Does gel thickness affect light intensity of the DNA? - (Jul/14/2006 )
When you take a photo of your gel, does the intensity of the light of your DNA bands depends not only on DNA amount but also the thickness of your gel?
Your DNA is in a vertical colum in the gel uniformily distributed along the colum. Then the light may be partly blocked somehow for the gel or the DNA below.
What do you think?
For agarose gel electrophoresis, I prefer thin gels which give me less white background so DNA band can stand out. So I make gels just thick enough for wells to hold the desired amount of sample.
Too thick can cause problem such as increase band width. Many things can go wrong: excessive heat generation, band not moving vertically synchronized (DNA located on the top and the bottom not moving at the same speed), etc.
Thanks a lot.
From now on, I will try to maje thinner gels and uniform between big tanks and small tanks.