Gel smiling is often caused by uneven heating of your gel, often because you’re running at too high of voltage.
Tips to avoid it:
- run at a lower voltage
- use a buffer with lower electrolyte concentrations (e.g. 0.5X TBE instead of 1X or one of the newer Tris-less buffers like sodium borate (SB))
- load 1X buffer in your empty lanes
- pre-run gels
- use a metal plate to even out heat distribution
- run in cold room or use ice pack in gel box
- make sure your buffer is well-mixed
- make sure your inner buffer chamber isn’t leaking
- wash out gel wells (especially for urea-PAGE)
I don’t have time to write text, but here are some resources:
History and principles of conductive media for standard DNA electrophoresis (2004) Jonathan R. Brody & Scott E. Kern, Analytical Biochemistry https://doi.org/10.1016/j.ab.2004.05.054
Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis (2018) Jonathan R. Brody & Scott E. Kern, BioTechniques https://doi.org/10.2144/04362BM02
Top 10 Fun Facts for DNA Electrophoresis, Reproduced from Life Technologies, Inc., Shanta Dube: https://bio.davidson.edu/courses/Molbio/tips/funDNAgel.html
Constant Current or Voltage in SDS-PAGE: The Great Debate, Zandile Nare, BiteSize Bio, April 15, 2021 https://bitesizebio.com/51744/constant-current-or-voltage-in-sds-page/#:~:text=An%20electric%20current%20can%20separate,base%20is%20around%20500%20Da
Modification of gel architecture and TBE/TAE buffer composition to minimize heating during agarose gel electrophoresis. (2014) Sanderson, B. A., Araki, N., Lilley, J. L., Guerrero, G., & Lewis, L. K. Analytical biochemistry, 454, 44–52. https://doi.org/10.1016/j.ab.2014.03.003
more on nucleic acid PAGE: blog form: http://bit.ly/ureapage ; YouTube: https://youtu.be/MHJqnur6yqk
more on agarose gel electrophoresis: http://bit.ly/agarosegelrunning
more on SDS-PAGE: http://bit.ly/sdspageruler
