Traditional methods of identifying molecular size and extracting DNA fragments in molecular cloning involve expensive procedures and commercial kits. This study presents a cost-effective alternative using a novel agarose-silica gel matrix. The mixture, comprising 0.5% agarose and silica gel in 1 x TAE buffer, was used for DNA separation and extraction without commercial kits. The resulting gel was clear, and DNA bands were well-defined, with a 90% recovery rate. This purified DNA is suitable for various applications. The silica-based gel is an economical, one-step solution, costing only a fraction of traditional methods.