Stutter Bands

[David Groth]

Can anyone suggest a cure for stutter bands when analysing 
dinucleotide microsatellites by PCR.  We are developing several 
microsatellites for use in population studies in a fresh water 
crustacean.  The loci identified so far all have very large repeat 
regions eg CA(50-70 repeats). These are usually perfect although they 
can be complex.  

When we do PCR we get 5-8 bands displaced 2bp in a ladder formation.  
This is a greater problem than I have seen in other species eg human.  
We have tried using DMSO, increasing the annealing temp, Taq gold 
without removing the problem. I have thought of using deaza-GTP 
instead of dGTP.  Has anyone tried this?

Dr David Groth
School of Biomedical Sciences
Curtin University
GPO Box U1987
Perth Western Australia
igrothd at info.curtin.edu.au