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The use of capillary electrophoresis for DNA polymorphism analysis

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Abstract

Capillary electrophoresis has advanced enormously over the last 10 yr as a tool for DNA sequencing, driven by the human and other major genome projects and by the need for rapid electrophoresis-based DNA diagnostic tests. The common need of these analyses is a platform providing very high throughput, high-quality data, and low process costs. These demands have led to capillary electrophoresis machines with multiple capillaries providing highly parallel analyses, to new electrophoresis matrices, to highly sensitive spectrofluorometers, and to brighter, spectrally distinct fluorescent dyes with which to label DNA. Capillary devices have also been engineered onto microchip formats, on which both the amount of sample required for analysis and the speed of analysis are increased by an order of magnitude. This review examines the advances made in capillary and chip-based microdevices and in the different DNA-based assays developed for mutation detection and genotype analysis using capillary electrophoresis. The automation of attendant processes such as for DNA sample preparation, PCR, and analyte purification are also reviewed. Together, these technological developments provide the throughput demanded by the large genome-sequencing projects.

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References

  1. Heller, C. (2001) Principles of DNA separation with capillary electrophoresis. Electrophoresis 22, 629–643.

    Article  PubMed  CAS  Google Scholar 

  2. Slater, G. W., Desruisseaux, C., and Hubert, S. J. (2001) DNA separation mechanisms during capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R. and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 27–42.

    Google Scholar 

  3. Xie, W., Yang, R., Xu, J., Zhang, L., Xing, W., and Cheng, J. (2001) Microchip-based capillary electrophoresis system, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 67–84.

    Google Scholar 

  4. Burns, M. A., Johnson, B. N., Brahmasandra, S. N., et al. (1998) An integrated nanoliter DNA analysis device. Science 282, 484–487.

    Article  PubMed  CAS  Google Scholar 

  5. Bruin, G. J. (2000) Recent developments in electrokinetically driven analysis on microfabricated devices. Electrophoresis 21, 3931–3951.

    Article  PubMed  CAS  Google Scholar 

  6. Koutny, L., Schmalzing, D., Salas-Solano, O., et al. (2000) Eight hundred-base sequencing in a micro-fabricated electrophoretic device. Anal. Chem. 72, 3388–3391.

    Article  PubMed  CAS  Google Scholar 

  7. Krishnan, M., Namasivayam, V., Lin, R., Pal, R., and Burns, M. A. (2001) Microfabricated reaction and separation systems. Curr. Opin. Biotechnol. 12, 92–98.

    Article  PubMed  CAS  Google Scholar 

  8. Cheng, J., Waters, L. C., Fortina, P., et al. (1998) Degenerate oligonucleotide primed-polymerase chain reaction and capillary electrophoresis analysis of human DNA on microchip-based devices. Anal. Biochem. 257, 101–106.

    Article  PubMed  CAS  Google Scholar 

  9. Schmalzing, D., Koutny, L., Adourian, A., Chisholm, D., Matsudaira, P., and Ehrlich, D. (2001) Genotyping by microdevice electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 163–174.

    Google Scholar 

  10. Gao, Q., Shi, Y., and Liu, S. (2001) Multiple-channel microchips for high-throughput DNA analysis by capillary electrophoresis. Fresenius J. Anal. Chem. 371, 137–145.

    Article  PubMed  CAS  Google Scholar 

  11. Hong, J.W., Hosokawa, K., Fujii, T., Seki, M., and Endo, I. (2001) Microfabricated polymer chip for capillary gel electrophoresis. Biotechnol. Prog. 17, 958–962.

    Article  PubMed  CAS  Google Scholar 

  12. Liu, Y., Ganser, D., Schneider, A., Liu, R., Grodzinski, P., and Kroutchinina, N. (2001) Microfabricated polycarbonate CE devices for DNA analysis. Anal. Chem. 73, 4196–4201.

    Article  PubMed  CAS  Google Scholar 

  13. Cheng, J., Sheldon, E. L., Wu, L., et al. (1998). Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips. Nat. Biotechnol. 16, 541–546.

    Article  PubMed  CAS  Google Scholar 

  14. Righetti, P. G., and Bossi, A. (1998) An isoelectrically trapped enzyme reactor operating in an electric field. Electrophoresis 19, 1075–1080.

    Article  PubMed  CAS  Google Scholar 

  15. Lu, S. X. and Yeung, E. S. (1999) Side-entry excitation and detection of square capillary array electrophoresis for DNA sequencing. J. Chromatogr. A 853, 359–369.

    Article  PubMed  CAS  Google Scholar 

  16. Hanning, A., Lindberg, P., Westberg, J. and Roeraade, J. (2000) Laser-induced fluorescence detection by liquid core waveguiding applied to DNA sequencing by capillary electrophoresis. Anal. Chem. 72, 3423–3430.

    Article  PubMed  CAS  Google Scholar 

  17. Manz, A., Bousse, L., Chow, A., Metha, T.B., Kopf-Sill, A., and Parce, J. W. (2001) Synchronized cyclic capillary electrophoresis using channels arranged in a triangle and low voltages. Fresenius J. Anal. Chem. 371, 195–201.

    Article  PubMed  CAS  Google Scholar 

  18. Liang, D., Song, L., Quesada, M. A., Tian, Z., Studier, F. W., and Chu, B. (2000) Formation of concentration gradient and its application to DNA capillary electrophoresis. Electrophoresis 21, 3600–3608.

