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Strange mobility behavior of PCR products on agarose gel


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#1 postdoc

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Posted 23 September 2004 - 12:49 AM

I am doing ChIP (chromatin immunoprecipitation) PCR which is not so easy to get amplicons, so I chose Gelstar which boasts of higher sensitivity than EB for gel staining. After running the gel which was prestained with GelStart, I found my PCR products were about 50 bp less than expected. So I thought my PCR failed and repeated twice with the same results. I then suspected that my marker was bad so I reprepared my marker and got the same results. As a last resort, I pre-stained my gel with EB, to my astonishment, the PCR products I got WAS the right size on EB stained gel. How come? In addition, some weak bands which didn't show up on Gelstar stained gel could be seen on EB gel!

Has anyone else experienced this?

#2 maarten

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Posted 24 September 2004 - 06:13 AM

check the graph on http://www.clarechem...com/gelstar.htm
here you see differences in migration distances with and without EB. this explains the smaller product you got than expected.

#3 postdoc

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Posted 24 September 2004 - 08:22 AM

ya, I see the difference too. Then why don't they indicate this fact and why doesn't the gelstar affect the migration of marker and PCR product equally?




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