RNA visualization

From Molecular Biology Wiki

RNA or ribonucleic acid may be visualized on agarose gels or polyacrilamide gels using ethidium bromide staining or SYBR dyes which are much safer.

See also RNA Gel Electrophoresis and Gel electrophoresis.

Ethidium Bromide Staining of RNA Agarose Gels

Ethidium bromide (EtBr) is added to the gels not the running buffer. This is a safety precaution as ethidium bromide is mutagenic.

Add 5ul from 10mg/ml stock of EtBr per 100 mL of 1X (or 0.5X depending on your apparatus) TAE or TBE buffer.

SYBR Visualization of RNA

If you are using SYBR Green, SYBR Orange or other SYBR staining you usually incubate your agarose gel after running in 5ul of SYBR with 50mL of 1X TAE or TBE buffer for 5-20 minutes. See manufacturer's instructions for more information!

RNA Visualization References

1. Eykholt, R., et al. (2000). Direct imaging of northern blots on an optical scanner using ethidium bromide. BioTechniques 28(5), 864-870.
2. Spiess, Andrej-Nikolai and Ivell, Richard, (1999). Normalization of RNA hybridization signals by means of SYBR Green II-stained 28S or 18S ribosomal RNA and a phosphor imager. BioTechniques 26(1) 46-50.