Electrophoresis Of DNA
What is it? DNA fragments have a constant charge/length ratio due to the net negative charge of the phosphate backbone. Therefore, DNA migrates toward the (+) electrode. The rate of migration of linear DNA mainly depends on the pore size of the gel and length of the DNA. During electrophoresis DNA molecules seem to snake through the pores in the gel head first. As the pore size decreases (i.e. the agarose or acrylamide concentration increases) it is harder for longer DNA molecules to orient properly to snake through the pores: smaller DNA fragments snake through the pores easier and hence migrate faster. Thus, the rate of migration of linear double stranded DNA is inversely proportional to the log of its molecular weight. By using gels with different concentrations of agarose or acrylamide, a wide range of DNA fragment sizes can be separated. The shape of the DNA molecule also affects its ability to snake through the pores in the gel. In general features that make the DNA less flexible or less compact slow the migration in a gel. The rate of migration of different forms of plasmid DNA is usually: supercoiled > linear > nicked circles. In addition, secondary structure and bends in linear DNA may affect the rate of migration.Added By: Kayla
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