    Article  PubMed  CAS  Google Scholar 

  19. Chiari, M., Cretich, M., Riva, S., and Casali, M. (2001) Performances of new sugar-bearing poly-(acrylamide) copolymers as DNA sieving matrices and capillary coatings for electrophoresis. Electrophoresis 22, 699–706.

    Article  PubMed  CAS  Google Scholar 

  20. Song, L., Liu, T., Liang, D., Fang, D., and Chu, B. (2001) Separation of double-stranded DNA fragments by capillary electrophoresis in interpenetrating networks of polyacrylamide and polyvinylpyrrolidone. Electrophoresis 22, 3688–3698.

    Article  PubMed  CAS  Google Scholar 

  21. Sudor, J., Barbier, V., Thirot, S., et al. (2001) New block-copolymer thermo-associating matrices for DNA sequencing: effect of molecular structure on rheology and resolution. Electrophoresis 22, 720–728.

    Article  PubMed  CAS  Google Scholar 

  22. Liu, T., Liang, D., Song, L., Nace, V. M., and Chu, B. (2001) Spatial open-network formed by mixed triblock copolymers as a new medium for double-stranded DNA separation by capillary electrophoresis. Electrophoresis 22, 449–458.

    Article  PubMed  CAS  Google Scholar 

  23. Buchholz, B. A., Doherty, E. A., Albarghouthi, M. N., Bogdan, F. M., Zahn, J. M., and Barron, A. E. (2001) Microchannel DNA sequencing matrices with a thermally controlled “viscosity switch.” Anal. Chem. 73, 157–164.

    Article  PubMed  CAS  Google Scholar 

  24. Albarghouthi, M. N., Buchholz, B. A., Doherty, E. A., Bogdan, F.M., Zhou, H., and Barron, A. E. (2001) Impact of polymer hydrophobicity on the properties and performance of DNA sequencing matrices for capillary electrophoresis. Electrophoresis 22, 737–747.

    Article  PubMed  CAS  Google Scholar 

  25. Chiari, M., and Cretich, M. (2001) Capillary coatings: choices for capillary electrophoresis of DNA, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 125–138.

    Google Scholar 

  26. Tian, H., Brody, L. C., Mao, D., and Landers, J. P. (2000) Effective capillary electrophoresis-based heteroduplex analysis through optimization of surface coating and polymer networks. Anal. Chem. 72, 5483–5492.

    Article  PubMed  CAS  Google Scholar 

  27. Righetti, P. G., Gelfi, C., Verzola, B., and Castelletti, L. (2001) The state of the art of dynamic coatings. Electrophoresis 22, 603–611.

    Article  PubMed  CAS  Google Scholar 

  28. Yoshida, C., Endo, Y., and Baba, Y. (2001) Enhanced throughput for DNA sequencing by capillary array electrophoresis with a gradient of electric field strength. Eur. J. Pharm. Sci. 13, 99–103.

    Article  PubMed  CAS  Google Scholar 

  29. Zhu, L., Lee, H. K., Lin, B., and Yeung, E. S. (2001) Spatial temperature gradient capillary electrophoresis for DNA mutation detection. Electrophoresis 22, 3683–3687.

    Article  PubMed  CAS  Google Scholar 

  30. Gelfi, C., Cremoresi, L., Ferrari, M., and Righetti, P. G. (2001) Point mutation detection by temperature-programmed capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 73–88.

    Google Scholar 

  31. Song, L., Liang, D., Fang, D., and Chu, B. (2001) Fast DNA sequencing up to 1,000 bases by capillary electrophoresis using poly(N,N-dimethylacrylamide) as a separation medium. Electrophoresis 22, 1987–1996.

    Article  PubMed  CAS  Google Scholar 

  32. Song, L., Liang, D., Chen, Z., Fang, D., and Chu, B. (2001) DNA sequencing by capillary electrophoresis using mixtures of polyacrylamide and poly(N,N-dimethylacrylamide). J. Chromatogr. A 915, 231–239.

    Article  PubMed  CAS  Google Scholar 

  33. Liang, D., Song, L., Chen, Z., and Chu, B. (2001) Clayenhanced DNA separation in low-molecular-weight poly(N,N-dimethylacrylamide) solution by capillary electrophoresis. Electrophoresis 22, 1997–2003.

    Article  PubMed  CAS  Google Scholar 

  34. Wei, W., and Yeung, E. S. (2001) DNA capillary electrophoresis in entangled dynamic polymers of surfactant molecules. Anal. Chem. 73, 1776–1783.

    Article  PubMed  CAS  Google Scholar 

  35. Hahn, M., Wilhelm, J., and Pingoud, A. (2001) Influence of fluorophor dye labels on the migration behavior of polymerase chain reaction-amplified short tandem repeats during denaturing capillary electrophoresis. Electrophoresis 22, 2691–2700.

    Article  PubMed  CAS  Google Scholar 

  36. Baskin, J. (2001) Determining dye-induced DNA mobility shifts for DNA sequencing fragments by capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 95–108.

    Google Scholar 

  37. Zhou, H., Miller, A. W., Sosic, Z., et al. (2000) DNA sequencing up to 1300 bases in two hours by capillary electrophoresis with mixed replaceable linear poly-acrylamide solutions. Anal. Chem. 72, 1045–1052.

    Article  PubMed  CAS  Google Scholar 

  38. Klepárník, K., Malá, Z., and Boçek, P. (2001) Fast separation of DNA sequencing fragments in highly alkaline solutions of linear polyacrylamide using electrophoresis in bare silica capillaries. Electrophoresis 22, 783–788.

    Article  PubMed  Google Scholar 

  39. Klepárník, K., Malá, Z. and Bo_ek, P. (2001) DNA analysis under highly denaturing conditions in bare fused silica capillaries, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 239–258.

    Google Scholar 

  40. Ferrance, J. and Landers, J.P. (2001) Exploiting sensitive laser-induced fluorescence detection on electrophoretic microchips for executing rapid clinical diagnostics. Luminescence 16, 79–88.

    Article  PubMed  CAS  Google Scholar 

  41. DeFrancesco, L. (2001) Capillary electrophoresis: finding a niche. Anal. Chem. 73, 497A-499A.

    Article  PubMed  CAS  Google Scholar 

  42. Righetti, P.G. and Gelfi, C. (1999). Capillary electrophoresis of DNA for molecular diagnostics: an update. J. Capillary Electrophor. 6, 119–124.

    CAS  Google Scholar 

  43. Barta, C., Ronai, Z., Sasvari-Szekely, M., and Guttman, A. (2001) Rapid single nucleotide polymorphism analysis by primer extension and capillary electrophoresis using polyvinyl pyrrolidone matrix. Electrophoresis 22, 779–782.

    Article  PubMed  CAS  Google Scholar 

  44. Matyas, G., Giunta, C., Steinmann, B., Hossle, J.P., and Hellwig, R. (2002). Quantification of single nucleotide polymorphisms: a novel method that combines primer extension assay and capillary electrophoresis. Hum Mutat. 19, 58–68.

    Article  PubMed  CAS  Google Scholar 

  45. Tian, H., Brody, L. C., Fan, S., Huang, Z., Landers, J. P. (2001) Capillary and microchip electrophoresis for rapid detection of known mutations by combining allele-specific DNA amplification with heteroduplex analysis. Clin. Chem. 47, 173–185.

    PubMed  CAS  Google Scholar 

  46. Li, T., Okano, K., and Kambara, H., (2001) DNA sequencing by selective PCR and multi-capillary gel electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 317–338.

    Google Scholar 

  47. Carrera, P., Righetti, P. G., Gelfi, C., and Ferrari, M. (2001) Amplification refractory mutation system analysis of point mutations by capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 95–108.

    Google Scholar 

  48. Cheng, J., Shoffner, M. A., Mitchelson, K. R., Kricka, L. J., and Wilding, P. (1996) Analysis of ligase chain reaction products amplified in a silicon-glass chip using capillary electrophoresis. J. Chromatogr. A 732, 151–158.

    Article  PubMed  CAS  Google Scholar 

  49. Butler, J. M., and Reeder, D. J. (2001) Detection of DNA polymorphisms using PCR-RFLP and capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 49–56.

    Google Scholar 

  50. Nachamkin, I., Panaro, N. J., Li, M., et al. (2001) Agilent 2100 bioanalyzer for restriction fragment length polymorphism analysis of the Campylobacter jejuni flagellin gene. J. Clin. Microbiol. 39, 754–747.

    Article  PubMed  CAS  Google Scholar 

  51. Moretti, T.R., Baumstark, A.L., Defenbaugh, D.A., Keys, K.M., Brown, A.L., and Budowle, B. (2001) Validation of STR typing by capillary electrophoresis. J. Forensic Sci. 46, 661–676.

    PubMed  CAS  Google Scholar 

  52. Mansfield, E. S., Wilson, R. B., and Fortina, P. (2001) Analysis of short tandem repeat markers by capillary array electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 151–162.

    Google Scholar 

  53. Nock, T., Dove, J., McCord, B., and Mao, D. (2001) Temperature and pH studies of short tandem repeat systems using capillary electrophoresis at elevated pH. Electrophoresis 22, 755–762.

    Article  PubMed  CAS  Google Scholar 

  54. Medintz, I. L., Lee, C. C., Wong, W. W., Pirkola, K., Sidransky, D., and Mathies, R. A. (2000) Loss of heterozygosity assay for molecular detection of cancer using energy-transfer primers and capillary array electrophoresis. Genome Res. 10, 1211–1218.

    Article  PubMed  CAS  Google Scholar 

  55. Hayashi, K., Wenz, H.-M., Inazuka, M., Tahira, T., Sasaki, T., and Atha, D. H. (2001) SSCP analysis of point mutations by capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 109–126.

    Google Scholar 

  56. Liu, M. S., Rampal, S., Hsiang, D., and Chen, F. T. (2000) Automated DNA mutation analysis by single-strand conformation polymorphism using capillary electrophoresis with laser-induced fluorescence detection. Mol. Biotechnol. 15, 21–27.

    Article  PubMed  Google Scholar 

  57. Kozlowski, P. and Krzyzosiak, W. J. (2001) Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection. Nucleic Acids Res. 29, e71.

    Google Scholar 

  58. Rozycka, M., Collins, N., Stratton, M. R., and Wooster, R. (2000) Rapid detection of DNA sequence variants by conformation-sensitive capillary electrophoresis. Genomics 70, 34–40.

    Article  PubMed  CAS  Google Scholar 

  59. Ekstrom, P. O., Wasserkort, R., Minarik, M., Foret, F., and Thilly, W. G. (2000) Two-point fluorescence detection and automated fraction collection applied to constant denaturant capillary electrophoresis. Biotechniques 29, 582–584, 586–589.

