After PFGE I got DNA bands in the Agarose gel. They were observed at normal UV light. But after putting it to the Gel documentation system, the bands were not appear in the gel. Then I re-stain the gel with EtBr. Bands were not there.
Sounds more like a technical problem with you Gel doc System. Wrong filter? Your Gel doc should have normal UV as well.
you have to be careful viewing DNA under UV light. Transilluminators have hard UV light filters on them to remove the very short wavelength uv light which is severely damaging to DNA. Simple UV lamps do not have these filters so may produce light around the 180-200nm range and the dna can be destroyed. If re staining produces no bands then this may have happened. You can also get this effect by leaving a gel on the transilluminator for too long when even the longer wavelength UV light will eventually destroy your sample. You could try examining a used pcr checker gel with your normal UV light and see if this is what is causing the problem. Even transilluninator filters can age badly over the years and allow too much hard UV through into your sample. If your pictures of the gel show good details of the UV lamp bulbs in the transilluminator then the filter may be failing or you may have an incorrect visualisation filter selected on your gel doc
In that case check if ur geldoc working fine? maybe any wire loose or lamp fused??
Maybe ask other labmates if that geldoc working fine? Otherwise I dont see any reason why u could not see bands in geldoc? After re-staining can u see bands normal UV light?? Do have ladder/marker in ur gel it might act as +ve control in both cases.
Dear Saranga Fonse,
In case of normal UV tray or open UV transilluminator , there is only one component like the UV light. But in Gel Documentation system there are several component that work together to make a perfect visualization of a gel and you will find there is several cable need to plug in separately for Camera and whole instrument as well, in case of instrument like Bio-rad Molecular Gel Doc Imager Xr+ .
For each run you need to select the option for satin or dye you have used to satin DNAs in the gel. If you select nothing then your band cant visualizes. So, try with other gels to find out the problem, sometimes you need to validate the focus and distance, when you made any filter or component changed.
So, make sure that you watching the gel but missing the DNA Band. Then you can find out whats going on and the problems also
So Good Luck !
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