Gel Electrophoresis

Gel electrophoresis is a technique used to separate charged molecules whether they are proteins or DNA fragments. The molecules of interest are placed on a gel filter made up of polyacrylamide or agarose or other appropriate substrate. When placed into an electrical field, these charged molecules will migrate toward the appropriate pole. The rate of migration depends on the charge, the charge density, size and shape of the molecule and density of the gel. The process of preparing and running a gel can be found here.

• Will a molecule migrate faster if it is large or small? Why?
• Will a molecule migrate faster if the molecule is globular or fibrous? Why?
• Will a molecule migrate faster in a 2% or 4% gel? Why?

Tracking dyes, radioisotopes and fluorescent markers can be used to monitor migration patterns. Electrophoresis can be done in one or two dimensions.

• When do you think you might use two dimensional gel electrophoresis to analyze molecules?

It has been noted that DNA or RNA fragments can be precisely separated even if they only differ by one nucleotide.

• Design an experiment where you could use gel electrophoresis to determine the nucleotide sequence of a DNA fragment.