Strategies for introducing non-radioactive labels during the automated sequence analysis of nucleic acids

Electronic Journal of Biotechnology

Volumn 1, Issue 1, 1998, Pages 23-30

  Igloi, Gabor L ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 54249142327     PISSN: 07173458     EISSN: 07173458     Source Type: Journal    
DOI: 10.2225/vol1-issue1-fulltext-3     Document Type: Review

References (78)

1. Agrawal, S., Christodoulou, C. and Gait, M.J. (1986). Efficient methods for attaching non-radioactive labels to the 5' ends of synthetic oligodeoxyribonucleotides. Nucleic Acids Research 14:6227-6245
2. Alexandrova, L.A., Lukin, M.A., Victorova, L.S. and Rozovskaya, T. (1991). Enzymatic incorporation of fluorescent labels into oligonucleotides. Nucleic Acids Symposium Series 24:277.
3. Ansorge, W., Rosenthal, A., Sproat, B., Schwager, C., Stegemann, J. and Voss, H. (1988). Non-radioactive automated sequencing of oligonucleotides by chemical degradation. Nucleic Acids Research 16:2203-2206
4. Ansorge, W., Sproat, B.S., Stegemann, J. and Schwager, C. (1986). A non-radioactive automated method for DNA sequence determination. Journal of Biochemical and Biophysical Methods 13:315-323.
5. Bauer, G.J. (1990). RNA sequencing using fluorescentlabeled dideoxynucleotides and automated fluorescence detection. Nucleic Acids Research 18:879-884.
6. Beck, S. (1987). Colorimetric-detected DNA sequencing. Analytical Biochemistry 164:514-520.
7. Berlin, Y.A., Korshun, V.A. and Boreskov, Y.G. (1991). Multiple non-radioactive labeling of oligonucleotides. Nucleic Acids Symposium Series 25:85-86.
8. Brumbaugh, J.A., Middendorf, L.R., Grone, D.L. and Ruth, J.L. (1988). Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores. Proceedings of the National Academy of Sciences USA 85:5610-5614.
9. Carothers, A.M., Urlaub, G., Mucha, J., Grunberger, D. and Chasin, L.A. (1989). Point mutation analysis in mammalian gene: rapid preparation of total RNA, PCR amplification of cDNA and Taq sequencing by a novel method. BioTechniques 7:494-499
10. Caruthers, M.H., Barone, A.D., Beaucage, S.L., Dodds, D.R., Isher, E.F.F., McBride, L.J., Matteucci, M., Stabinsky, Z. and Tang, J.-Y. (1987). Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. Methods in Enzymology 154:287-313.
11. Cech, D., Schubert, F. and Möller, U. (1991). Non-radioactive labelling of oligonucleotides with prefunctionalized phosphoramidites or H-phosphonates during automated synthesis. Nucleic Acids Symposium Series 24:205-206.
12. Connolly, B.A. (1985). Chemical synthesis of oligonucleotides containing a free sulphydryl group and subsequent attachment to thiol specific probes. Nucleic Acids Research 13:4485-4502.
13. Connolly, B.A. (1987). The synthesis of oligonucleotides containing a primary amino group at the 5' terminus. Nucleic Acids Research 15:3131-3139.
14. Craesey, A., D'Angio, L. Jr., Dunne, T.S., Kissinger, C., O'Keefe, T., Perry-O'Keefe, H., Moran, L.S., Roskey, M., Schildkraut, I., Sears, L.E. and Slatko, B. (1991). Application of a novel chemiluminescence-based DNA detection method to single-vector and multiplex DNA sequencing. BioTechniques 11:102-109.
15. DeBellis, G., Pergolizzi, R., Debernardi, S., Invernizzi, L. and Luzzana, M. (1995). Fluorescence-based automated DNA sequencing by limited primer labeling. BioTechniques 19:66-70.
16. Flick, P.K.(1995). DNA sequencing by non-isotopic methods. In:Non-isotopic probing, blotting and sequencing. 2nd.ed.L.J.Kricka. SanDiego, Academic Press, pp.475-492.
17. Guzaev, A., Azhayeva, E., Hovinen, J., Azhayev, A. and Lönnberg, H. (1994). Synthesis and primer properties of oligonucleotides containing 3'-deoxypsicothymidine units, labeled with fluorescein at their 1'-position. Bioconjugate Chemistry 5:501-503.
18. Haralambidis, J., Chai, M. and Tregear, G.W. (1987). Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into oligodeoxyribonucleotides. Nucleic Acids Research 15:4857-4876.
19. Hawkins, T.L., Du, Z., Halloran, N.D. and Wilson R.K. (1992). Fluorescent chemistries for automated primer-directed DNA sequencing. Electrophoresis 13:552-559.
