The desired fragment is always contaminated with small amount of unexpected fragment, particularly smaller ones.
For example, when I PCR amplified tDimer 2 gene which is about 1.4 kb, the purification pruduct is contaminated with a 0.7 kb fragment. This may because of the tandem repeat of tDimer 2 gene. However,
I found this problem happen a bit frequently when purify other PCR products.
Edited by albatross, 01 September 2009 - 07:43 AM.