    PubMed  CAS  Google Scholar 

  60. Khrapko, K., Collier, H. A., Li-Sucholeiki, X.-C., André, P. C., and Thilly, W. G. (2001) High resolution analysis of point mutations by constant denaturant capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 57–72.

    Google Scholar 

  61. Lim, E.L., Tomita, A.V., Thilly, W.G., and Polz, M.F. (2001) Combination of competitive quantitative PCR and constant-denaturant capillary electrophoresis for high-resolution detection and enumeration of microbial cells. Appl. Environ. Microbiol. 67, 3897–3903.

    Article  PubMed  CAS  Google Scholar 

  62. Andersen, P. S., Larsen, L. A., Kanters, Jr. et al. (1998) Mutation detection by cleavase in combination with capillary electrophoresis analysis: application to mutations causing hypertrophic cardiomyopathy and long-QT syndrome. Mol. Diagnos. 3, 105–111.

    Article  CAS  Google Scholar 

  63. Siles, B. A., O’Neil, K. A., Tung, D. L., Bazar, L., Collier, G. B., and Lovelace, C. I. (1998) The use of dynamic size-sieving capillary and mismatch repair enzymes for mutant DNA analysis. J. Capillary Electrophor. 5, 51–58.

    PubMed  CAS  Google Scholar 

  64. Bazar, L. S., Collier, G. B., Vanek, P. G., et al. (1999) Mutation identification DNA analysis system (MIDAS) for detection of known mutations. Electrophoresis 20, 1141–1148.

    Article  PubMed  CAS  Google Scholar 

  65. Ren, J. (2001) Chemical mismatch cleavage analysis by capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 231–240.

    Google Scholar 

  66. Li, Y., White, J., Stokes, D., Sayler, G., and Sepaniak, M. (2001) Capillary electrophoresis as a method to study DNA reassociation. Biotechnol. Prog. 17, 348–354.

    Article  PubMed  CAS  Google Scholar 

  67. Butler, J. M., Ruitberg, C. M., and Vallone, P. M. (2001) Capillary electrophoresis as a tool for optimization of multiplex PCR reactions. Fresenius J. Anal. Chem. 369, 200–205.

    Article  PubMed  CAS  Google Scholar 

  68. Baele, M., Storms, V., Haesebrouck, F., et al. (2001) Application and evaluation of the interlaboratory reproducibility of tRNA intergenic length polymorphism analysis (tDNA-PCR) for identification of Streptococcus species. J. Clin. Microbiol. 39, 1436–1442.

    Article  PubMed  CAS  Google Scholar 

  69. Siles, B.A., O’Neil, K.A., Fox, M.A., et al. (2000) Genetic fingerprinting of grape plant (Vitis vinifera) using random amplified polymorphic DNA (RAPD) analysis and dynamic size-sieving capillary electrophoresis. J. Agric. Food Chem. 48, 5903–5912.

    Article  PubMed  CAS  Google Scholar 

  70. Dresler-Nurmi, A., Terefework, Z., Kaijalainen, S., Lindstrom, K., and Hatakka, A. (2000) Silver stained polyacrylamide gels and fluorescence-based automated capillary electrophoresis for detection of amplified fragment length polymorphism patterns obtained from white-rot fungi in the genus Trametes. J. Microbiol. Methods 41, 161–172.

    Article  PubMed  CAS  Google Scholar 

  71. Schatzmann-Turhani, D., Greber-Platzer, S., Cairns, N., and Lubec, G. (1999) Determination of the protooncogene ets-2 gene transcript in human brain at the atto-gram-level by the use of competitive RT/PCR. Amino Acids 16, 13–19.

    Article  PubMed  CAS  Google Scholar 

  72. Borson, N. D., Strausbauch, M. A., Wettstein, P. J., Oda, R. P., Johnston, S. L., and Landers, J. P. (1998) Direct quantitation of RNA transcripts by competitive single-tube RT-PCR and capillary electrophoresis. Biotechniques 25, 130–137.

    PubMed  CAS  Google Scholar 

  73. Williams, S. J. and Williams, P. M. (2001) Quantitation of mRNA by competitive PCR using capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 243–252.

    Google Scholar 

  74. Zhao, X. and George, K. S. (2001) Differential display analysis by capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 259–268.

    Google Scholar 

  75. Liu, S., Shi, Y., Ja, W. W., and Mathies, R. A. (1999) Optimization of high-speed DNA sequencing on microfabricated capillary electrophoresis channels. Anal. Chem. 71, 566–573.

    Article  PubMed  CAS  Google Scholar 

  76. Kim, Y. and Yeung, E. S. (1997) DNA sequencing with pulsed-field capillary electrophoresis in poly(ethylene oxide) matrix. Electrophoresis 18, 2901–2908.

    Article  PubMed  CAS  Google Scholar 

  77. Voss, K. O., Roos, H.P., and Dovichi, N.J. (2001) The effect of temperature oscillations on DNA sequencing by capillary electrophoresis. Anal. Chem. 73, 1345–1349.

    Article  PubMed  CAS  Google Scholar 

  78. Xiong, Y., Park, S. R., and Swerdlow, H. (1998) Base stacking: pH-mediated on-column sample concentration for capillary DNA sequencing. Anal. Chem. 70, 3605–3611.

