Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1990 Feb 11;18(3):569–575. doi: 10.1093/nar/18.3.569

Molecular detrapping and band narrowing with high frequency modulation of pulsed field electrophoresis.

C Turmel 1, E Brassard 1, G W Slater 1, J Noolandi 1
PMCID: PMC333463  PMID: 2408015

Abstract

In high electric fields, megabase DNA fragments are found to be trapped, i.e. to enter or migrate in the gel only very slowly, if at all, leading to very broad electrophoretic bands and loss of separation. As a consequence, low electric fields are usually used to separate these molecules by pulsed field electrophoretic methods. We report here that high-frequency pulses eliminate the molecular trapping found in continuous fields. When high frequency pulses are used to modulate the longer pulses used in pulsed field electrophoresis, narrower bands result, and higher fields can be used. We suggest that this is due to effects that occur on the length scale of a single pore.

Full text

PDF
569

Images in this article

570Image
on p.570
571Image
on p.571
572Image
on p.572
573Image
on p.573
573Image
on p.573

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bancroft I., Wolk C. P. Pulsed homogeneous orthogonal field gel electrophoresis (PHOGE). Nucleic Acids Res. 1988 Aug 11;16(15):7405–7418. doi: 10.1093/nar/16.15.7405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Birren B. W., Hood L., Lai E. Pulsed field gel electrophoresis: studies of DNA migration made with the programmable, autonomously-controlled electrode electrophoresis system. Electrophoresis. 1989 May-Jun;10(5-6):302–309. doi: 10.1002/elps.1150100506. [DOI] [PubMed] [Google Scholar]
  3. Carle G. F., Frank M., Olson M. V. Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science. 1986 Apr 4;232(4746):65–68. doi: 10.1126/science.3952500. [DOI] [PubMed] [Google Scholar]
  4. Carle G. F., Olson M. V. Separation of chromosomal DNA molecules from yeast by orthogonal-field-alternation gel electrophoresis. Nucleic Acids Res. 1984 Jul 25;12(14):5647–5664. doi: 10.1093/nar/12.14.5647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chu G., Vollrath D., Davis R. W. Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science. 1986 Dec 19;234(4783):1582–1585. doi: 10.1126/science.3538420. [DOI] [PubMed] [Google Scholar]
  6. Clark S. M., Lai E., Birren B. W., Hood L. A novel instrument for separating large DNA molecules with pulsed homogeneous electric fields. Science. 1988 Sep 2;241(4870):1203–1205. doi: 10.1126/science.3045968. [DOI] [PubMed] [Google Scholar]
  7. Gardiner K., Laas W., Patterson D. Fractionation of large mammalian DNA restriction fragments using vertical pulsed-field gradient gel electrophoresis. Somat Cell Mol Genet. 1986 Mar;12(2):185–195. doi: 10.1007/BF01560665. [DOI] [PubMed] [Google Scholar]
  8. Gardiner K., Patterson D. Transverse alternating field electrophoresis and applications to mammalian genome mapping. Electrophoresis. 1989 May-Jun;10(5-6):296–302. doi: 10.1002/elps.1150100505. [DOI] [PubMed] [Google Scholar]
  9. Holzwarth G., McKee C. B., Steiger S., Crater G. Transient orientation of linear DNA molecules during pulsed-field gel electrophoresis. Nucleic Acids Res. 1987 Dec 10;15(23):10031–10044. doi: 10.1093/nar/15.23.10031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lalande M., Noolandi J., Turmel C., Brousseau R., Rousseau J., Slater G. W. Scrambling of bands in gel electrophoresis of DNA. Nucleic Acids Res. 1988 Jun 24;16(12):5427–5437. doi: 10.1093/nar/16.12.5427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lalande M., Noolandi J., Turmel C., Rousseau J., Slater G. W. Pulsed-field electrophoresis: application of a computer model to the separation of large DNA molecules. Proc Natl Acad Sci U S A. 1987 Nov;84(22):8011–8015. doi: 10.1073/pnas.84.22.8011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Levene S. D., Zimm B. H. Separations of open-circular DNA using pulsed-field electrophoresis. Proc Natl Acad Sci U S A. 1987 Jun;84(12):4054–4057. doi: 10.1073/pnas.84.12.4054. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Noolandi J, Rousseau J, Slater GW, Turmel C, Lalande M. Self-trapping and anomalous dispersion of DNA in electrophoresis. Phys Rev Lett. 1987 Jun 8;58(23):2428–2431. doi: 10.1103/PhysRevLett.58.2428. [DOI] [PubMed] [Google Scholar]
  14. Orbach M. J., Vollrath D., Davis R. W., Yanofsky C. An electrophoretic karyotype of Neurospora crassa. Mol Cell Biol. 1988 Apr;8(4):1469–1473. doi: 10.1128/mcb.8.4.1469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Schwartz D. C., Cantor C. R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984 May;37(1):67–75. doi: 10.1016/0092-8674(84)90301-5. [DOI] [PubMed] [Google Scholar]
  16. Slater G. W., Rousseau J., Noolandi J., Turmel C., Lalande M. Quantitative analysis of the three regimes of DNA electrophoresis in agarose gels. Biopolymers. 1988 Mar;27(3):509–524. doi: 10.1002/bip.360270311. [DOI] [PubMed] [Google Scholar]
  17. Smith C. L., Cantor C. R. Purification, specific fragmentation, and separation of large DNA molecules. Methods Enzymol. 1987;155:449–467. doi: 10.1016/0076-6879(87)55030-3. [DOI] [PubMed] [Google Scholar]
  18. Stellwagen N. C. Effect of the electric field on the apparent mobility of large DNA fragments in agarose gels. Biopolymers. 1985 Dec;24(12):2243–2255. doi: 10.1002/bip.360241207. [DOI] [PubMed] [Google Scholar]
  19. Sturm J, Weill G. Direct observation of DNA chain orientation and relaxation by electric birefringence: Implications for the mechanism of separation during pulsed-field gel electrophoresis. Phys Rev Lett. 1989 Mar 27;62(13):1484–1487. doi: 10.1103/PhysRevLett.62.1484. [DOI] [PubMed] [Google Scholar]
  20. Turmel C., Lalande M. Resolution of Schizosaccharomyces pombe chromosomes by field inversion gel electrophoresis. Nucleic Acids Res. 1988 May 25;16(10):4727–4727. doi: 10.1093/nar/16.10.4727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Vollrath D., Davis R. W. Resolution of DNA molecules greater than 5 megabases by contour-clamped homogeneous electric fields. Nucleic Acids Res. 1987 Oct 12;15(19):7865–7876. doi: 10.1093/nar/15.19.7865. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES