Skip to main content
SpringerLink
Log in

The Application of Capillary Electrophoresis in the Analysis of PCR Products Used in Forensic DNA Typing

  • Chapter
Book cover Clinical and Forensic Applications of Capillary Electrophoresis

Part of the book series: Pathology and Laboratory Medicine ((PLM))

Abstract

The development of methods for the amplification and detection of specific regions of the DNA molecule using the polymerase chain reaction (PCR) has resulted in rapid and dramatic advances in biochemical analysis (1). With the advent of the PCR it is now possible to easily produce analytically significant amounts of a specified DNA product. A typical PCR reaction can produce microgram quantities of target DNA, allowing rapid and efficient screening of genetic defects, cancer susceptibility, and low level bacterial contamination (2). The sensitivity of the technique has freed biochemists from the many laborious processes necessary to isolate and examine small quantities of DNA. In the forensic arena, PCR methods have permitted rapid and specific tests of evidence produced in a crime (2).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Mullis, K. B. and Faloona, F. A. (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155, 335–350.

    Article  PubMed  CAS  Google Scholar 

  2. Erlich, H. A. (ed.) (1989) PCR Technology. Stockton Press, New York, NY.

    Google Scholar 

  3. Gibbs, R. A. (1990) DNA Amplification by the polymerase chain reaction. Anal. Chem. 62, 1202–1214.

    Google Scholar 

  4. Kasper, T. J., Melera, M., Gozel, P., and Brownlee, R. G. (1988) Separation and detection of DNA by capillary electrophoresis J. Chromatogr. 458, 303–312.

    Article  PubMed  CAS  Google Scholar 

  5. Cohen, A. S., Paulus, A., and Karger, B. L. (1987) High-performance capillary electrophoresis using open tubes and gels. Chromatographia 24, 15–24.

    Article  CAS  Google Scholar 

  6. Cohen, A. S. and Karger, B. L. (1987) High performance sodium dodecyl sulfate polyacrylamide gel capillary electrophoresis of peptides and proteins. J. Chromatogr. 409, 697.

    Google Scholar 

  7. Zhu, M., Hansen, D. L., Burd, S., and Gannon, F. (1989) Factors affecting free zone electrophoresis and isoelectric focusing in capillary electrophoresis. J. Chromatogr. 480, 311–319.

    Article  CAS  Google Scholar 

  8. Barron, A. E., Blanch, H. W., and Soane, D. S. (1994) A transient entanglement coupling mechanism for DNA separation by capillary electrophoresis in ultra-dilute polymer solutions. Electrophoresis 15, 597–615.

    Article  PubMed  CAS  Google Scholar 

  9. Ogston, A. G. (1958) The spaces in a uniform random suspension of fibres. Tran. Faraday Soc. 54, 1754–1757.

    Google Scholar 

  10. Lerman, L. S. and Frisch, H. L. (1982) Why does the electrophoretic mobility of DNA in gels vary with the length of the molecule? Biopolymers 21, 995–997.

    Article  PubMed  CAS  Google Scholar 

  11. Grossman, P. D. and Soane, D. S. (1991) Capillary electrophoresis of DNA in entangled polymer solutions. J. Chromatogr. 559, 257–266.

    Article  PubMed  CAS  Google Scholar 

  12. Barron, A. E., Sunada, W. M., and Blanch, H. W. (1996) The effect of polymer properties on DNA separations by capillary electrophoresis in uncrosslinked polymer solutions. Electrophoresis 17, 744–757.

    Article  PubMed  CAS  Google Scholar 

  13. Heiger, D. N., Cohen, A. S., and Karger, B. L. (1990) Separation of DNA restriction fragments by high performance capillary electrophoresis with low and zero crosslinked polyacrylamide using continuous and pulsed electric fields. J. Chromatogr. 558, 33–48.

    Google Scholar 

  14. Srinivasan, K., Morris, S. C., Girard, J. E., Kline, M. C., and Reeder, D. J. (1993) Use of TOTO and YOYO intercalating dyes to enhance detection of PCR products with laser induced fluorescence-capillary electrophoresis. Appl. Theor. Electrophoresis 3, 235–239.

    Google Scholar 

  15. Clark, B. K., Nickles, C. L., Morton, K. C., Kovac, J., and Sepaniak, M. J. (1994) Rapid separation of DNA restriction digests using size selective capillary electrophoresis with application to DNA fingerprinting. J. Microcol. Sep. 6, 503–513.

    Google Scholar 

  16. Kim, Y. and Morris, M. D. (1994) Separation of nucleic acids by capillary electrophoresis in cellulose solutions with mono-and bis-intercalating dyes. Anal. Chem. 66, 168–174.