    Article  PubMed  CAS  Google Scholar 

  79. Lindberg, P. and Roeraade, J. (2001) DNA sequencing at elevated temperature by capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 289–308.

    Google Scholar 

  80. Ueda, M., Endo, Y., Abe, H., et al. (2001) Field-inversion electrophoresis on a microchip device. Electrophoresis 22, 217–221.

    Article  PubMed  CAS  Google Scholar 

  81. Madabhushi, R. S. (2001) DNA sequencing in noncovalently coated capillaries using low viscosity polymer solutions, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 309–316.

    Google Scholar 

  82. Morris, M. D., Schwinefus, J. J., and de Carmejane, O. (2001) Megabase DNA analysis and pulsed-field capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 307–322.

    Google Scholar 

  83. Heller, C., Magnúsdóttir, S., and Viovy, J.-L. (2001) Robust field inversion capillary electrophoretic separation of long DNA fragments, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 293–306.

    Google Scholar 

  84. Kabatek, Z., Klepárník, K., and Gas, B. (2001) Effect of temperature on the separation of long DNA fragments in polymer solution. J. Chromatogr. A 916, 305–310.

    Article  PubMed  CAS  Google Scholar 

  85. Klepárník, K., Müller, O. M., and Foret, F. (2001) Ultra-fast DNA separations using capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 19–40.

    Google Scholar 

  86. Zhang, J., Voss, K. O., Shaw, D. F., et al. (1999) A multiple-capillary electrophoresis system for small-scale DNA sequencing and analysis. Nucleic Acids Res. 27, e36.

    Google Scholar 

  87. Zhong X. B., Lizardi, P. M., Huang, X. H., Bray-Ward, P. L., and Ward, D. C. (2001) Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification. Proc. Natl. Acad. Sci. USA 98, 3940–3945.

    Article  PubMed  CAS  Google Scholar 

  88. Leone, G., van Schijndel, H., van Gemen, B., Kramer, F. R., and Schoen, C. D. (1998) Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res. 26, 2150–2155.

    Article  PubMed  CAS  Google Scholar 

  89. Lyamichev, V., Mast, A. L., Hall, J. G et al. (1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17, 292–296.

    Article  PubMed  CAS  Google Scholar 

  90. Lagally, E. T., Medintz, I., and Mathies, R. A. (2001) Single-molecule DNA amplification and analysis in an integrated microfluidic device. Anal. Chem. 73, 565–570.

    Article  PubMed  CAS  Google Scholar 

  91. Shortreed, M. R., Li, H., Huang, W. H., and Yeung, E. S. (2000) High-throughput single-molecule DNA screening based on electrophoresis. Anal. Chem. 72, 2879–2885.

    Article  PubMed  CAS  Google Scholar 

  92. Nilsson, P., Larsson, A., Lundeberg, J., Uhlén, M., and Nygren, P. A. (1999) Mutational scanning of PCR products by subtractive oligonucleotide hybridization analysis. Biotechniques 26, 308–316.

    PubMed  CAS  Google Scholar 

  93. Woolley, A. T., Lao, K., Glazer, A. N., and Mathies, R. A. (1998) Capillary electrophoresis chips with integrated electrochemical detection. Anal. Chem. 70, 684–688.

    Article  PubMed  CAS  Google Scholar 

  94. Basile, A., Giuliani, A., Pirri, G. and Chiari, M. (2002) Use of peptide nucleic acid probes for detecting DNA single-base mutations by capillary electrophoresis. Electrophoresis 23, 926–929.

    Article  PubMed  CAS  Google Scholar 

  95. Baba, Y. (2001) Capillary affinity gel electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 347–354.

    Google Scholar 

  96. German, I., Buchanan, D. D., and Kennedy, R. T. (1998) Aptamers as ligands in affinity probe capillary electrophoresis. Anal. Chem. 70, 4540–4545.

    Article  PubMed  CAS  Google Scholar 

  97. Wan, Q. H., and Le, X. C. (2000) Studies of protein-DNA interactions by capillary electrophoresis/laser-induced fluorescence polarization. Anal. Chem. 72, 5583–5589.

    Article  PubMed  CAS  Google Scholar 

  98. Ma, Y., Shortreed, M. R., Li, H., Huang, W., and Yeung, E. S. (2001) Single-molecule immunoassay and DNA diagnosis. Electrophoresis 22, 421–426.

    Article  PubMed  CAS  Google Scholar 

  99. LeCaptain, D. J., Michel, M. A., and Van Orden, A. (2001) Characterization of DNA-protein complexes by capillary electrophoresis-single molecule fluorescence correlation spectroscopy. Analyst 126, 1492.

    Article  Google Scholar 

  100. Weinfeld, M., Xing, J. Z., Lee, J., Leadon, S. A. and Le, X. C. (2002) Immunofluorescence detection of radiation-induced DNA base damage. Mil. Med. 167, (Suppl.) 2–4.

    PubMed  Google Scholar 

  101. Xian, J. (2001) Capillary DNA-protein mobility shift assay, in Capillary Electrophoresis of Nucleic Acids, Vol. 2 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 355–368.

    Chapter  Google Scholar 

  102. Yindeeyoungyeon, W., and Schell, M. A. (2000) Footprinting with an automated capillary DNA sequencer. Biotechniques 29, 1034–1036, 1038, 1040–1041.

    PubMed  CAS  Google Scholar 

  103. Foulds, G. J., and Etzkorn, F. A. (2001) Protein-DNA binding affinities determined by capillary electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 369–378.

