Hello everyone, I'm working on DNA cloning and I got some problem for agarose gel electrophoresis after RE digestion.
From the internet, I saw the 100ng of DNA will be shown as a sharp and clean band in electrophoresis. However, I could only see very weak band even I load 1ug of DNA per well. I cut the plasmid with two restriction endonuclease, for 4 hours in 50ul reaction. (buffer types and reaction temperature were perfect for bothe enzyme)
Since I was planning to load 1ug of DNA per well, I put total 2.5ug of DNA and 10U of RE for the reaction tubes. After reaction, I mixed 6x loading dye and load total 24ul of mix in a well. I found two bands at the right sites, but the intensity was too weak. To check if it is a amount problem or not, I loaded same amount of uncut plasmid on the last well. The intensity was good, unlike RE digested samples. Does anyone have an idea what is the problem in my experiment?
(* Target band size was 2.7kb and 1.9kb, I used 1% agarose gel. The gel contains redsafe DNA staining solution. I put 5ul of redsafe for 100ml of agarose gel solution. As I can detect the band of uncut plasmid clearly, I think it is not a problem of gel itslef)
I added a result image. I used 100bp ladder, each band in the marker lane is 3kb, 2kb, 1.5kb and so on. For the first two lanes, I loaded 10ng and 100ng of cut plasmid. In the 3rd and 4th lane, 500ng and 1ug of cut plasmid was loaded. The last lane is uncut plasmid.