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I'm working with a GFP-tagged protein and am routinely using a fluorescence imager (GE Typhoon) and a standard optical scanner to capture fluorescent and absorption images, respectively, of my SDS-PAGE gels. The Typhoon supports multiple channels, so is there some way that I can scan for the two on the same device (GFP + total protein)? I assume I can't do absorption on a fluorescence scanner..

I could manually register the two images, but it would be laborious as they are at different resolutions, slightly different rotations, and the gel can stretch ever-so-slightly when placing it on the platens.

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Can you explain how you get actual fluorescence images from your gels in which GFP is denatured? –  leonardo Oct 19 '12 at 12:06
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@leonardo the standard running/gel/loading buffers do not seem to be so aggressive as to destroy (all) the GFP; it may be denatured in the loading dye, but when washed out into the gel buffer it seems to recover. On the other hand, putting the gel into destain or fixing solution is very effective at obliterating the fluorescence. –  Nick T Oct 21 '12 at 18:13
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Coomassie blue fluoresces in infrared when bound to protein, so if your reader has the appropriate filter set, it should be possible.

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