    Google Scholar 

  17. Strege, M. and Lagu, A. (1991) Separation of DNA restriction fragments by capillary electrophoresis using coated fused silica capillaries. Anal. Chem. 63, 1233–1236.

    Google Scholar 

  18. MacCrehan, W. A., Rasmussen, H. T., and Northrop, D. M. (1992) Size-selective capillary electrophoresis (SSCE) separation of DNA fragments. J. Liq. Chromatogr. 15, 1063–1080.

    Google Scholar 

  19. Baba, Y., Ishimaru, N., Samata, K., and Tsuhako, M. (1993) High-resolution separation of DNA restriction fragments by capillary electrophoresis in cellulose derivative solutions. J. Chromatogr. 653, 329–335.

    Article  CAS  Google Scholar 

  20. Nathakarnkitkool, S., Oefner, P. J., Bartsch, G., Chin, M. A., and Bonn, G. K. (1992) High-resolution capillary electrophoretic analysis of DNA in free solution. Electrophoresis 13, 18–31.

    Article  PubMed  CAS  Google Scholar 

  21. Kleemiss, M. H., Gilges, M., and Schomburg, G. (1993) Capillary electrophoresis of DNA restriction fragments with solutions of entangled polymers. Electrophoresis 14, 515–522.

    Article  PubMed  CAS  Google Scholar 

  22. Butler, J. M., McCord, B. R., Jung, J. M., Lee, J. A., Budowle, B., and Allen, R. O. (1995) Application of dual internal standards for precise sizing of polymerase chain reaction products using capillary electrophoresis. Electrophoresis 16, 974–980.

    Article  PubMed  CAS  Google Scholar 

  23. Barron, A. E., Soane, D. S., and Blanch, H. W. (1993) Capillary electrophoresis of DNA in uncrosslinked polymer solutions. J. Chromatogr. 652, 3–16.

    Article  CAS  Google Scholar 

  24. Pearce, M. J. and Watson, N. D. (1993) Rapid analysis of PCR components and products by acidic non-gel capillary electrophoresis, in DNA Fingerprinting: State of the Science ( Pena, S. D. J., Chakraborty, R., Epplen, J., and Jeffreys, A. J., eds.), Birkauser Verlag, Basel, Switzerland, pp. 117–124.

    Chapter  Google Scholar 

  25. Schwartz, H. E., Ulfelder, K., Sunzeri, F. J., Busch, M. P., and Brownlee, R. G. (1991) Analysis of DNA restriction fragments and polymerase chain reaction products towards detection of AIDS (HIV-1) virus in blood. J. Chromatogr. 559, 267–283.

    Article  PubMed  CAS  Google Scholar 

  26. Kim, Y. and Morris, M. D. (1994) Separation of nucleic acids by capillary electrophoresis in cellulose solutions with mono-and bis-intercalating dyes. Anal. Chem. 66, 1168–1174.

    Google Scholar 

  27. Chan, K. C., Whang, C. W., and Yeung, E. S. (1993) Separation of DNA Restriction fragments using capillary electrophoresis. J. Liq. Chromatogr. 16, 1941–1962.

    Google Scholar 

  28. Chang, H.-T. and Yeung, E. S. (1995) Poly(ethyleneoxide) for high-resolution and high-speed separation of DNA by capillary electrophoresis. J. Chromatogr. B, 669, 113.

    Google Scholar 

  29. Chian, M., Nesi, M., and Righetti, P. G. (1994) Capillary zone electrophoresis of DNA fragments in a novel polymer network: poly ( N-acryloylaminoethoxyethanol ). Electrophoresis 15, 616–622.

    Google Scholar 

  30. Lazaruk, K., Walsh, P. Oaks, F., Gilbert, F., Rosenblum, D., Barnett, B., Menchen, S. et al. (1998) Genotyping of forensic short tandem repeat ( STR) systems based on sizing precision in a capillary electrophoresis instrument. Electrophoresis 19, 86–93.

    Google Scholar 

  31. Fung, E. N. and Yeung, E. S. (1995) High speed DNA sequencing by using mixed poly(ethyleneoxide) solution in uncoated capillary columns. Anal. Chem. 67, 1913–1919.

    Google Scholar 

  32. Rosenblum, B. B., Oaks, F., Menchen, S., and Johnson, B. (1997) Improved single-strand DNA sizing accuracy in capillary electrophoresis. Nucleic Acids Res. 25 (19), 3925–3929.

