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. 1989 Aug 11;17(15):5989–6003. doi: 10.1093/nar/17.15.5989

A systematic study of field inversion gel electrophoresis.

C Heller 1, F M Pohl 1
PMCID: PMC318255  PMID: 2528121

Abstract

The mobilities of oligomers of phage lambda DNA and of yeast chromosomes in agarose gels during field inversion gel electrophoresis (FIGE) were measured at different pulse times and electric fields. Also the ratios between forward and backward pulse times and/or field gradients were varied. The problem of 'band inversion' during FIGE, leading to an ambiguity in the mobility of large DNA fragments, was solved by using two dimensional gel electrophoresis with different parameters in the first and second dimension. The results are compared with those obtained with other pulsed electrophoresis systems and with a theoretical model.

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Selected References

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  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., Lai E., Clark S. M., Hood L., Simon M. I. Optimized conditions for pulsed field gel electrophoretic separations of DNA. Nucleic Acids Res. 1988 Aug 11;16(15):7563–7582. doi: 10.1093/nar/16.15.7563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Birren B. W., Lai E., Hood L., Simon M. I. Pulsed field gel electrophoresis techniques for separating 1- to 50-kilobase DNA fragments. Anal Biochem. 1989 Mar;177(2):282–286. doi: 10.1016/0003-2697(89)90052-3. [DOI] [PubMed] [Google Scholar]
  4. Bostock C. J. Parameters of field inversion gel electrophoresis for the analysis of pox virus genomes. Nucleic Acids Res. 1988 May 25;16(10):4239–4252. doi: 10.1093/nar/16.10.4239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Carle G. F., Olson M. V. Orthogonal-field-alternation gel electrophoresis. Methods Enzymol. 1987;155:468–482. doi: 10.1016/0076-6879(87)55031-5. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Chu B., Xu R., Wang Z. Low-field transient electric birefringence of DNA in agarose gels. Biopolymers. 1988 Dec;27(12):2005–2009. doi: 10.1002/bip.360271211. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. 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]
  11. Deutsch J. M. Theoretical studies of DNA during gel electrophoresis. Science. 1988 May 13;240(4854):922–924. doi: 10.1126/science.3363374. [DOI] [PubMed] [Google Scholar]
  12. Deutsch JM. Dynamics of pulsed-field electrophoresis. Phys Rev Lett. 1987 Sep 14;59(11):1255–1258. doi: 10.1103/PhysRevLett.59.1255. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Graham M. Y., Otani T., Boime I., Olson M. V., Carle G. F., Chaplin D. D. Cosmid mapping of the human chorionic gonadotropin beta subunit genes by field-inversion gel electrophoresis. Nucleic Acids Res. 1987 Jun 11;15(11):4437–4448. doi: 10.1093/nar/15.11.4437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Herrmann B. G., Barlow D. P., Lehrach H. A large inverted duplication allows homologous recombination between chromosomes heterozygous for the proximal t complex inversion. Cell. 1987 Mar 13;48(5):813–825. doi: 10.1016/0092-8674(87)90078-x. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. 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]
  18. Lerman L. S., Frisch H. L. Why does the electrophoretic mobility of DNA in gels vary with the length of the molecule? Biopolymers. 1982 May;21(5):995–997. doi: 10.1002/bip.360210511. [DOI] [PubMed] [Google Scholar]
  19. Lumpkin O. J., Déjardin P., Zimm B. H. Theory of gel electrophoresis of DNA. Biopolymers. 1985 Aug;24(8):1573–1593. doi: 10.1002/bip.360240812. [DOI] [PubMed] [Google Scholar]
