Ever heard not of Prime Dimers but Primer Multimers? - (Mar/05/2007 )

One of our students is facing a primer problem. She was always getting a double band at roughly 300 bp (even in the water control with only forward primer). We thought, it would be a contamination issue and ordered new primers.
And now, she is getting the same bands with the new stock! The water can't be contaminated since the band didn't show up in a neg. control with a different pair of primers...

So now I was having a look at the primer and am thinking... Are Multimer constructs possible? What would it look like in a gel? (More like a smear or like our double band?)

Theoretically, this construct (and quite a few others) would be possible:

...ATHGATGARAARTGGTTC..ATHGATGARAARTGGTTC..ATHGATGARAARTGGTTC..ATHGATGARAARTGGTT
...........|||....:::..||||||..|||....:::..||||||..|||....:::..||||||:::..::..||
...........CTTGGTRAARAGTAGHTA..CTTGGTRAARAGTAGHTA..CTTGGTRAARAGTAGHTACTTGGTRAARA

(The dots are spaces)

Do I live in dreamland or can this occur in reality as well?

Tony

I think even if you could have primer multimers, you would be battling to get to 300bp worth!
Perhaps another one of your PCR reagents (not the water) is contaminated...