    Google Scholar 

  104. Mangru, S. D. and Harrison, D. J. (1998) Chemiluminescence detection in integrated post-separation reactors for microchip-based capillary electrophoresis and affinity electrophoresis. Electrophoresis 19, 2301–2307.

    Article  PubMed  CAS  Google Scholar 

  105. Le, X. C., Wan, Q. H., and Lam, M. T. (2002) Fluorescence polarization detection for affinity capillary electrophoresis. Electrophoresis 23, 903–908.

    Article  PubMed  CAS  Google Scholar 

  106. Medintz, I. L., Berti, L., Emrich, C. A., Tom, J., Scherer, J. R., and Mathies, R. A. (2001) Genotyping energy-transfer-cassette-labeled short-tandem-repeat amplicons with capillary array electrophoresis microchannel plates. Clin. Chem. 47, 1614–1621.

    PubMed  CAS  Google Scholar 

  107. Shibata, K., Itoh, M., Aizawa, K., et al. (2000) RIKEN integrated sequence analysis (RISA) system—384-format sequencing pipeline with 384 multicapillary sequencer. Genome Res. 10, 1757–1771.

    Article  PubMed  CAS  Google Scholar 

  108. Zhang, J., Yang, M., Puyang, X., Fang, Y., Cook, L. M., and Dovichi, N. J. (2001) Two-dimensional direct-reading fluorescence spectrograph for DNA sequencing by capillary array electrophoresis. Anal. Chem. 73, 1234–1239.

    Article  PubMed  CAS  Google Scholar 

  109. http://www.amershambiosciences.com/; http://home.appliedbiosystems.com/; appliedbiosystems.com/; http://www.spectrumedix.com/; http://www.visgen.com/

  110. He, H. and McGown, L. B. (2000) DNA sequencing by capillary electrophoresis with four-decay fluorescence detection. Anal. Chem. 72, 5865–5873.

    Article  PubMed  CAS  Google Scholar 

  111. Sauer, M., Angerer, B., Ankenbauer, W., et al. (2001) Single molecule DNA sequencing in submicrometer channels: state of the art and future prospects. J. Biotechnology 86, 181–201.

    Article  CAS  Google Scholar 

  112. Brazill, S. A., Kim, P. H. and Kuhr, W. G. (2001) Capillary gel electrophoresis with sinusoidal voltammetric detection: a strategy to allow four-“color” DNA sequencing. Anal. Chem. 73, 4882–4890.

    Article  PubMed  CAS  Google Scholar 

  113. Zhu, R. and Kok, W. T. (1998) Post-column derivatization for fluorescence and chemiluminescence detection in capillary electrophoresis. J. Pharm. Biomed. Anal. 17, 985–999.

    Article  PubMed  CAS  Google Scholar 

  114. Swerdlow, H., Wu, S., Harke, H. and Dovichi, N. J. (1990) Capillary gel electrophoresis for DNA sequencing: Laser-induced fluorescence detection with the sheath flow cuvette. J. Chromatogr. 516, 61–67.

    Article  PubMed  CAS  Google Scholar 

  115. Crabtree, H. J., Bay, S. J., Lewis, D. F., et al. (2000) Construction and evaluation of a capillary array DNA sequencer based on a micromachined sheath-flow cuvette. Electrophoresis 21, 1329–1335.

    Article  PubMed  CAS  Google Scholar 

  116. Mitnik L, Novotny M, Felten C, Buonocore S, Koutny L, and Schmalzing D. (2001). Recent advances in DNA sequencing by capillary and microdevice electrophoresis. Electrophoresis 22, 4104–4117.

    Article  PubMed  CAS  Google Scholar 

  117. Salimi-Moosavi, H., Jiang, Y., Lester, L., McKinnon, G. and Harrison, D. J. (2000) A multi-reflection cell for enhanced absorbance detection in microchip-based capillary electrophoresis devices. Electrophoresis 21, 1291–1299.

    Article  PubMed  CAS  Google Scholar 

  118. Metzker, M. L., Lu, J., and Gibbs, R. A. (1996) Electrophoretically uniform fluorescent dyes for automated DNA sequencing. Science 271, 1420–1422.

    Article  PubMed  CAS  Google Scholar 

  119. McWhorter, S. and Soper, S. A. (2000) Near-infrared laser-induced fluorescence detection in capillary electrophoresis. Electrophoresis 21, 1267–1280.

    Article  PubMed  CAS  Google Scholar 

  120. Soper, S. A., Ford, S. M., Xu, Y., et al. (1999) Nanoliter-scale sample preparation methods directly coupled to polymethylmethacrylate-based microchips and gel-filled capillaries for the analysis of oligonucleotides. J. Chromatogr. A 853, 107–120.

    Article  PubMed  CAS  Google Scholar 

  121. Soper, S. A., Williams, D. C., Xu, Y., et al. (1998) Sanger DNA-sequencing reactions performed in a solid-phase nanoreactor directly coupled to capillary gel electrophoresis. Anal. Chem. 70, 4036–4043.

    Article  PubMed  CAS  Google Scholar 

  122. Blomstergren, A., O’Meara, D., Luckacs, M., Uhlén, M., and Lundeberg, J. (2000) Cooperative oligonucleotides in purification of cycle sequencing products. BioTechniques 29, 352–363.

