Many of the procedures used in recombinant DNA technology rely on a researcher's ability to purify a DNA fragment of interest. In an important procedure called agarose gel electrophoresis, DNA fragments are separated by size as they move through a gel matrix. In this animation, we will examine how gel electrophoresis is performed and then describe a method called blotting, which allows researchers to identify the DNA fragments of interest along the length of a gel.
In gel electrophoresis, charged molecules migrate through a matrix in an electric field. DNA molecules are negatively charged along their length, so they migrate toward the positive electrode. Within an agarose matrix, the DNA molecules become separated according to size during their travel—the pores in the agarose gel allow short DNA molecules to snake through easily, but cause more friction for the longer DNA molecules, slowing their progress. Therefore, the shorter the DNA fragment, the quicker it can travel through an agarose gel.
The electrophoresis procedure can be a starting point for additional identification and isolation of the DNA fragments. For example, the DNA fragments within an agarose gel can be transferred to a solid support, such as a nylon filter—making a blot of the DNA fragments in the gel—for further analysis. DNA fragments of interest can also be sliced out of a gel and used in recombinant DNA applications.
Textbook Reference: Concept 13.1 Recombinant DNA Can Be Made in the Laboratory