Skip to main content

Toward Effective PCR-Based Amplification of DNA on Microfabricated Chips

  • Protocol
Book cover Capillary Electrophoresis of Nucleic Acids

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 163))

Abstract

The polymerase chain reaction (PCR) has rapidly become the most valuable tool in the clinical diagnostic arsenal for determining specific diseases or detecting infectious agents. Primers, short pieces of DNA complementary to the DNA sequence of interest, are mixed with nucleotides, a small amount of template DNA from the sample of interest, and Taq DNA polymerase enzyme in the appropriate buffer. Using temperature cycling, a short piece of DNA (50-1000 bp in length), defined by the primers chosen, is rapidly amplified from the few initial template molecules added to the mixture. The amplification product is then analyzed using an electrophoretic separation. The entire process, shown in Fig. 1, includes the “sample preparation” which typically involves isolating the appropriate cells, from which the DNA is extracted prior to PCR amplification. To utilize this sequence most efficiently there should be a continuous flow from sample collection to diagnosis. This would eliminate both delays due to the transfer of material between each step and the need for intervention before the next step could begin. In the ideal world, this diagnosis would be immediate—the real goal is to decrease the time to as short as possible. Towards this end, the integration of the steps detailed in Fig. 1 into a single platform is of obvious and critical importance (see Note 1).

Overall scheme for clinical and genetic analyses.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

References

  1. 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.

    Article  PubMed  CAS  Google Scholar 

  2. Freemantle, M. (1999) Downsizing chemistry. C & E News 77, 27–36.

    Google Scholar 

  3. Wilding, P., Shoffner, M. A., and Kricka, L. J. (1994) PCR in a silicon microstructure. Clin. Chem. 40, 1815–1818.

    PubMed  CAS  Google Scholar 

  4. 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 in a microfabricated DNA analysis device. Anal. Chem. 68, 4081–4086.

    Article  PubMed  CAS  Google Scholar 

  5. Kopp, M. T., deMello, A. J., and Manz, A. (1998) Chemical amplification: continuousflow PCR on a chip. Science 280, 1046–1048.

    Article  PubMed  CAS  Google Scholar 

  6. Wittwer, C. T., Reed, G. B., and Ririe, K. M. (1994) Rapid cycle DNA amplification, in The Polymerase Chain Reaction (Mullis, K. B., Ferré, F., and Gibbs R. A., eds.), Birkhauser, Boston, pp. 175–181.

    Google Scholar 

  7. Friedman, N. A. and Meldrum, D. R. (1998) Capillary tube resistive thermal cycling. Anal. Chem. 70, 2997–3002.

    Article  PubMed  CAS  Google Scholar 

  8. Oda, R. P., Strausbauch, M. A., Huhmer, A. F. R., Borson, N., Jurrens, S. R., Craighead, J., et al. (1998) Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA. Anal. Chem. 70, 4361–4368.

    Article  PubMed  CAS  Google Scholar 

  9. Shoffner, M. A., Cheng, J., Hvichia, G. E., Kricka, J. J., and Wilding, P. (1996) Chip PCR. I. Surface passivation of microfabricated silicon-glass chips for PCR. Nucleic Acids Res. 24, 375–379.

    Article  PubMed  CAS  Google Scholar 

  10. Xie, W., Yang, R., Xu, J., Zhang, L., Xing, W., and Cheng, J. (2001) Microchip-based capillary electrophoresis systems, in Capillary Electrophoresis of Nucleic Acids, Vol. 1 (Mitchelson, K. R., and Cheng, J., eds.), Humana Press, Totowa, NJ, pp. 67–83.

    Google Scholar 

  11. Ibrahim, M. S., Lofts, R. S., Jahrling, P. B., Henchal, E. A., Weedn, V.W., Northrup, M. A., and Belgrader, P. (1998) Real-time microchip PCR for detecting single-base differences in viral and human DNA. Anal. Chem. 70, 2013–2017.

    Article  PubMed  CAS  Google Scholar 

  12. Kalinina, O., Lebedeva, I., Brown, J., and Silver, J. (1997) Nanoliter scale PCR with TaqMan detection. Nucleic Acids Res. 25, 1999–2004.

    Article  PubMed  CAS  Google Scholar 

  13. Oda, R. P, Strausbauch, M. A., Hühmer, A. F. R., Borson, N., Jurrens, S. R., Craighead, J., et al. (1998) Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA. Anal. Chem. 70, 4361–4368.

    Article  PubMed  CAS  Google Scholar 

  14. Waters, L. C., Jacobson, S. C., Kroutchinina, N., Khandurina, J., Foote, R. S., and Ramsey, J. M. (1998) Multiple sample PCR amplification and electrophoretic analysis on a microchip. Anal. Chem. 70, 5172–5176.

    Article  PubMed  CAS  Google Scholar 

  15. Harrison, D. J., Fluri, K., Chiem, N., Tang, T., and Fan, Z. (1996) Micromachining chemical and biochemical analysis and reaction systems on glass substrates. Sensors and Actuators B. 33, 105–109.

    Article  Google Scholar 

  16. Tarigan, H. J., Neill, P., Kenmore, C. K., and Bornhop, D. J. (1996) Capillary-scale refractive index detection by interferometric backscatter. Anal. Chem. 68, 1762–1770.

    Article  CAS  Google Scholar 

  17. Khandurina, J., Jacobson, S. C., Waters, L. C., Foote, R. S., Ramsey, J. M. (1999) Microfabricated porous membrane structure for sample concentration and electrophoretic analysis. Anal. Chem. 71, 1815–1819.

    Article  PubMed  CAS  Google Scholar 

  18. Schmalzing, D., Adourian, A., Koutny, L., Ziaugra, L., Matsudaira, P., and Ehrlich, D. (1998) DNA sequencing on microfabricated electrophoretic devices. Anal Chem. 70, 2303–2310.

    Article  PubMed  CAS  Google Scholar 

  19. Hofgaertner, W., Hühmer, A. F. R., Landers J. P., and Kant, J. (1999) Rapid diagnosis of HSV-induced encephalitis: Electrophoresis of PCR products on microchips. Clin. Chem. 45, 2132–2140.

    Google Scholar 

  20. Munro, N. J., Snow, K., Kant, J., and Landers, J. P. (1999) Molecular diagnostics on microfabricated electrophoretic devices: Translating slab gel-based T-and B-cell lymphomoproliferative disorder assays from the capillary to the microchip. Clin. Chem. 45, 1906–1917.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2001 Humana Press Inc.

About this protocol

Cite this protocol

Ferrance, J.P., Giordano, B., Landers, J.P. (2001). Toward Effective PCR-Based Amplification of DNA on Microfabricated Chips. In: Mitchelson, K.R., Cheng, J. (eds) Capillary Electrophoresis of Nucleic Acids. Methods in Molecular Biology™, vol 163. Humana Press. https://doi.org/10.1385/1-59259-116-7:191

Download citation

  • DOI: https://doi.org/10.1385/1-59259-116-7:191

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-765-6

  • Online ISBN: 978-1-59259-116-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics