Separating PCR products on agarose gel with similar bp length

Peter Ellis via (by pjie2 from
Fri Dec 4 17:24:55 EST 2009

umwong25 from wrote:
> Hi,
> I am trying to separate 745bp, 646bp, and 655bp fragments on an agarose 
> gel. I've separated the 745bp fragment but the other two fragments are 
> not separating on a 2.5% agarose gel, running at 55V for 3.5 hours. I 
> also want a crisp band because I am planning to cut these fragments out 
> and extract the DNA for sequencing. Any suggestions?

Would it be simpler to clone the mixture and then just sequence half a 
dozen clones until you get the right one?  Or is the band you want much 
weaker than the others?


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