    Article  PubMed  CAS  Google Scholar 

  33. Weinberger, R. (1993) Practical Capillary Electrophoresis. Academic, San Diego, CA.

    Google Scholar 

  34. Muth, J., Williams, P. M, Williams, S. J., Brown, M. D., Wallace, D. C., and Karger, B. L. (1996) Fast capillary electrophoresis-laser induced fluorescence analysis of ligase chain reaction products: human mitochondrial point mutations causing Lebers hereditary optic neuropathy, Electrophoresis 17, 1875–1883.

    Article  PubMed  CAS  Google Scholar 

  35. Mansfield, E. S. and Kronick, M. N. (1993) Alternative labeling techniques for automated fluorescence based analysis of PCR products. BioTechniques 15, 274–279.

    Google Scholar 

  36. McCord, B. R., Budowle, B., Isenberg, A. R., and Allen, R. O. (1996) Capillary electrophoresis for the automated analysis of multiplexed STRs using multi wavelength detection, Proceedings of the Seventh International Symposium on Human Identification. Promega Corporation, pp. 116–122.

    Google Scholar 

  37. Schwartz, H. E. and Ulfelder, K. J. (1992) Capillary electrophoresis with laser-induced fluorescence detection of PCR fragments using Thiazole Orange. Anal. Chem. 64, 1737–1740.

    Google Scholar 

  38. McCord, B. R., McClure, D. M., and Jung, J. M. (1993) Capillary electrophoresis of PCR-amplified DNA using fluorescence detection with an intercalating dye. J. Chromatogr. 652, 75–82.

    Article  CAS  Google Scholar 

  39. Zhu, H., Clark, S. M., Benson, S. C., Rye, H. S., Glazer, A. N., and Mathies, R. A. (1994) High-sensitivity capillary electrophoresis of double-stranded DNA fragments using monomeric and dimeric fluorescent intercalating dyes. Anal. Chem. 66, 1941–1948.

    Google Scholar 

  40. Berka, J., Pariat, Y. F., Müller, O., Hebenbrock, K., Heiger, D. N., Foret, F., and Karger, B. (1995) Sequence dependent migration behavior of double-stranded DNA in capillary electrophoresis. Electrophoresis 16, 377–388.

    Article  PubMed  CAS  Google Scholar 

  41. Butler, J. M., McCord, B. R., Jung, J. M., Wilson, M. R., Budowle, B., and Allen, R. O. (1994) Quantitation of polymerase chain reaction products by capillary electrophoresis using laser fluorescence. J. Chromatogr. 658, 271–280.

    Article  CAS  Google Scholar 

  42. Marino, M. A., Turni, L. A., Del Rio, S. A., and Williams, P. E. (1994) Molecular size determinations of DNA restriction fragments and polymerase chain reaction products using capillary gel electrophoresis. J. Chromatogr. A, 676, 185–189.

    Google Scholar 

  43. McCord, B. R., Jung, J. M., and Holleran, E. A. (1993) High resolution capillary electrophoresis of forensic DNA using a non-gel sieving buffer. J. Liq. Chromatogr. 16, 1963–1981.

    Google Scholar 

  44. Wilson, M. R., Polanskey, D., Butler, J. M., DiZinno, J. A., Replogle, J., and Budowle, B. (1995) Extraction, PCR amplification and sequencing of mitochondrial DNA from human hair shafts. BioTechniques, 18, 662.

    Google Scholar 

  45. Elmer Applied Biosciences Division protocols for ABD 310 Genetic Analyzer and AmpF1STR Profiler Plus (1995) Foster City, CA.

    Google Scholar 

  46. Chan, K. C., Muschik, G. M., and Issaq, H. J. (1997) High-speed electrophoretic separation of DNA fragments using a short capillary. J. Chromatogr. B 695, 113–115.

    Article  CAS  Google Scholar 

  47. Woolley, A. T., Hadley, D., Landre, P., DeMello, A. J., Mathies, R. A., and Northrup, M. A. (1996) Functional integration of PCR amplification and capillary electrophoresis on a microfabricated DNA analysis device. Anal. Chem. 68, 4081.

    Google Scholar 

  48. Clark, B. K. and Sepaniak, M. J. (1993) Evaluation of on-column labeling with intercalating dyes for fluorescence detection of DNA fragments separated by capillary electrophoresis. J. Microcol. Sep. 5, 275–282.

    Google Scholar 

  49. Schwartz, H. E., Ulfelder, K. J., Chen, F. A., and Pentoney, S. L., Jr. (1994) The utility of laser-induced fluorescence detection in applications of capillary electrophoresis. J. Cap. Elec. 1, 36–54.

