I agree primer-dimer at the bottom of the gel. Bad design isn't the only reason to see them though. They are often seen with lack of template. So even though dimer formation is not favourable in the abscence of anything else to bind to the stick to themselves.
Zeb
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Cathal Garvey <cathalgarvey@gmail.com> wrote:
Those fuzzy bands at the bottom, if they are not loading dye, are 'primer dimers'. You get them when your primers are able to prime one another or self-prime, causing lots of wasted primer and 'distracting' the the reaction from the real product.
One way to avoid this is to carefully avoid primers which can prime one another. Another way is to raise the annealing temperature step in your reaction to somewhere closer to the primer melting temperature, so that it's less likely that only-partially matching DNA will bond.
pcrbro <princeofnam@gmail.com> wrote:
>
>
>The following is my 1% PCR gel run.
>
>As you can see the products have strangely run all the way until the
>end. The products also look to be further than the dye looks to be on
>the
>gel itself. I'm relatively new to PCR and not completely sure how to
>trouble shoot this. The first row is a 1 kb ladder and the third row
>is a
>control. The expected product should have had a product length of 611.
> I
>ran the PCR at 4 annealing temperatures 5 C below the Tm. Does anyone
>know
>where I should start in determining what may have gone wrong with my
>PCR/gel run?
>
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