Taq Pol and 3' primer mismatch?

Shahram Mori smori at nmsu.edu
Fri Sep 23 20:21:55 EST 1994


Carlisle Landel (landel at helios) wrote:

: Will Taq polymerase work if the primer has a 3' mismatch of a single base?
: How many bases of mismatch does it take before the polymerase won't work?
: Does anybody know a reference?

: We are trying to PCR a specific member of a highly conserved multi-gene
: family.  I seem to remember hearing that Taq absolutely requires a 3'
: match in the primer to work, but I don't know for sure that it is true.

: Thanks for your help!

: Carlisle Landel
: landel at helios.medsci.udel.edu
Actually this depends on the sequence at the 3' end. I can't remember the
reference but somebody from california did studies and said that sequence
with 3' ends  high in G and T mismatches will almost always get extented
and to a lesser extent A:C. It may be a good idea ( especially in
differential display ) to use primers having high concentration of TG or
AC at the 3' end. 
cheers,
 
-- 
Shahram Mori					   _/\_
Program in Molecular Biology			  _\  /_
Dept. of chemistry and Biochemistry Box 3C	  \_  _/
NMSU  Las Cruces NM				    ||



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