  20. Mathew M. K., Smith C. L., Cantor C. R. High-resolution separation and accurate size determination in pulsed-field gel electrophoresis of DNA. 1. DNA size standards and the effect of agarose and temperature. Biochemistry. 1988 Dec 27;27(26):9204–9210. doi: 10.1021/bi00426a019. [DOI] [PubMed] [Google Scholar]
  21. Mathew M. K., Smith C. L., Cantor C. R. High-resolution separation and accurate size determination in pulsed-field gel electrophoresis of DNA. 2. Effect of pulse time and electric field strength and implications for models of the separation process. Biochemistry. 1988 Dec 27;27(26):9210–9216. doi: 10.1021/bi00426a020. [DOI] [PubMed] [Google Scholar]
  22. Mortimer R. K., Schild D. Genetic map of Saccharomyces cerevisiae, edition 9. Microbiol Rev. 1985 Sep;49(3):181–213. doi: 10.1128/mr.49.3.181-213.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pyle L. E., Corcoran L. N., Cocks B. G., Bergemann A. D., Whitley J. C., Finch L. R. Pulsed-field electrophoresis indicates larger-than-expected sizes for mycoplasma genomes. Nucleic Acids Res. 1988 Jul 11;16(13):6015–6025. doi: 10.1093/nar/16.13.6015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. 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]
  25. Schwartz D. C., Koval M. Conformational dynamics of individual DNA molecules during gel electrophoresis. Nature. 1989 Apr 6;338(6215):520–522. doi: 10.1038/338520a0. [DOI] [PubMed] [Google Scholar]
  26. Serwer P. The mechanism of DNA's fractionation during pulsed-field agarose gel electrophoresis: a hypothesis. Appl Theor Electrophor. 1988;1(1):19–22. [PubMed] [Google Scholar]
  27. Slater G. W., Rousseau J., Noolandi J. On the stretching of DNA in the reptation theories of gel electrophoresis. Biopolymers. 1987 Jun;26(6):863–872. doi: 10.1002/bip.360260607. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Slater GW, Noolandi J. New biased-reptation model for charged polymers. Phys Rev Lett. 1985 Oct 7;55(15):1579–1582. doi: 10.1103/PhysRevLett.55.1579. [DOI] [PubMed] [Google Scholar]
  30. Smith C. L., Matsumoto T., Niwa O., Klco S., Fan J. B., Yanagida M., Cantor C. R. An electrophoretic karyotype for Schizosaccharomyces pombe by pulsed field gel electrophoresis. Nucleic Acids Res. 1987 Jun 11;15(11):4481–4489. doi: 10.1093/nar/15.11.4481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Smith S. B., Aldridge P. K., Callis J. B. Observation of individual DNA molecules undergoing gel electrophoresis. Science. 1989 Jan 13;243(4888):203–206. doi: 10.1126/science.2911733. [DOI] [PubMed] [Google Scholar]
  32. Southern E. M., Anand R., Brown W. R., Fletcher D. S. A model for the separation of large DNA molecules by crossed field gel electrophoresis. Nucleic Acids Res. 1987 Aug 11;15(15):5925–5943. doi: 10.1093/nar/15.15.5925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Stellwagen N. C. Effect of pulsed and reversing electric fields on the orientation of linear and supercoiled DNA molecules in agarose gels. Biochemistry. 1988 Aug 23;27(17):6417–6424. doi: 10.1021/bi00417a033. [DOI] [PubMed] [Google Scholar]
  34. Stellwagen N. C. Orientation of DNA molecules in agarose gels by pulsed electric fields. J Biomol Struct Dyn. 1985 Oct;3(2):299–314. doi: 10.1080/07391102.1985.10508418. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. Willis C. E., Willis D. G., Holmquist G. P. An equation for DNA electrophoretic mobility in agarose gels. Appl Theor Electrophor. 1988;1(1):11–18. [PubMed] [Google Scholar]
  37. Zimm BH. Size flucuations can explain anomalous mobility in field-inversion electrophoresis of DNA. Phys Rev Lett. 1988 Dec 26;61(26):2965–2968. doi: 10.1103/PhysRevLett.61.2965. [DOI] [PubMed] [Google Scholar]

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