20. Hou, W. and Smith, L.M. (1993) Fluorescence-based DNA sequencing with hexamer primers. Nucleic Acids Research 21:3331-3332.
21. Hung, S.-C., Ju, J., Mathies, R.A. and Glazer, A.N. (1996a). Cyanine dyes with high absorption cross section as donor chromophores in energy transfer primers. Analytical Biochemistry 243:15-27.
22. Hung, S.-C., Ju, J., Mathies, R.A. and Glazer, A.N. (1996b). Energy transfer primers with 5- or 6-carboxyrhodamine-6G as acceptor chromophores. Analytical Biochemistry 238:165-170.
23. Hunkapillar, T., Kaiser, R.J., Koop, B.F. and Hood, L. (1991). Large-scale and automated DNA sequence determination. Science 254:59-67.
24. Igloi, G.L. (1996a). Substrate properties of fluorescent ribonucleotides in the terminal-transferase-catalyzed labelling of DNA sequencing primers. BioTechniques 21: 1084-1092.
25. Igloi, G.L. (1996b). Non-radioactive labeling of RNA. Analytical Biochemistry 233:124-129.
26. Igloi, G.L. and Schiefermayr, E. (1993). Enzymatic addition of fluorescein- or biotin-riboUTP to oligonucleotides results in primers suitable for DNA sequencing and PCR. BioTechniques 15:486-497.
27. Jang, G.Y. and Steffens, D.L. (1997). Ligation mediated fluorescent labeling of DNA sequencing primers. Nucleic Acids Research 25:922-923.
28. Ju, J., Glazer, A.N. and Mathies, R.A. (1996). Cassette labeling for facile construction of energy transfer fluorescent primers. Nucleic Acids Research 24:1144-1148.
29. Ju, J., Kheterpal, I., Scherer, J.R., Ruan, C., Fuller, C.W., Glazer, A.N. and Mathies, R.A. (1995a). Design and synthesis of fluorescence energy transfer dye-labeled primers and their application for DNA sequencing and analysis. Analytical Biochemistry 231:131-140.
30. Ju, J., Ruan, C., Fuller, C.W., Glazer, A.N. and Mathies, R.A. (1995b). Fluorescent energy transfer dye-labeled primers for DNA sequence analysis. Proceedings of the National Academy of Sciences USA 92:4347-4351.
31. Kambara, H., Nagai, K. and Hayasaka, S. (1991). Real time automated simultaneous double-stranded DNA sequencing using two-color fluorophore labeling. Bio/technology 9:648-651.
32. Kawashima, E.H. and Chollet, A. (1985). Biotin labeled synthetic oligodeoxyribonucleotides: chemical synthesis and uses as hybridization probes. Nucleic Acids Research 13:1529-1541.
33. Kempe, T., Sundquist, W.I., Chow, F. and Hu, S.-L. (1985). Chemical and enzymatic biotin-labeling of oligodeoxyribonucleotides. Nucleic Acids Research 13:45-57.
34. Kessler, C. (1995). Methods for nonradioactive labeling of nucleic acids. In:Non-isotopic probing, blotting and sequencing. 2nd.ed.L.J.Kricka. SanDiego, Academic Press, pp.41-109.
35. Kinoshita, Y., Nishigaki, K. and Husimi, Y. (1997). Fluorescence-, isotope- or biotin-labeling of the 5'-end of single-stranded DNA/RNA using T4 RNA ligase. Nucleic Acids Research 25:3747-3748.
36. Kössel, H. and Roychoudhury, R. (1971). Synthetic polynucleotides. The terminal addition of riboadenylic acid to deoxyoligonucleotides by terminal deoxynucleotidyl transferase as a tool for the specific labelling of deoxyoligonucleotides at the 3' ends. European Journal of Biochemistry 22: 271-276.
37. Kumar, A., Tchen, P., Roullet, F. and Cohen, J. (1988). Nonradioactive labeling of synthetic oligonucleotide probes with terminal deoxynucleotidyl transferase. Analytical Biochemistry 169:376-382.
38. Lee, L.G., Connell, C.R., Woo, S.L., Cheng, R.D., McArdle, B.F., Fuller, C.W., Halloran, N.D. and Wilson, R.K. (1992). DNA sequencing with dye-labeled terminators and T7 DNA polymerase: effect of dyes and dNTPs on incorporation of dye-terminators and probability analysis of termination fragments. Nucleic Acids Research 20:2471-2483.
39. 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. (1997). New energy transfer dyes for DNA sequencing. Nucleic Acids Research 25, 2816-2822.
