Usually agarose gel electrophoresis is performed at constant low voltage (5 – 10 V/cm). High voltage results in excessive heat generation due to current, leading to distorted bands and low resolution (Sanderson et al., 2014).
The following tips can help minimize excessive heat generation by reducing the current and you can run the gel at high voltage (20 – 25 V/cm). This reduces the electrophoresis time considerably (≈ 3 fold) and also minimizes diffusion of DNA molecules that results in better resolution especially of low-molecular weight DNA fragments.
- Use electrophoresis buffer without EDTA (e.g., electrophoresis buffer containing Tris and borate, no EDTA) (Sanderson et al., 2014).
- Do not overfill electrophoresis buffer (2 mm height above the gel top surface) (Sanderson et al., 2014).
- Prepare thin gel
- Do not use low melting agarose
Sanderson et al., 2014. Modification of gel architecture and TBE/TAE buffer composition to minimize heating during agarose gel electrophoresis. Anal Biochem. 454, 44-52. PMID-24637158; Full-text links: sciencedirect, PMC4021863 (download PDF)