    Google Scholar 

  50. Lee, L. G., Chen, C. H., and Chiu, L. A. (1986) Thiazole Orange: a new dye for reticulocyte analysis. Cytometry 7, 508–517.

    Article  PubMed  CAS  Google Scholar 

  51. Isenberg, A. R., McCord, B. R., Koons, B. W., Budowle, B., and Allen, R. O. (1996) DNA typing of a polymerase chain reaction amplified D1S80/ amelogenin multiplex using capillary electrophoresis and a mixed entangled polymer matrix. Electrophoresis 17, 1505.

    Article  PubMed  CAS  Google Scholar 

  52. Lu, W., Han, D. S., Yuan, J., and Andrieu, J. M. (1994) Multi-target PCR analysis by capillary electrophoresis and laser-induced fluorescence. Nature 368, 269–271.

    Article  PubMed  CAS  Google Scholar 

  53. Wang, Y., Ju, J., Carpenter, B., Atherton, J. M., Sensabaugh, G. F., and Mathies, R. A. (1995) High-speed, high-throughput THO1 allelic sizing using energy transfer fluorescent primers and capillary array electrophoresis. Anal. Chem. 67, 1197–1203.

    Google Scholar 

  54. Pariat, Y. F., Berka, J., Heiger, D. N., Schmitt, T., Vilenchik, M., Cohen, A. S., Foret, F., et al. (1993) Separation of DNA fragments by capillary electrophoresis using replacable linear polyacrylamide matrices. J. Chromatogr. 652, 57–66.

    Article  CAS  Google Scholar 

  55. Butler, J. M. (1995) Sizing and quantitation of polymerase chain reaction products by capillary electrophoresis for use in DNA typing. University of Virginia, Ph. D. dissertation.

    Google Scholar 

  56. ABI Prism 310 Genescan Chemistry Guide, Perkin Elmer, Foster City, CA (1995)

    Google Scholar 

  57. Righetti, P. G. and Gelfi, C. (1997) Recent advances in capillary electrophoresis of DNA fragments and PCR products in poly(N-substituted acrylamides). Anal. Biochem. 244, 195–207.

    Google Scholar 

  58. Cheng, J., Kasuga, T., Watson, N. D., and Mitchelson, K. R. (1995) Enhanced Single-stranded DNA conformation polymorphism analysis by entangled solution capillary electrophoresis. J. Cap. Elec. 2, 24–29.

    Google Scholar 

  59. Ulfelder, K. J. and McCord, B. R. (1996) Separation of DNA by capillary electrophoresis, in Handbook of Capillary Electrophoresis, ( Landers, J. P., ed.), CRC, New York.

    Google Scholar 

  60. Butler, J. M. (1997) Separation of DNA restriction fragments and PCR products, in Analysis of Nucleic Acids by Capillary Electrophoresis (Heller, C., ed.), Vieweg, Germany, Chapter 8, pp. 195–217.

    Chapter  Google Scholar 

  61. Hammond, H. A., Jin, L., Zhong, Y., Caskey, C. T., and Chakraborty, R. (1994) Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am. J. Hum. Genet. 55, 175–189.

    Google Scholar 

  62. Mansfield, E. S., Vainer, M., Enad, S., Barker, D. L., Harris, D., Rappaport E., and Fortina, P. (1996) Sensitivity, reproducibility and accuracy in short tandem repeat genotyping using capillary array electrophoresis. Genome Res. 6, 893.

    Article  PubMed  CAS  Google Scholar 

  63. Isenberg, A. R., Allen, R. O., Keys, K. M., Smerick, J. B., Budowle, B., and McCord, B. R. (1998) Analysis of two multiplexed short tandem repeats using capillary electrophoresis with multiwavelength fluorescence detection. Electrophoresis 19, 94–100.

    Article  PubMed  CAS  Google Scholar 

  64. McCord, B. R., Budowle, B., Isenberg, A. R., and Allen, R. O. (1997) Precision and resolution studies utilizing capillary electrophoresis: investigations of the effect of polymer type and concentration, Proceedings from the Eighth International Symposium on Human Identification, p. 192.

    Google Scholar 

  65. Walsh, P. S., Fildes, N. J., and Reynolds, R. (1996) Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA. Nucleic Acids Res. 24 (14), 2807–2812.

    Article  PubMed  CAS  Google Scholar 

  66. Dimo-Simonin, N., Grange, F., Kratzer, A., Brandt-Casadevall, C., and Mangin, P. (1998) Forensic validation of the short tandem repeat HUMACTBP2 using capillary electrophoresis. Electrophoresis 19, 256–261.

