Dna sequencing using fluorescence detection

Biomedical Photonics: Handbook

Volumn , Issue , 2003, Pages 53-1-53-48

  Soper, Steven A ^a   Owens, Clyde V ^a   Lassiter, Suzanne J ^a   Xu, Yichuan ^a   Waddell, Emanuel ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

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EID: 32444438760     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (56)

1. Watson, J.D. and Crick, F.H.C., Molecular structure of nucleic acid: a structure of deoxyribonucleic acid, Nature, 171, 737, 1953.
2. Chen, E.Y., Schlessinger, D., and Kere, J., Ordered shotgun sequencing, a strategy for integrated mapping and sequencing of YAC clones, Genomics, 17, 651, 1993.
3. Maxam, A.M. and Gilbert, W., A new method for sequencing DNA, Proc. Natl. Acad. Sci. U.S.A., 74, 560, 1977.
4. Sanger, F., Nicklen, S., and Coulson, A.R., DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. U.S.A., 74, 5463, 1977.
5. Fung, E.N. and Yeung, E.S., High-speed DNA sequencing by using mixed poly(ethylene oxide) solutions in uncoated capillary columns, Anal. Chem., 67, 1913, 1995.
6. Smith, L.M., Saunders, J.Z., Kaiser, R.J., Hughes, P., Dodd, C.R., Connell, C.R., Heiner, C., Kent, S.B.H., and Hood, L.E., Fluorescence detection in automated DNA sequence analysis, Nature, 321, 674, 1986.
7. Prober, J.M., Trainor, G.L., Dam, R.J., Hobbs, F.G., Robertson, C.W., Zagursky, R.J., Cocuzza, A.J., Jensen, M.A., and Baumeister, K., A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides, Science, 238, 336, 1987.
8. Ansorge, W., Sproat, B., Stegeman, J., Schwager, C., and Zenke, M., Automated DNA sequencing: ultrasensitive detection of bands during electrophoresis, Nucleic Acids Res., 15, 4593, 1987.
9. Metzker, M.L., Lu, J., and Gibbs, R.A., Electrophoretically uniform fluorescent dyes for automated DNA sequencing, Science, 271, 1420, 1996.
10. Lee, L.G., Connell, C., Woo, S., Cheng, R., McArdle, B., Fuller, C., Halloran, N., and Wilson, R., DNA sequencing with dye-labeled terminators and T7 DNA polymerase: effects of dyes and dNTPs on incorporation of dye-terminators and probability analysis of termination fragments, Nucleic Acids Res., 20, 2471, 1992.
11. Tabor, S. and Richardson, C.C., A single residue in DNA polymerase from E. coli DNA polymerase I family is critical for distinguishing between deoxy-and dideoxynucleotides, PNAS, 92, 6339, 1995.
12. Rosenblum, B.B., Lee, L.G., Spurgeon, S.L., Khan, S.H., Menchen, S.M., Heiner, C.R., and Chen, S.M., New dye-labeled terminators for improved DNA sequencing patterns, Nucleic Acids Res., 25, 4500, 1997.
13. Hung, S.-C., Mathies, R.A., and Glazer, A.N., Optimization of spectroscopic and electrophoretic properties of energy transfer primers, Anal. Biochem., 252, 78, 1997.
14. Hung, S.-C., Mathies, R.A., and Glazer, A.N., Comparison of fluorescence energy transfer primers with different donor-acceptor dye combinations, Anal. Biochem., 255, 32, 1998.
15. Ju, J., Ruan, C., Fuller, C.W., Glazer, A.N., and Mathies, R.A., Fluorescence energy transfer dyelabeled primers for DNA sequencing and analysis, Proc. Natl. Acad. Sci. U.S.A., 92, 4347, 1995.
16. Lee, L.G., Spurgeon, S.L., Heiner, C.R., Benson, S.C., Rosenblum, B.B., Menchen, S.M., Graham, R.J., Constantinescu, A., Upadhya, K.G., and Cassel, J.M., New energy transfer dyes for DNA sequencing, Nucleic Acids Res., 25, 2816, 1997.
17. Williams, D.C. and Soper, S.A., Ultrasensitive near-IR fluorescence detection for capillary gel electrophoresis and DNA sequencing applications, Anal. Chem., 67, 3427, 1995.
18. Middendorf, L.R., Bruce, J.C., Bruce, R.C., Eckles, R.D., Grone, D.L., Roemer, S.C., Sloiker, G.D., Steffens, D.L., Sutter, S.L., Brumbaugh, J.A., and Patonay, G., Continuous, on-line DNA sequencing using a versatile infrared laser scanner/electrophoresis apparatus, Electrophoresis, 13, 487, 1992.
19. Shealy, D.B., Lipowska, M., Lipwoski, J., Narayanan, N., Sutter, S., Strekowski, L., and Patonay, G., Synthesis, chromatographic separation and characterization of near-infrared-labeled DNA oligomers for use in DNA sequencing, Anal. Chem., 67, 247, 1995.
20. Soper, S.A. and Mattingly, Q., Steady-state and picosecond laser fluorescence studies of nonradiative pathways in tricarbocyanine dyes: implications to the design of near-IR fluorochromes with high fluorescence efficiencies, J. Am. Chem. Soc., 116, 3447, 1994.
21. Huang, X.C., Quesada, M.A., and Mathies, R.A., Capillary array electrophoresis using laser-excited confocal fluorescence detection, Anal. Chem., 64, 967, 1992.
22. Huang, X.C., Quesada, M.A., and Mathies, R.A., DNA sequencing using capillary array electrophoresis. Anal. Chem., 64, 2149, 1992.
23. Soper, S.A., Shera, E., Davis, L., Nutter, H., and Keller, R., The photophysical constants of several visible fluorescent dyes and their effects on ultrasensitive fluorescence detection, Photochem. Photobiol., 57, 972, 1993.
24. Kambara, H. and Takahashi, S. Multiple-sheathflow capillary array DNA analyzer, Nature, 361, 565, 1993.
25. Takahashi, S., Murakami, K., Anazawa, T., and Kambara, H., Multiple sheath-flow gel capillaryarray electrophoresis for multicolor fluorescent DNA detection, Anal. Chem., 66, 1021, 1994.
26. Swerdlow, H., Wu, S., Harke, H., and Dovichi, N., Capillary gel electrophoresis for DNA sequencing: laser-induced fluorescence detection with the sheath flow cuvette, J. Chromatogr., 516, 61, 1990.
27. Swerdlow, H., Zhang, J.Z., Chen, D.Y., Harke, H.R., Grey, R., Wu, S., and Dovichi, N.J., Three DNA sequencing methods using capillary gel electrophoresis and laser-induced fluorescence, Anal. Chem., 63, 2835, 1991.
28. Ewing, B., Hillier, L., Wendl, M., and Green, P., Base-calling of automated sequencer traces using Phred. I. Accuracy assessment, Genomics, 8, 175, 1998.
29. Tu, O., Knott, T., Marsh, M., Bechtol, K., Harris, D., Barker, D., and Bashkin, J., The influence of fluorescent dye structure on the electrophoretic mobility of end-labeled DNA, Nucleic Acids Res., 26, 2797, 1998.
30. Ansorge, W., Zimmermann, C., Schwager, C., Stegemann, J., Erfle, H., and Voss, H., One label, one tube, Sanger DNA sequencing in one and two lanes on a gel, Nucleic Acids Res., 18, 3419, 1990.
31. Chen, D., Swerdlow, H.P., Harke, H.R., Zhang, J.Z., and Dovichi, N.J., Single-color laser-induced fluorescence detection and capillary gel electrophoresis for DNA sequencing, Proc. Int. Soc. Opt. Eng., 1435, 161, 1991.
32. Tabor, S. and Richardson, C.C., DNA sequence analysis with a modified bacteriophage T7 DNA polymerase, Proc. Natl. Acad. Sci. U.S.A., 84, 4767, 1987.
33. Tabor, S. and Richardson, C.C., DNA sequence analysis with a modified bacteriophage T7 DNA polymerase, J. Biol. Chem., 14, 8322, 1990.
34. Chen, D.Y., Harke, H.R., and Dovichi, N.J., Two-label peak-height encoded DNA sequencing by capillary gel electrophoresis: three examples, Nucleic Acids Res., 20, 4873, 1992.
35. Li, Q. and Yeung, E., Simple two-color base-calling schemes for DNA sequencing based on standard four-label Sanger chemistry, Appl. Spectrosc., 49, 1528, 1995.
36. Starke, H.R., Yan, J., Zhang, Z., Muhlegger, K., Effgen, K., and Dovichi, N., Internal fluorescence labeling with fluorescent deoxoynucleotides in two-label peak-height encoded DNA sequencing by capillary electrophoresis, Nucleic Acids Res., 22, 3997, 1994.
37. Soper, S.A., Legendre, B.L., and Williams, D.C., On-line fluorescence lifetime determinations in capillary electrophoresis, Anal. Chem., 67, 4358, 1995.
