Hi all, just a small question.
I run DNA gel using NEB 6x DNA loading dye as the loading dye and Gel red as DNA stain. Sometimes when I have very heavy DNA bands (e.g., after PCR) I can even see the red DNA bands (a bit faint though) directly in the agarose gel without using UV light. What could cause this? As far as I know, the loading dye serves to track the electrophoresis progress and precipitate the DNA sample into wells but has no ability to bind to DNA, while the DNA stain does help visualise DNA but is only visible under UV (at least Gel red requires it). So I am a bit puzzled here.
Gelred has a second longer wavelength absorption of around 500nm as well as the stronger absorption maximum around 280nm and an emission spectrum at around 600nm. This makes the blue part of the visible spectrum in normal light conditions capable of exciting the gel red which then produces an emission also in the visible range
Fully agreed with Paul Rutland. This is a very interesting phenomenon that occurs because GelRed has two emission maxima; one at ~ 280nm (in the UV range) and the other one at ~ 600 nm (near-visible range). That is why one can visualize faint bands of DNA with naked eyes too, Jian Wang.
Also I forgot to mention that even in England in winter there is a small amount of UV in the ambient light so this may contribute to seeing a very faint fluorescence of a strongly amplified product
You can see the same phenomenon with EtBr whenever the DNA quantity is high. With EtBr, you are not observing fluorescence. Instead, you are seeing the red light is reflected from the ambient light source. It is the same phenomenon that is observed with the dry powder form of EtBr. If GelRed is doing the same thing, it will be easier to see the bands with a white background behind the gel. If it is fluorescence, it will be easier to see with a black background. Even fluorescent dyes can have a color independent of fluorescence.
Thank you Jian Wang for the interesting question
many thanks Paul Rutland for your nice answer
Hello, is that the same with SYBR Safe? We also observed bands without UV light on our agarose gel.
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