RNA electrophoresis

Curators

Anyone should feel free to add themselves as a curator for this consensus protocol. You do not need to be a curator in order to contribute.

Abstract

Electrophoresis permits assessment of RNA by size and amount. In general, electrophoresis of RNA is done as a step prior to Northern analysis.

Materials

List everything necessary to perform the protocol here. Include all information about suppliers, ordering details, etc. Links to the suppliers' page on that material are also appropriate and encouraged. Please be aware that users of this protocol may not be working in the same country as you.

Reagents

Biological resources e.g. cell lines, buffers (link to a method for making them), enzymes, chemicals, kits, etc.

Equipment

Any equipment used to perform the protocol (link to a method for using them).

Procedure

A step by step guide to the experimental procedure.

Critical steps

• RNA secondary structure can strongly impact how RNA electrophoreses through the gel. Therefore, electrophoresis of RNA is usually done under denaturing conditions.
• The choice of gel matrix depends on the size range of RNAs to be analyzed. Use 3-20% polyacrylamide for RNAs < 500bp. For RNAs between 0.5-8.0 kb, use 1.5% denaturing agarose gel. For a larger size range (typically necessary for Northern analysis), use 1.0-1.2% denaturing agarose gel.

Troubleshooting

• RNases are the biggest problem in RNA work. Use proper precautions.
• The electrophoresis apparatus can be contaminated with RNases. At a minimum, soak comb in solution of 3% H₂O₂ or 0.5% SDS, 50mM EDTA and then rinse with large amounts of autoclaved H₂O.

Notes

• For best resolution, pour gels as thin as possible (0.5-0.75cm is typical especially for efficient blotting later) and run at low voltage. [1]
• Tom Knight strongly recommends using glyoxal denaturation rather than formaldehyde denaturation due to the safety issues of formaldehyde.
• Many protocols call for recirculation of buffer during electrophoresis of glyoxylated RNA. However, recent electrophoresis buffers (like 10X BPTE electrophoresis buffer) are more stable and do not require this.

References

1. ISBN:0-12-249695-7

2. Molecular Cloning: Separation of RNA According to Size: Electrophoresis of Glyoxylated RNA through Agarose Gels

3. Molecular Cloning: Separation of RNA According to Size: Electrophoresis of RNA through Agarose Gels Containing Formaldehyde

4. Northern Hybridization of RNA Denatured by Glyoxal/DMSO Treatment

Specific Protocols

1. Endy:Northern Blot, 32P End-Labeled Probes#Process the Gel (3-4 hours)
2. Knight:RNA electrophoresis