40. Maier, R.M., Neckermann, K., Igloi, G.L. and Kössel, H. (1995). Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Journal of Molecular Biology 251: 614-628.
41. Markiewicz, W.T., Gröger, G., Rösch, R., Zebrowska, A., Markiewicz, M., Klotz, M., Hinz, M., Godzina, P. and Seliger, H. (1997). A new method of synthesis of fluorescently labelled oligonucleotides and their application in DNA sequencing. Nucleic Acids Research 25:3672-3680.
42. Martin, C., Bresnick, L., Juo, R.-R.., Voyta, J.C. and Bronstein, I. (1991). Improved chemiluminescent DNA sequencing. BioTechniques 11:110-113.
43. Matsuki, T., Ito, R., Yokogawa, T. and Nishikawa, K. (1993). Sequence analysis of low-molecular-weight RNAs by the use of non-radioactive labeling. Nucleic Acids Symposium Series 29: 75-76.
44. Maxam, A.M. and Gilbert, W. (1977). A new method for sequencing DNA. Proceedings of the National Academy of Sciences USA 74:560-564.
45. Metzker, M.L., Lu, J. and Gibbs, R.A. (1996). Electrophoretically uniform fluorescent dyes for automated DNA sequencing. Science 271:1420-1422.
46. Middendorf, L.R., Bruce, J.C., Bruce, R.C., Eckles, R.D., Grone, D.L., Roemer, S.C., Sloniker, G.D., Steffens, D.L., Sutter, S.C., Brumbaugh, J.A. and Patonay, G. (1992). Continuous, on-line DNA sequencing using a versatile infrared scanner/electrophoresis apparatus. Electrophoresis 13:487-494.
47. Mineno, J., Ishino, Y., Ohminami, T. and Kato, I. (1993). Fluorescent labeling of a DNA sequencing primer. DNA Sequence 4:135-141.
48. Murasugi, A. and Wallace, R.B. (1984). Biotin-labeled oligonucleotides: enzymatic synthesis and use as hybridisation probes. DNA 3:269-277.
49. Naeve, C.W., Buck, G.A., Niece, R.L., Pon, R.T., Robertson, M. and Smith, A.J. (1995). Accuracy of automated DNA sequencing: a multilaboratory comparison of sequencing results. BioTechniques 19:448-453.
50. Nelson, P.S., Kent, M. and Muthini, S. (1992). Oligonucleotide labeling methods 3. Direct labeling of oligonucleotides employing a novel, non-nucleosidic, 2-aminobutyl-1, 3-propanediol backbone. Nucleic Acids Research 20:6253-6259.
51. Ohara, R., Tanaka, A. and Ohara, O. (1997). Automated fluorescent DNA sequencing by a simplified solid-phase chemical sequencing method. BioTechniques 22:653-656.
52. Olesen, C.E.M., Martin, C.S. and Bronstein, I. (1993). Chemiluminescent DNA sequencing with multiplex labeling. BioTechniques 15:480-485.
53. Parker, L.T., Deng, Q., Zakeri, H., Carlson, C., Nickerson, D.A. and Kwok, P.Y. (1995). Peak height variation s in automated sequencing of PCR products using dye-terminator chemistry. BioTechniques 19:116-121.
54. Patel, A. and Nash, B. (1995). Innovations in non-isotopic DNA sequencing: using an electrotransfer unit to blot sequencing gels and an automated membrane processor for detecting DNA sequences. BioTechniques 18:328-333.
55. Pohl, F. M. and Beck, S. (1987). Direct transfer electrophoresis used for DNA sequencing. Methods in Enzymology 155:250-259.
56. Pohl, T.M. and Maier, E.(1995). Sequencing 500kb of yeast DNA using a GATC 1500 direct blotting electrophoresis system. BioTechniques 19:482-486.
57. Prober, J.M., Trainor, G.L., Dam, R.J., Hobbs, F.W., Robertson, C.W., Zagursky, R.J., Cocuzza, A.J., Jensen, M.A. and Baumeister, K. (1987). A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238:336-341.
58. Purschke, W.G. and Schäfer, G. (1996). An alternative to digoxigenin-labeled primers for manual non-radioactive sequencing allows reading of more than 700 bases. Analytical Biochemistry 238:98-100.
59. Quesada, M.A. and Zhang, S. (1996). Multiple capillary DNA sequencer that uses fiber-optic illumination and detection. Electrophoresis 17:1841-1851.
60. Richterich, P. (1989). Non-radioactive chemical sequencing of biotin labelled DNA. Nucleic Acids Research 17:2181-2186.
