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. 1994 Sep 25;22(19):4002–4008. doi: 10.1093/nar/22.19.4002

Capillary electrophoresis as a technique to analyze sequence-induced anomalously migrating DNA fragments.

H M Wenz 1
PMCID: PMC308402  PMID: 7937124

Abstract

Sequence-induced anomalous migration of double-stranded (ds) DNA in native gel electrophoresis is a well known phenomenon. The retardation of migration is more obvious in polyacrylamide compared with agarose gels, and is greatly affected by the concentration of the gel and the temperature. This anomalous migration results in a difference between calculated and actual sizes of the affected DNA fragments. A low viscosity polymer solution (DNA Fragment Analysis Reagent) under investigation for use in dsDNA analysis by capillary electrophoresis is shown to be useful for the visualization of anomalies in migration of dsDNA fragments. Comparable with traditional slab gel systems, the retardation effect, indicative of bent or curved DNA, is strongly dependent on polymer concentration and separation temperature. These dependencies have implications on the accurate sizing of dsDNA fragments with unknown sequences and secondary structures.

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Selected References

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  1. Bianchi N., Mischiati C., Feriotto G., Gambari R. Polymerase-chain reaction: analysis of DNA/DNA hybridization by capillary electrophoresis. Nucleic Acids Res. 1993 Jul 25;21(15):3595–3596. doi: 10.1093/nar/21.15.3595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bocek P., Chrambach A. Capillary electrophoresis of DNA in agarose solutions at 40 degrees C. Electrophoresis. 1991 Dec;12(12):1059–1061. doi: 10.1002/elps.1150121212. [DOI] [PubMed] [Google Scholar]
  3. Cohen A. S., Najarian D. R., Paulus A., Guttman A., Smith J. A., Karger B. L. Rapid separation and purification of oligonucleotides by high-performance capillary gel electrophoresis. Proc Natl Acad Sci U S A. 1988 Dec;85(24):9660–9663. doi: 10.1073/pnas.85.24.9660. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Crothers D. M., Drak J. Global features of DNA structure by comparative gel electrophoresis. Methods Enzymol. 1992;212:46–71. doi: 10.1016/0076-6879(92)12005-b. [DOI] [PubMed] [Google Scholar]
  5. Diekmann S. Analyzing DNA curvature in polyacrylamide gels. Methods Enzymol. 1992;212:30–46. doi: 10.1016/0076-6879(92)12004-a. [DOI] [PubMed] [Google Scholar]
  6. Hagerman P. J. Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry. 1985 Dec 3;24(25):7033–7037. doi: 10.1021/bi00346a001. [DOI] [PubMed] [Google Scholar]
  7. Hagerman P. J. Sequence-directed curvature of DNA. Annu Rev Biochem. 1990;59:755–781. doi: 10.1146/annurev.bi.59.070190.003543. [DOI] [PubMed] [Google Scholar]
  8. Heiger D. N., Cohen A. S., Karger B. L. Separation of DNA restriction fragments by high performance capillary electrophoresis with low and zero crosslinked polyacrylamide using continuous and pulsed electric fields. J Chromatogr. 1990 Sep 7;516(1):33–48. doi: 10.1016/s0021-9673(01)90202-x. [DOI] [PubMed] [Google Scholar]
  9. Hsieh C. H., Wu M., Yang J. M. The sequence-directed bent DNA detected in the replication origin of Chlamydomonas reinhardtii chloroplast DNA is important for the replication function. Mol Gen Genet. 1991 Jan;225(1):25–32. doi: 10.1007/BF00282638. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Maschke H. E., Frenz J., Belenkii A., Karger B. L., Hancock W. S. Ultrasensitive plasmid mapping by high performance capillary electrophoresis. Electrophoresis. 1993 May-Jun;14(5-6):509–514. doi: 10.1002/elps.1150140178. [DOI] [PubMed] [Google Scholar]
  13. Noll M. Internal structure of the nucleosome: DNA folding in the conserved 140-base-pair core particle. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 1):77–85. doi: 10.1101/sqb.1978.042.01.009. [DOI] [PubMed] [Google Scholar]
  14. Paulus A., Hüsken D. DNA digest analysis with capillary electrophoresis. Electrophoresis. 1993 Jan-Feb;14(1-2):27–35. doi: 10.1002/elps.1150140106. [DOI] [PubMed] [Google Scholar]
  15. Ryder K., Silver S., DeLucia A. L., Fanning E., Tegtmeyer P. An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen. Cell. 1986 Mar 14;44(5):719–725. doi: 10.1016/0092-8674(86)90838-x. [DOI] [PubMed] [Google Scholar]
  16. Ryder K., Vakalopoulou E., Mertz R., Mastrangelo I., Hough P., Tegtmeyer P., Fanning E. Seventeen base pairs of region I encode a novel tripartite binding signal for SV40 T antigen. Cell. 1985 Sep;42(2):539–548. doi: 10.1016/0092-8674(85)90111-4. [DOI] [PubMed] [Google Scholar]
  17. Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
  18. Schwartz H. E., Ulfelder K., Sunzeri F. J., Busch M. P., Brownlee R. G. Analysis of DNA restriction fragments and polymerase chain reaction products towards detection of the AIDS (HIV-1) virus in blood. J Chromatogr. 1991 Oct 18;559(1-2):267–283. doi: 10.1016/0021-9673(91)80077-t. [DOI] [PubMed] [Google Scholar]
  19. Schwartz H. E., Ulfelder K., Sunzeri F. J., Busch M. P., Brownlee R. G. Analysis of DNA restriction fragments and polymerase chain reaction products towards detection of the AIDS (HIV-1) virus in blood. J Chromatogr. 1991 Oct 18;559(1-2):267–283. doi: 10.1016/0021-9673(91)80077-t. [DOI] [PubMed] [Google Scholar]
  20. Stellwagen N. C. Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels. Biochemistry. 1983 Dec 20;22(26):6186–6193. doi: 10.1021/bi00295a023. [DOI] [PubMed] [Google Scholar]
  21. Ulfelder K. J., Schwartz H. E., Hall J. M., Sunzeri F. J. Restriction fragment length polymorphism analysis of ERBB2 oncogene by capillary electrophoresis. Anal Biochem. 1992 Feb 1;200(2):260–267. doi: 10.1016/0003-2697(92)90463-h. [DOI] [PubMed] [Google Scholar]
  22. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]

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