Electrophoresis related apparatus, fluorescent stains

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Electrophoresis related apparatus, fluorescent stains

The Biomolecular Research Facility has equipment which may be useful for electrophoretic separations.

  • Bio-Rad GS-800 scanner for Coomassie and silver stained gels, blots and films (self service)
  • Bio-Rad FX fluorescent scanner (core operated)
  • IEF apparatus, Bio-Rad and Amersham and some associated gel apparatus (user operated, unsupported)
  • Bio-Rad Rotofor (user operated, unsupported)

Fluorescent gel scanning

The Bio-Rad FX fluorescent scanner, operated by the core (fee for service) scans gels stained with:
  • Sypro Ruby
  • Pro-Q Diamond phospho-protein stain
  • Cy3, Cy5
  • Pro-Q Emerald glycoprotein stain
  • others excited by lasers with wavelengths of 488 nm, 532 nm, 635 nm, on Bio-Rad list of fluorescent stains


The image files from both scanners can be converted to TIFF format for export. Images of 2-D gels can be analyzed with Bio-Rad PDQuest software, a  time consuming process because of streaks and faint spots amidst other factors.

Fluorescent stains for gels

Fluorescent protein stains like the Sypro series and Deep Purple are alternatives to Coomassie and silver. Advantages and disadvantages are listed below.



Advantages of fluorescent stains

Disadvantages of fluorescent stain


more sensitive
greater dynamic range

not visible by eye


greater dynamic range
fewer chemical interferences
less chance of cross linking reactions preventing MS analysis
less hands on time

not visible by eye
greater time to complete staining
less sensitive

The best known total protein stain is Sypro Ruby from Molecular Probes. This stain may be available from other vendors at a slightly lower price. There are other Sypro stains, which are both less sensitive and less expensive. Some people reuse or dilute Sypro Ruby, although Molecular Probes has data showing that dilution or reuse reduces sensitivity. There are reports of making a stain equivalent to Sypro Ruby, although with less sensitivity; some who have tried their own synthesis have been dissatisfied.

Although the protocols from suppliers suggest only one destain step, we recommend multiple changes of destain solution to avoid having a high background. Note that for the last step, put the gel in water. Some sources advise against using latex gloves with Sypro stained gels because the gloves can contribute to the background. An annoyance of  Sypro Ruby is the presence of speckles cause by precipitation of the dye.

An alternative to Sypro Ruby is Deep Purple stain from GE HealthCare (formerly Amersham). This stain is claimed to be a little more sensitive than Sypro Ruby and free of the speckling problem, although our initial experience shows speckles. Bio-Rad sell Flamingo Pink fluorescent stain which is claimed to be more sensitive than Sypro Ruby.


Fluorescent stains with interesting specificity

There are some novel fluorescent stains available for which visible stains are not available, or have much less sensitivity.

Molecular Probes is the best known supplier of fluorescent protein stains and sells some in packages, which must be used in the specified order. Suitable molecular weight markers may be included to verify that the stain is detecting the specified type of protein.


ProQ-Diamond stain is very selective for phosphoproteins. Some who have used it find more proteins than expected. The phosphoprotein stains must be used before Sypro Ruby for total protein. Molecular Probes suggest using known proteins to establish a ratio of phosphoprotein stain to total protein stain to distinguish between phosphorylated proteins and non-phosphorylated proteins.

Investigators here have used this stain to follow relative phosphorylation of a a few target proteins on 1-D gels, and in another project to compare the extent of phosphorylation of two proteins.

Non-specific staining may be reduced by extensive washing. Background papers are:

Steinberg, T.H., Agnew, B.J., Gee, K.R, Leung, W-Y, Goodman, T, Schulenberg, B., Hendrickson, J. Beechem, J.M., Haugland, R.P., Patton, W.F. Proteomics 2003, 3, 1128–1144

Schulenberg, B, Aggeler R, Beechem J.M.. Capaldi, R.A. and Patton, W.F. (2003) J. Biol. Chem. 278 27251-27255



Molecular Probes sell a fluorescent stain for glycoproteins, using traditional chemistry, but with a fluorescent dye attached. Note that there are two versions of the stain, one requiring illumination with UV light, the other with visible light. The former can be seen on a a UV transilluminator but not the scanner used by the BRF, while the latter stain can be viewed with the BRF fluorescent scanner.

Transmembrane proteins.

Molecular Probes sell a stain selective for transmembrane proteins. They claim that unlike some older stains, it stains transmembrane proteins rather than hydrophobic proteins.