61. Ricterich, P. and Church, G.M. (1993). DNA sequencing with direct transfer electrophoresis and non-radioactive detection. Methods in Enzymology 218:187-222.
62. Rosenblum, B.B., Lee, L.G., Spurgeon, S.L., Khan, S.H., Menchen, S.M., Heiner, C.R. and Chen, S.M. (1997). New dye-labeled terminators for improved DNA sequencing patterns. Nucleic Acids Research 25:4500-4504.
63. Rosenthal, A., Sproat, B., Voss, H., Stegemann, J., Schwager, C., Erfle, H., Zimmermann, J., Coutelle, C. and Ansorge, W. (1990). Automated sequencing of fluorescently labelled DNA by chemical degradation. DNA Sequence 1: 63-71.
64. Sanger, F., Nicklen, S. and Coulson, A.R. (1977). DNA sequencing with chain terminator inhibitors. Proceedings of the National Academy of Sciences USA 74:5463-5467.
65. Schubert, F., Ahlert, K., Cech, D. and Rosenthal, A. (1990). One-step labelling of oligonucleotides with fluoresceine during automated synthesis. Nucleic Acids Research 18:3427.
66. Schubert, F., Cech, D., Reinhardt, R. and Wiesner, P. (1992). Fluorescent labelling of sequencing primers for automated oligonucleotide synthesis. DNA Sequence 2:273-279.
67. Smith, L.M., Fung, S., Hunkapillar, M.W., Hunkapillar, T.J. and Hood, L.E. (1985). The synthesis of oligonucleotides containing an aliphatic amino group at the 5' terminus: synthesis of fluorescent DNA primers for use in DNA sequence analysis. Nucleic Acids Research 13:2399-2412.
68. Smith, L.M., Sanders, J.Z., Kaiser, R.J., Hughes, P., Dodd, C., Connell, C.R., Heiner, C., Kent, S.B.H. and Hood, L.E. (1986). Fluorescence detection in automated DNA sequence analysis. Nature 321:674-679.
69. Starke, H.R., Yan, J.Y., Zhang, J.Z., Muhlegger, K., Effgen, K. and Dovichi, N.J. (1994). Internal labeling with fluorescent deoxynucleotides in two-label peak-height encoded DNA sequencing by capillary electrophoresis. Nucleic Acids Research 22:3997-4001.
70. Steffens, D.L., Jang, G.Y., Sutler, S.L., Brumbaugh, J.A., Middendorf, L.R., Mühlegger, K., Mardis, E.R., Weinstock, L.A. and Wilson, R.K. (1995). An infrared fluorescent dATP for labeling DNA. Genome Research 5:393-399.
71. Tabor, S. and Richardson, C.C. (1995). A single residue in DNA polymerases of the Escherichia Coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. Proceedings of the National Academy of Sciences USA 92:6339-6343.
72. Theisen, P., McCollum, C. and Andrus, A. (1992). Fluorescent dye phosphoramidite labelling of oligonucleotides. Nucleic Acids Symposium Series 27:99-100.
73. Voss, H., Nentwich, U., Duthie, S., Wiemann, S., Benes, V., Zimmermann, J. and Ansorge, W. (1997). Automated cycle sequencing with Taquenase: protocols for internal labeling, dye primer and "doublex" simultaneous sequencing. BioTechniques 23:312-318.
74. Voss, H., Schwager, C., Wirkner, U., Zimmermann, J., Erfle, H., Hewitt, N.A., Rupp, T., Stegemann, J. and Ansorge, W. (1991). A new procedure for automated DNA sequencing with multiple internal labelling by fluorescent dUTP. Methods in Molecular and Cellular Biology 3:30-34.
75. Wiemann, S., Rupp, T., Zimmermann, J., Voss, H., Schwager, C. and Ansorge, W. (1995). Primer design for automated DNA sequencing utilizing T7 DNA polymerase and internal labeling with fluorescein-15-dATP. BioTechniques 18:688-697.
76. Wiemann, S., Schilke, A., Rechmann, S., Zimmermann, J., Voss, H. and Ansorge, W. (1996). Reducing "double sequences" in automated DNA sequencing with T7 DNA polymerase and internal labeling. BioTechniques 20:791-792.
77. Wiemann, S., Stegemann, J., Grothues, D., Bosch, A., Estvill, X., Schwager, C., Zimmermann, J., Voss, H. and Ansorge, W. (1995). Simultaneous on-line DNA sequencing of both strands with two fluorescent dyes. Analytical Biochemistry 224:117-121.
78. Wu, T., Ruan K. and Liu, W. (1996). A fluorescence-labeling method for sequencing small RNA on polyacrylamide gel. Nucleic Acids Research 24:3472-3473.