What type of electrophoresis is best for separating larger fragments of DNA?

Pulsed Field Electrophoresis (PFE) is particularly effective for separating larger DNA fragments, typically those greater than 50 kilobases. This method utilizes alternating electric fields to move DNA through an agarose gel, which helps to resolve the larger molecules more efficiently than traditional gel electrophoresis. The alternating electrical fields allow for better separation by facilitating the linearization of larger DNA fragments and preventing them from becoming entangled.

While polyacrylamide gel electrophoresis can separate smaller fragments of DNA effectively due to its smaller pore size, it is not ideal for larger fragments. Horizontal gel electrophoresis generally refers to agarose gel electrophoresis that may not be suited for the resolution of very large DNA fragments either. Two-dimensional electrophoresis is primarily used for protein separation and does not apply to DNA separation in this context. Thus, Pulsed Field Electrophoresis stands out as the best choice for the separation of larger DNA fragments due to its unique mechanism and capabilities.