POTENTIAL USE OF SEAWEED AGAR AS A SUBSTITUTE FOR AGAROSE GEL IN DNA ELECTROPHORESIS

Abstract

Polymerase Chain Reaction (PCR) has become the gold standard test in molecular diagnostics owing to its high sensitivity. The results of DNA amplification from PCR were visualised using gel agarose electrophoresis. However, agarose is expensive and creates an obstacle for molecular examination in Indonesia. This means that not all health facilities in Indonesia can always have a ready stock of agarose, so a replacement for agarose with a good enough result for visualisation with a cheaper one is needed. This study aimed to evaluate the potential use of seaweed agar as a substitute for agarose, and to optimise the optimal conditions for seaweed agar in DNA electrophoresis. This study used a true-experimental research method with a post-test-only control group design. We optimised several parameters of seaweed agar (Swallow brand), including seaweed agar concentration, TAE buffer concentration, voltage variations, and amplicon volume. All electrophoresis results were compared with those of the control. This study shows that seaweed agar can be used as a substitute for commercial agarose gel in DNA electrophoresis under the best conditions, such as using a 2% concentration of seaweed agar, 1x concentration of TAE buffer, 80 volts for 1 h, and 12 µL of DNA amplicons. The limitation of using seaweed agar is that the size of the DNA that can be detected is less than 700 bp.