38. Köllner, M., Fischer, A., Arden-Jacob, J., Drexhage, K.-H., Müller, R., Seeger, S., and Wolfrum, J., Fluorescence pattern recognition for ultrasensitive molecule identification: comparison of experimental data and theoretical approximations, Chem. Phys. Lett., 250, 355, 1996.
39. Legendre, B.L., Williams, D.C., Soper, S.A., Erdmann, R., Ortmann, U., and Enderlein, J., An all solid-state near-infrared time-correlated single photon counting instrument for dynamic lifetime measurements in DNA sequencing applications, Rev. Sci. Instrum., 67, 3984, 1996.
40. Lieberwirth, U., Arden-Jacob, J., Drexhage, K.H., Herten, D.P., Muller, R., Neumann, M., Schulz, A., Siebert, A., Siebert, S., Sagner, G., Klingel, S., Sauer, M., and Wolfrum, J., Multiplexed dye DNA sequencing in capillary gel electrophoresis by diode laser-based time-resolved fluorescence detection, Anal. Chem., 70, 4771, 1998.
41. Sauer, M., Arden-Jacob, J., Drexhage, K.H., Marx, N.J., Karger, A.E., Lieberwirth, U., Muller, R., Neumann, M., Nord, S., Schulz, A., Seeger, S., Zander, C., and Wolfrum, J., On-line diode laser based time-resolved fluorescence detection of labeled oligonucleotides in capillary gel electrophoresis, Biomed. Chromatogr., 11, 81, 1997.
42. Soper, S.A. and Legendre, B.L., Error analysis of simple algorithms for determining fluorescence lifetimes in ultradilute dye solutions, Appl. Spectrosc., 48, 400, 1994.
43. Waddell, E., Stryjewski, W., and Soper, S.A., A fiber-optic-based multichannel time-correlated single photon-counting device with subnanosecond time resolution, Rev. Sci. Instrum., 70, 32, 1999.
44. He, H., Nunnally, B.K., Li, L.C., and McGowen, L.B., On-the-fly fluorescence lifetime detection of dye-labeled primers for multiplexed analysis, Anal. Chem., 70, 3413, 1998.
45. Li, L.C. and McGowen, L.B., On-the-fly frequency-domain fluorescence lifetime detection in capillary electrophoresis, Anal. Chem., 68, 2737, 1996.
46. Li, L.C., He, H., Nunnally, B.K., and McGowen, L.B., On-the-fly fluorescence lifetime detection of labeled DNA primers, J. Chromatogr., 695, 85, 1997.
47. Li, L. and McGowen, L.B., Effects of gel material on fluorescence lifetime detection of dyes and dye-labeled DNA primers in capillary electrophoresis, J. Chromatogr., 841, 95, 1999.
48. Nunnally, B.K., He, H., Li, L.C., Tucker, S.A., and McGowen, L.B., Characterization of visible dyes for four-decay fluorescence detection, Anal. Chem., 69, 2392, 1997.
49. Hall, P. and Sellinger, B., Better estimates of exponential decay parameters, J. Phys. Chem., 85, 2941, 1981.
50. Ballew, R.M. and Demas, J.N., An error analysis of the rapid lifetime determination method for the evaluation of single exponential decays, Anal. Chem., 61, 30, 1989.
51. Flanagan, J.H., Owens, C.V., Romero, S.E., Waddell, E., Kahn, S.H., Hammer, R.P., and Soper, S.A., Near-infrared heavy-atom-modified fluorescent dyes for base-calling in DNA-sequencing applications using temporal discrimination, Anal. Chem., 70, 2676, 1998.
52. Fairfield, E.R., Jett, J., Keller, R., Hahn, J., Krakowski, L., Marrone, B., Martin, J., Ratliff, R., Shera, E., and Soper, S., Rapid DNA sequencing based upon single molecule detection, Gen. Anal., 8, 1, 1991.
53. Shera, E.B., Seitzinger, N., Davis, L., Keller, R., and Soper, S., Detection of single fluorescent molecules, Chem. Phys. Lett., 174, 553, 1990.
54. Soper, S.A., Hahn, J., Nutter, H., Shera, E., Martin, J., Jett, J., and Keller, R., Single molecule detection of R-6G in ethanolic solutions utilizing CW excitation, Anal. Chem., 63, 432, 1991.
55. Soper, S.A., Mattingly, Q.L., and Vegunta, P., Photon burst detection of single near infrared fluorescent dye molecules, Anal. Chem., 65, 740, 1993.
56. Soper, S.A., Davis, L., and Shear, E.B., Detection and identification of single molecules in solution, J. Opt. Soc. Am. B, 9, 1761, 1992.