    Article  PubMed  CAS  Google Scholar 

  67. Mansfield, E. S., Robertson, J. M., Vainer, M., Isenberg, A. R., Frazier, R. R., Ferguson, K., et al. (1998) Analysis of multiplexed short tandem repeat ( STR) systems using capillary array electrophoresis. Electrophoresis 19, 101–107.

    Google Scholar 

  68. Marchi, E. and Pasacreta, R. J. (1997) Capillary electrophoresis in court: the landmark decision of the people of Tennessee versus Ware. J. Cap Electr. 4 (4), 145–156.

    CAS  Google Scholar 

  69. Butler, J. M., Wilson, M. R., and Reeder, D. J. (1998) Rapid mitochondrial DNA typing using restriction enzyme digestion of polymerase chain reaction amplicons followed by capillary electrophoretic separation with fluorescence detection. Electrophoresis 19, 119–124.

    Article  PubMed  CAS  Google Scholar 

  70. Clark, S. M. and Mathies, R. A. (1993) High-speed parallel separation of DNA restriction fragments using capillary array electrophoresis. Anal. Biochem. 215, 163–170.

    Google Scholar 

  71. Belgrader, P., Del Rio, S. A., Turner, K. A., Marino, M. A., Weaver, K. R., and Williams, P. E. (1995) Automated DNA purification and amplification from blood stained cards using a robotic workstation. BioTechniques 19, 427.

    Google Scholar 

  72. Belgrader, P., Devaney, J. M., Del Rio, S. A., Turner, K. A., Weaver, K. R., and Marino, M. A. (1996) Automated polymerase chain reaction sample preparation for capillary electrophoresis. J. Chromatogr. B Biomed. Appl. 683, 109.

    Google Scholar 

  73. Jacobson, S. C. and Ramsey, J. M. (1996) Integrated microdevice for DNA restriction fragment analysis. Anal. Chem. 68, 720.

    Google Scholar 

  74. Manz, A. (1997) Ultimate speed and sample volumes in electrophoresis. Biochem. Soc. Trans. 25, 278.

    Google Scholar 

  75. Effenhauser, C. S., Paulus, A., Manz, A., and Widmer, H. M. (1994) Highspeed separation of antisense oligonucleotides on a micromachined capillary electrophoresis device. Anal. Chem. 66, 2949–2953.

    Google Scholar 

  76. Woolley, A. T. and Mathies, R. A. (1994) Ultra-high-speed DNA fragment separations using microfabricated capillary array electrophoresis chips. Proc. Natl. Acad. Sci. USA 91, 11,348–11, 352.

    Google Scholar 

  77. Burns, M. A., Mastrangelo, C. H., Sammarco, T. S., Man, F. P., Webster, J. R., Johnson, B. N., et al. (1996) Microfabricated structures for integrated DNA analysis. Proc. Natl. Acad. Sci. USA 93, 5556.

    Google Scholar 

  78. Service, R. F. (1995) Genomics: DNA chips survey an entire genome. Science 268, 26.

    Google Scholar 

  79. Schmalzing, D., Koutny, L., Adourian, A., Matsudiara, P., Ehrlich, D., and Belgrader, P. (1998) Ultrafast STR analysis by microchip gel analysis. Proceedings from the Eighth International Symposium on Human Identification, Promega Corp., Madison, WI.

    Google Scholar 

  80. Schmalzing, D., Koutny, L., Adourian, A, Belgrader, P., Matsudiara, P., and Ehrlich, D. (1997) DNA typing in thirty seconds with a microfabricated device. Proc. Natl. Acad. Sci. USA 94, 10,273–10, 278.

    Google Scholar 

  81. Wallin, J. M., Buoncristiani, M. R., Lazaruk, K., Fildes, N., Holt, C. L., and Walsh, P. S. (1998) Validation of the AmpF1STR bluePCR amplification kit for forensic casework analysis. J. Forensic Sci. 43, 854–870.

    PubMed  CAS  Google Scholar 

Download references

Authors
  1. Bruce R. McCord
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John M. Butler
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Texas Medical Branch, Galveston, TX, USA

    John R. Petersen  & Amin A. Mohammad  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2001 Springer Science+Business Media New York

About this chapter

Cite this chapter

McCord, B.R., Butler, J.M. (2001). The Application of Capillary Electrophoresis in the Analysis of PCR Products Used in Forensic DNA Typing. In: Petersen, J.R., Mohammad, A.A. (eds) Clinical and Forensic Applications of Capillary Electrophoresis. Pathology and Laboratory Medicine. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-120-6_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-59259-120-6_14

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61737-113-4

  • Online ISBN: 978-1-59259-120-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation