[9] Gel electrophoresis of restriction fragments

Gel electrophoresis of restriction fragments of deoxyribonucleic acid (DNA) in agarose or polyacrylamide gels is discussed, which is often useful to identify a particular sequence in the DNA fragments separated by gel electrophoreis.

Abstract

This chapter discusses gel electrophoresis of restriction fragments. There are many designs of an apparatus that can be used for the electrophoresis of deoxyribonucleic acid (DNA) in agarose or polyacrylamide gels. Some of them are very easy to make from glass or perspex, and a simple apparatus can give excellent results. It is often useful to identify a particular sequence in the DNA fragments separated by gel electrophoresis. At present, there are a number of methods available to achieve this purpose. Restriction fragments that bind to a protein may be separated as a complex by filtration through a membrane filter. Radioactive restriction fragments that hybridize to a particular ribonucleic acid (RNA) molecule can be measured by gel electrophoresis after nonhybridized parts of the fragments are digested with the single-strand-specific nuclease S1. Alternatively, nonradioactive restriction fragments, after they are separated by agarose gel electrophoresis, can be probed with radioactive RNA or DNA to mark the positions of specific sequences.