computer Assisted Analytical Spectroscopy. 1996;61-80 Wiley, Chichester, England.
17. Goodwin P.M., Ambrose W.P., Keller R.A. Single-molecule detection in liquids by laser-induced fluorescence. Acc. Chem. Res. 29:1996;607-613.
18. Goodwin P.M., Cai H., Jett J.H., Ishaug-Riley S.L., Machara N.P., Semin D.J., Van Orden A., Keller R.A. Application of single molecule detection to DNA sequencing. Nucleosides Nucleotides. 16:1997;543-550.
19. Harris T.D., Lytle F.E. Kliger D.S. Ultrasensitive Laser Spectroscopy. 1983;369-433 Academic Press, New York.
20. Hinz M., Gura A., Nitzan B., Seliger H. Polymer support for exonucleolytic sequencing. J. Biotechnol. 86:2001;281-288.
21. Jett J.H., Keller R.A., Martin J.C., Marrone B.L., Moyzis R.K., Ratliff R.L., Seitzinger N.K., Shera E.B., Stewart C.C. High speed DNA sequencing: an approach based upon fluorescence detection of single molecules. J. Biomol. Struct. Dynam. 7:1989;301-309.
22. Jett, J.H., Keller, R.A., Martin, J.C., Moyzis, R.K., Ratliff, R.L., Shera, E.B., Stewart, C.C., 1990. Method for rapid base sequencing in DNA and RNA. US Patent 4,962,037.
23. Jett, J.H., Hammond, M.L., Keller, R.A., Martin, J.C., Posner, R.G., Marrone, B.L., Simpson, D.J., 1995. Method for rapid base sequencing in DNA and RNA with two base labeling. US Patent 5,405,747.
24. Machara N.P., Goodwin P.M., Enderlein J., Semin D.J., Keller R.A. Efficient detection of single molecules eluting off an optically trapped microsphere. Bioimaging. 6:1998;33-42.
25. Messing J., Crea R., Seeburg P.H. A system for shotgun DNA sequencing. Nucleic Acids Res. 9:1981;309-321.
26. Reha-Krantz, L.J., Goodman, M.F., 1999a. Variant DNA polymerases. United States Patent 5,928,919.
27. Reha-Krantz, L.J., Goodman, M.F., 1999b. Synthesis of fluorophore-labeled DNA. United States Patent 5,945,312.
28. Sauer M., Zander C. Zander C., Enderlein J., Keller R.A. Single Molecule Detection in Solution. 2002;260-267 Wiley-VCH, Berlin.
29. Sauer M., Arden-Jacob J., Drexhage K.H., Göbel F., Lieberwirth U., Mühlegger K., Müller R., Wolfrum J., Zander C. Time-resolved identification of individual mononucleotide molecules in aqueous solution with pulsed semiconductor lasers. Bioimaging. 6:1998;14-24.
30. Sauer M., Angerer B., Han K.-T., Zander C. Detection and identification of single dye labeled mononucleotide molecules released from an optical fiber in a microcapillary: first steps towards a new single molecule DNA sequencing technique. Phys. Chem. Chem. Phys. 1:1999;2471-2477.
31. Sauer M., Angerer B., Ankenbauer W., Földes-Papp Z., Göbel F., Han K.-T., Rigler R., Schulz A., Wolfrum J., Zander C. Single molecule DNA sequencing in submicrometer channels: state of the art and future prospects. J. Biotechnol. 86:2001;181-201.
32. Schecker J.A., Goodwin P.M., Affleck R.L., Wu M., Martin J.C., Jett J.H., Keller R.A. DNA sequencing via single molecule detection of enzymatically cleaved fluorescent nucleotides. Proc. SPIE. 2386:1995;4-12.
33. Seela F., Feiling E., Gross J., Hillenkamp F., Ramzaeva N., Rosemeyer H., Zulauf M. Fluorescent DNA: the development of 7-deazapurine nucleoside triphosphates applicable for sequencing at the single molecule level. J. Biotechnol. 86:2001;269-279.
34. Shera E.B., Seitzinger N.K., Davis L.M., Keller R.A., Soper S.A. Detection of single fluorescent molecules. Chem. Phys. Lett. 174:1990;553-557.
35. Stephan J., Dörre K., Brakmann S., Winkler T., Wetzel T., Lapczyna M., Stuke M., Angerer B., Ankwnbauer W., Földes-Papp Z., Rigler R., Eigen M. Towards a general procedure for sequencing single DNA molecules. J. Biotechnol. 86:2001;255-267.
36. Van Orden A., Machara N.P., Goodwin P.M., Keller R.A. Single-molecule identification in flowing sample streams by fluorescence burst size and intraburst fluorescence decay rate. Anal. Chem. 70:1998;1444-1451.
37. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.Q.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J.H., Miklos G.L.G., Nelson C., Broder S., Clark A.G., Nadeau C., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z.M., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W.M., Gong F.C., Gu Z.P., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z.X., Ketchum K.A., Lai Z.W., Lei Y.D., Li Z.Y., Li J.Y., Liang Y., Lin X.Y., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B.X., Sun J.T., Wang Z.Y., Wang A.H., Wang X., Wang J., Wei M.H., Wides R., Xiao C.L., Yan C.H., et al. The sequence of the human genome. Science. 291:2001;1304-1351.
38. Wang W., Liu Y., Sonek G.J., Berns M.W., Keller R.A. Optical trapping and fluorescence detection in laminar-flow streams. Appl. Phys. Lett. 67:1995;1057-1059.
39. Werner J.H., Cai H., Goodwin P.M., Keller R.A. Current status of DNA sequencing by single molecule detection. Proc. SPIE. 3602:1999;355-366.