SECTION 9-2 - Analysis of DNA Fragments After Enzymatic Cleavage: Agarose Gel Electrophoresis

Abstract

This chapter discusses the analysis of DNA fragments after enzymatic cleavage. The method describes some basic principles of agarose gel electrophoresis performed on a larger scale. The larger-scale gel allows for longer electrophoresis and a better resolution of fragments and can also resolve fragments from preparative digests of plasmids for making DNA probes. These gels are well suited for Southern blotting. Their disadvantage compared to minigels is the longer electrophoretic time required. The time required to carry out the procedure for analyzing the DNA fragment is a minimum of four hours. The procedure requires a horizontal agarose gel electrophoresis apparatus, some well-forming combs, and gel mold. The chapter also lists the reagents that are required in this method, such as ethidium bromide, a 40 × TAE buffer, and a gel loading solution. RE digest of the DNA samples is prepared in advance, and progress of digestion with a minigel is also checked side by side.