Dinucleotide Repeat PCR

[berschic at convex.rz.uni-duesseldorf.de]

One possible reason for producing shorter fragments is that primers are not
clean and also shorter primer fragments are in the sample. These products
could be seen if you are using labeled samples.
I worked with STR (4 bp) and I often got "extra" bands greater than 
the product if heterozygous samples were amplified. This is due to
heteroduplex structures. You can check this by using two homozygous samples
of different alleles (these should not have these extra bands) mix and amplify 
them. Then heteroduplex structures could be detected. For more information about 
this read:
PCR Methds. & Appl. Vol. 3, pp. 7-12, 1993
PCR Methds. & Appl. Vol. 3, pp. 112-116, 1993

Hope this helps
Peter (berschic at convex.rz.uni-duesseldorf.de)