Oligonucleotide VisualizationThis is a question asked quite a bit, most recently (late September, 1995) in the bionet.molbio.methds-reagnts newsgroup. Here are two methods, and who submitted them.
UV ShadowingElectrophorese the oligo via PAGE. Place the gel on a piece of saran wrap on an X-ray cassette intensifying screen (or a thin-layer chromatography plate). Then illuminate with a hand-held UV light source. The oligo absorbs the UV, preventing it reaching the screen. Where there is no oligo, the screen fluoresces, so the DNA appears as a black band. This also works if you use parafilm instead of the intensifying screen, but at about 10% efficiency.
From: email@example.com (Brian Grimwade)
Subject: Re: Oligonucleotide staining
Date: Tue, 26 Sep 95 19:59:00 GMT
Organization: CuraGen Corporation
Methylene Blue StainingRun the oligo into a mini PAGE and when finished, soak the gel in a soln of 0.0002% Methylene Blue and 0.1X TBE. Find something to do for 4 hours like growing your other stuff and reading a journal. Come back and walla! Bands appear. Cut out the bands and do your usual elution procedure, desalt.