Knight:RNA electrophoresis/Denaturing

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Electrophoresis permits assessment of RNA by size and amount. In general, electrophoresis of RNA is done as a step prior to Northern analysis. However, this protocol is for visualizing the RNA in the gel.


  • 10X BPTE electrophoresis buffer (The final pH of this 10x buffer is ~6.5.)
    • 100 mM PIPES
    • 300 mM Bis-Tris
    • 10 mM EDTA
  • HPLC grade or better DMSO
  • Glyoxal
    • Commercially available stock solutions of glyoxal contain both hydrated forms of glyoxal and oxidation products that can degrade RNA. These must be removed.
  • Glyoxal reaction mixture (divide into small aliquots and store at -70°C)
    • 6mL DMSO
    • 2mL deionized glyoxal
    • 1.2mL of 10X BPTE electrophoresis buffer
    • 0.6mL of 80% glycerol
  • RNA gel loading buffer
  • RNAse free water (make lots for rinsing glassware and electrophoresis chambers)
    • Add DEPC to final concentration of 0.1%.
    • Incubate 1hr at 37°C.
    • Autoclave for 15 mins at 15 psi.
  • SYBR Gold


Make up BPTE electrophoresis buffer

  1. Prepare by adding the following to 90 ml of distilled H2O
    • 3 g of PIPES (free acid)
    • 6 g of Bis-Tris (free base)
    • 2 ml of 0.5 M EDTA
  2. Treat the solution with final concentration of 0.1% DEPC for 1 hour at 37°C
  3. Autoclave.



  1. Molecular Cloning: Separation of RNA According to Size: Electrophoresis of Glyoxylated RNA through Agarose Gels [MolecularCloning]