Single error in Primer

[Olivier Gandrillon]

Patrick HJ Falckh wrote:
> 
> 'lo Netters,
> 
> I was wondering if someone could advise me if it is feasible to have a
> single error in a PCR primer but still have it bind to a specific
> region?
> The situation is that I have a 21mer primer that is specific for a
> given product (a class of enzyme).  I have found that this primer is
> ~95% homologous to a subclass of the enzyme with the difference being
> an 'A' substitution for a 'T'; 7 bases upstream from the 3' end.  I
> was think that this would not cause too much of a distortion .... am I
> correct in this assumption or should I remake the primer? Either side
> of the substitution is a 'TGC' and a 'GGT'.
> 
> Your advise is appreciated.
> 
> --
> 
>    Patrick HJ Falckh PhD                                 #     #
>    Key Centre for Applied & Nutritional Toxicology      # # # # #
>    RMIT - City Campus                                    # Q Q #
>    GPO Box 2467V, Melbourne  Vic  3001                   #  o  #
>                                                           # ~ #
>    Telephone  : 03 9660 3136                             ##<->##
>    Fax No.    : 03 9663 6087                            #       #
>    Email      : p.falckh at rmit.edu.au                   # #     # #
>                                                        ##       ##
>    "No matter how tall your grandfather                  #  \/  #
>        was, you have to do your own growing"              # /\ #
>                                                          ooO  Ooo


Hi

This should not be a problem. I have personnal experience of succesful 
PCR amplification using primers with a couple (2 or 3) differences with 
the template. What is important is their how far they are from the 
3-prime end (the closer, the worst): 7 bases should work just fine.


-- 
Olivier Gandrillon AKA ogandril at cri.ens-lyon.fr

Meet me at http://www.ens-lyon.fr:80/~ogandril

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³Il ne suffit pas de flipper, il faut encore savoir pourquoi.²

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