What type of gel is typically used for Southern Blot analysis?

Agarose gel is typically used for Southern Blot analysis because of its favorable properties for separating larger DNA fragments. In Southern Blotting, the goal is to detect specific DNA sequences within a complex mixture, and agarose gel electrophoresis provides an effective way to separate these fragments based on size. Agarose can be easily prepared and offers a wide range of gel concentrations, allowing for the resolution of various DNA sizes, which is essential for accurately analyzing and identifying DNA fragments during the blotting process.

In contrast, polyacrylamide gels are more commonly employed for the separation of smaller nucleic acids or proteins due to their higher resolution capabilities but are not ideal for larger DNA fragments often analyzed in Southern Blots. Cellulose acetate gels are less commonly used for this type of analysis as well, primarily because they do not provide the same level of resolution for larger DNA fragments as agarose gels. The concept of a combined gel is not standard in Southern Blot methodologies, making agarose the clear choice for this technique.