PRIMERS

[Patrick HJ Falckh]

If a single primer is producing product then it is functioning as both 
an unstream and downstream primer (or forward and reverse primer); the 
problem is with your design of the primer.  A cheap way to check where 
your primer may be binding is to have the sequence of your expected 
fragment in a word processing package (like MS Word) and then use the 
'Find' option to search the sequence using a small number of the bases 
from the 3' end of the primer eg 5'> ....ATgCtggCTAC>3' then have 'Find' 
look for CTAC sites (and CATC sites for the reverse phase).... something 
like looking for restriction enzyme cuts.  This may give you possible 
sites that are binding from which you can calculate the fragment 
lengths, compare to your gel and deduce the putative binding.  In the 
end you are still going to have to redesign the primers.
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   Patrick HJ Falckh PhD                                 #     #     
   Key Centre for Applied & Nutritional Toxicology      # # # # #    
   RMIT - City Campus                                    # Q Q #     
   GPO Box 2467V, Melbourne  Vic  3001                   #  o  #     
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   Telephone  : 03 9660 3136                             ##<->##     
   Fax No.    : 03 9663 6087                            #       #    
   Email      : p.falckh at rmit.edu.au                   # #     # #   
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   "No matter how tall your grandfather                  #  \/  #    
       was, you have to do your own growing"              # /\ #
                                                         ooO  Ooo