Electrophoresis of PCR products

Scott Coutts scott.coutts at med.monash.edu.au
Sat Dec 16 01:38:26 EST 2000

Probably genomic DNA if it stays in the well and you're running it on a
normal (TAE/TBE etc) agarose gel. You can get a smeary looking lane if
you've used too much template (I assume you are using genomic DNA as
template) and that would account for the fact that it is so apparent in
the wells. How much are you using for each reaction?

Damien wrote:
> Hello,
> I am looking for help about a problem I encounter often with agarose
> electrophoresis of PCR products: in some lanes, there is a strong signal at
> the location of the well, and a continuous smear through the whole length of
> the gel, with no visible band. It seems like most of the DNA is still inside
> the well and has not migrated through the gel. The marker lane is fine (all
> bands are apparent, no smear is visible, and the well is empty).
> How can I interpret this? Is it just genomic DNA that is too long to go
> through the gel (I use 1.5 to 2% agarose)? Or can it be some PCR product
> that is in a form (precipitated?) that prevents it from entering the gel?
> Thank you in advance for your help. Please copy by e-mail to
> marsicd at email.uah.edu
> Damien Marsic

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