RS 09:10, 27 August 2007 (EDT): At what annealing temperature did you do this expt? Presumably, increasing the annealing temperature during PCR should mitigate this effect.
Sam 13:34, 28 August 2007 (EDT): I did a gradient PCR to see if increasing the annealing temperature would help. The results of it are here and are now linked from the first paragraph.