Design of a molecular weight analysis system for proteins using sodium dodecyl sulfate-agarose gel

Methods for separating proteins according to molecular weight are usually based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). However, the toxicity of acrylamide and its handling during gel preparation constitute a significant problem. Therefore, we determined the molecular weights of proteins using agarose gel instead of polyacrylamide. We used the Mupid electrophoretic apparatus, because it is small, easy to use, and time-saving. We evaluated different types of agarose and buffer solutions, and parameters such as gel concentration, buffer SDS concentration, and quantity of gel (central thickness). The optimal gel was made from 5ml (central gel thickness 2mm) 4% NuSieve 3:1 agarose. An electrophoresis buffer containing 25mM Tris, 190mM glycine (pH8.3), and 0.1% SDS is optimal for protein separation. With this method, the standard curve was linear for reference proteins in the range of molecular weights from 14.4×103 to 97×103.