    PubMed  CAS  Google Scholar 

  123. Mitchelson, K. R., Selway, J., Ward, W and Findlay, I. (2002) Returns on investment in automation of DNA sequencing. Today’s Life Sciences, 14, 22–27.

    Google Scholar 

  124. Zhang, N., Tan, H., and Yeung, E. S. (1999) Multiplexed automated DNA sequencing directly from single bacterial colonies. Anal. Chem. 71, 5018–5025.

    Article  PubMed  CAS  Google Scholar 

  125. Pang, H. M. and Yeung, E. S. (2000) Automated one-step DNA sequencing based on nanoliter reaction volumes and capillary electrophoresis. Nucleic Acids Res. 28, e73.

    Google Scholar 

  126. He, Y., Pang, H.M., and Yeung, E. S. (2000) Integrated electroosmotically-driven on-line sample purification system for nanoliter DNA sequencing by capillary electrophoresis. J. Chromatogr. A 894, 179–190.

    Article  PubMed  CAS  Google Scholar 

  127. Haab, B. B. and Mathies, R. A. (1999) Single-molecule detection of DNA separations in microfabricated capillary electrophoresis chips employing focused molecular streams. Anal. Chem. 71, 5137–5145.

    Article  PubMed  CAS  Google Scholar 

  128. Findlay, I., Matthews, P. L., Mulcahy, B. K., and Mitchelson, K. R. (2001). Using MF-PCR to diagnose multiple defects from single cells: implications for PGD. Molec. Cell. Endocrinology 183, S5-S12.

    Article  CAS  Google Scholar 

  129. Han, F. and Lillard, S. J. (2000) In-situ sampling and separation of RNA from individual mammalian cells. Anal. Chem. 72, 4073–4079.

    Article  PubMed  CAS  Google Scholar 

  130. Zabzdyr, J. L. and Lillard, S. J. (2001) Measurement of single-cell gene expression using capillary electrophoresis. Anal. Chem. 73, 5771–5775.

    Article  PubMed  CAS  Google Scholar 

  131. Tang, T., Badal, M. Y., Ocvirk, G., et al. (2002) Integrated microfluidic electrophoresis system for analysis of genetic materials using signal amplification methods. Anal. Chem. 74, 725–733.

    Article  PubMed  CAS  Google Scholar 

  132. Foquet, M., Korlach, J., Zipfel, W., Webb, W. W. and Craighead, H. G. (2002) DNA fragment sizing by single molecule detection in submicrometer-sized closed fluidic channels. Anal. Chem. 74, 1415–1422.

    Article  PubMed  CAS  Google Scholar 

  133. Jiang, G., Attiya, S., Ocvirk, G., Lee, W. E. and Harrison, D. J. (2000) Red diode laser induced fluorescence detection with a confocal microscope on a microchip for capillary electrophoresis. Biosens. Bioelectron. 14, 861–869.

    Article  PubMed  CAS  Google Scholar 

  134. Woods, L. A., Roddy, T. P., Paxon, T. L. and Ewing, A. G. (2001) Electrophoresis in nanometre inner diameter capillaries with electrochemical detection. Anal. Chem. 73, 3687–3690.

    Article  PubMed  CAS  Google Scholar 

  135. Giordano, B. C., Ferrance, J., Swedberg, S., Huhmer, A. F., and Landers, J. P. (2001) Polymerase chain reaction in polymeric microchips: DNA amplification in less than 240 seconds. Anal. Biochem. 291, 124–132.

    Article  PubMed  CAS  Google Scholar 

  136. Krylov, S. N. Starke, D. A. Arriaga, E. A., et al. (2000). Instrumentation for chemical cytometry. Anal. Chem. 72, 872–877.

    Article  PubMed  CAS  Google Scholar 

  137. Nirode, W. F. Staller, T. D. Cole, R. O., and Sepaniak, M. J. (1998) Fluorescence derivatization of DNA fragments separated by capillary electrophoresis. Anal. Chem. 70, 182–186.

    Article  CAS  Google Scholar 

  138. Chen, S. and Lillard, S. J. (2001) Continuous cell introduction for the analysis of individual cells by capillary electrophoresis. Anal. Chem. 73, 111–118.

    Article  PubMed  CAS  Google Scholar 

  139. Fang, Q., Xu, G.-M., and Fang, Z.-L. (2002) A high-throughput continuous sample introduction interface for microfluidic chip-based capillary electrophoresis systems. Anal. Chem. 74, 1223–1231.

    Article  PubMed  CAS  Google Scholar 

  140. Rezenom, Y. H., Lancaster, J. M. III, Pittman, J. L., and Gilman, S. D. (2002) Laser ablation construction of on-column reagent addition devices for capillary electrophoresis. Anal. Chem. 74, 1572–1577.

    Article  PubMed  CAS  Google Scholar 

  141. Xue, G., Pang, H. M., and Yeung, E. S. (2001) Online nanoliter cycle sequencing reaction with capillary zone electrophoresis purification for DNA sequencing. J. Chromatogr. A 914, 245–256.

    Article  PubMed  CAS  Google Scholar 

  142. Hadd, A. G., Goard, M. P., Rank, D. R., and Jovanovich, S. B. (2000) Sub-microliter DNA sequencing for capillary array electrophoresis. J. Chromatogr. A 894, 191–201.

