Abstract
Agarose-gel electrophoresis is used to separate DNA molecules on the basis of size and shape (1-4). Since DNA is negatively charged, the charge-to-mass ratio is constant. Thus, migration through agarose is inversely proportional to the size of the molecule. However, the electrophoretic mobility of DNA in agarose is also affected by the shape of the DNA, the pore size of the matrix (agarose concentration), temperature, the ionic strength of the electrophoresis buffer, the applied voltage/field strength, and the presence of intercalators (reviewed in 5,6).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Thorne, H. V. (1967) Electrophoretic characterization and fractionation of polyoma virus DNA. J. Mol. Biol. 24, 203–211.
Keller, W. (1975) Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc. Natl. Acad. Sci. USA 72, 4876–4880.
Depew, D. E. and Wang, J. C. (1975) Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. USA 72, 4275–4279.
Bates, A. D. and Maxwell, A. (1993) DNA Topology. Oxford University Press, New York.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
Voytas, D. (1988) Resolution and recovery of large DNA fragments, in Current Protocols in Molecular Biology, vol. 1 (Ausubel, F. M., Brent, R., Kingston, R. E., (eds.) Wiley, NY, pp. 2.5.1–2.5.9.
Fisher, M. P. and Dingman, C. W. (1971) Role of molecular conformation in determining the electrophoretic properties of polynucleotides in agarose-acrylamide composite gels. Biochemistry 10, 1895–1899.
Aaij, C. and Borst, P. (1972) The gel electrophoresis of DNA. Biochim. Biophys. Acta 269, 192–200.
Helling, R. B., Goodman, H. M., and Boyer, H. W. (1974) Analysis of endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis. J. Virol. 14, 1235–1244.
Wang, J. C. (1974) The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J. Mol. Biol. 89, 783–801.
Pulleyblank, D. E. and Morgan, A. R. (1975) The sense of naturally occurring superhelices and the unwinding angle of intercalated ethidium. J. Mol. Biol. 91, 1–13.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Humana Press Inc.
About this protocol
Cite this protocol
Bjornsti, MA., Megonigal, M.D. (1999). Resolution of DNA Molecules by One-Dimensional Agarose-Gel Electrophoresis. In: Bjornsti, MA., Osheroff, N. (eds) DNA Topoisomerase Protocols. Methods in Molecular Biology, vol 94. Humana, Totowa, NJ. https://doi.org/10.1385/1-59259-259-7:9
Download citation
DOI: https://doi.org/10.1385/1-59259-259-7:9
Published:
Publisher Name: Humana, Totowa, NJ
Print ISBN: 978-0-89603-444-0
Online ISBN: 978-1-59259-259-3
eBook Packages: Springer Protocols