    Article  PubMed  CAS  Google Scholar 

  143. Yuen, P.K., Kricka, L. J., Fortina, P., Panaro, N. J., Sakazume, T., and Wilding, P. (2001) Microchip module for blood sample preparation and nucleic acid amplification reactions. Genome Res. 11, 405–412.

    Article  PubMed  CAS  Google Scholar 

  144. Bakajin, O., Duke, T. A., Tegenfeldt, J., et al. (2001). Separation of 100-kilobase DNA molecules in 10 seconds. Anal. Chem. 73, 6053–6056.

    Article  PubMed  CAS  Google Scholar 

  145. Chou, C.F., Austin, R.H., Bakajin, O., et al. (2000). Sorting biomolecules with microdevices. Electrophoresis 21, 81–90.

    Article  PubMed  CAS  Google Scholar 

  146. Ronai, Z., Barta, C., Sasvari-Szekely, M., and Guttman, A. (2001) DNA analysis on electrophoretic microchips: effect of operational variables. Electrophoresis 22, 294–299.

    Article  PubMed  CAS  Google Scholar 

  147. Salas-Solano, O., Schmalzing, D., Koutny, L., et al. (2000) Optimization of high performance DNA sequencing on short microfabricated electrophoretic devices. Anal. Chem. 72, 3129–3137.

    Article  PubMed  CAS  Google Scholar 

  148. Regnier, F. E., He, B., Lin, S., and Busse, J. (1999) Chromatography and electrophoresis on chips: critical elements of future integrated, microfluidic analytical systems for life science. Trends Biotechnol. 17, 101–106.

    Article  PubMed  CAS  Google Scholar 

  149. Marzilli, L. A., Koertje, C., and Vouros, P. (2001) Capillary electrophoresis — mass spectrometric analysis of DNA adducts, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 395–406.

    Google Scholar 

  150. Ding, J. and Vouros, P. (2000) Capillary electro-chromatography-mass spectrometry for the separation and identification of isomeric polyaromatic hydrocarbon DNA adducts derived from in vitro reactions. J. Chromatogr. A 887, 103–113.

    Article  PubMed  CAS  Google Scholar 

  151. Deforce, D. L. and Van den Eeckhout, E. E. (2001) Analysis of DNA-damage using capillary zone electrophoresis and electrospray mass spectrometry, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 429–442.

    Google Scholar 

  152. Zhang, N., Tan, H., and Yeung, E. S. (1999) Automated and integrated system for high-throughput DNA genotyping directly from blood. Anal. Chem. 71, 1138–1145.

    Article  PubMed  CAS  Google Scholar 

  153. Hong, J. W., Fujii, T., Seki, M., Yamamoto, T., and Endo, I. (2001) Integration of gene amplification and capillary gel electrophoresis on a polydimethyl-siloxane-glass hybrid microchip. Electrophoresis 22, 328–333.

    Article  PubMed  CAS  Google Scholar 

  154. Sassi, A. P., Paulus, A., Cruzado, I. D., Bjornson, T., and Hooper, H. H. (2000) Rapid, parallel separations of d1S80 alleles in a plastic microchannel chip. J. Chromatogr. A 894, 203–217.

    Article  PubMed  CAS  Google Scholar 

  155. Ying, F., Mastrangelo, C. H., Burke, D. T., and Burns, M. A. (1998) Electrophoretic separations using sweeping fields. Electrophoresis 19, 1388–1393.

    Article  PubMed  CAS  Google Scholar 

  156. Ren, H., Karger, A. E., Oaks, F., Menchen, S., Slater, G. W., and Drouin, G. (1999) Separating DNA sequencing fragments without a sieving matrix. Electrophoresis 20, 2501–2509.

    Article  PubMed  CAS  Google Scholar 

  157. Ahmadian, A., Gharizadeh, B., Gustafsson, A.C., et al. (2000) Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280, 103–110.

    Article  PubMed  CAS  Google Scholar 

  158. Kenis, P. J., Ismagilov, R. F., and Whitesides, G. M. (1999) Microfabrication inside capillaries using multiphase laminar flow patterning. Science 285, 83–85.

    Article  CAS  Google Scholar 

  159. Paegel, B. M., Hutt, L. D., Simpson, P. C., and Mathies, R. A. (2000) Turn geometry for minimizing band broadening in microfabricated capillary electrophoresis channels. Anal. Chem. 72, 3030–3037.

    Article  PubMed  CAS  Google Scholar 

  160. Chen, X., Wu, H., Mao, C., and Whitesides, G. M. (2002) A prototype two-dimensional capillary electrophoresis system fabricated in poly(dimethylsiloxane). Anal. Chem. 74, 1772–1778.

    Article  PubMed  CAS  Google Scholar 

  161. Magnúsdóttir, S., Heller, C., Sergot, P., and Viovy, J.-L. (2001) Collection of capillary electrophoresis fractions on a moving membrane, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 323–332.

    Google Scholar 

  162. Minarik, M., Foret, F., and Karger, B. L. (2000) Fraction collection in micropreparative capillary zone electrophoresis and capillary isoelectric focusing. Electrophoresis 21, 247–254.

    Article  PubMed  CAS  Google Scholar 

  163. Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.

    Article  PubMed  CAS  Google Scholar 

  164. The International SNP Map Working Group. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933.

    Article  Google Scholar 

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    Keith R. Mitchelson

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Mitchelson, K.R. The use of capillary electrophoresis for DNA polymorphism analysis. Mol Biotechnol 24, 41–68 (2003). https://doi.org/10.1385/MB:24:1:41

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