tm calculation for tagged primers

Peter Ellis via (by pjie2 from
Tue Nov 3 07:31:05 EST 2009

On Mon, 2 Nov 2009, cjmcdermottroe from wrote:
> based on the definition of tm, it follows that since binding will not 
> (or at least should not) occur between the template and your added 
> restriction site, you should not therefore factor it in when calculating 
> tms, gc etc.  Fyi, adding flag/myc tags etc on a primer will give you 
> crazy tms. Again, no binding so dont worry about them. Gl

To be more precise - during the first few cycles of PCR, you will be 
priming directly off your DNA template, and so the added parts will not 
match.  For these cycles, you need to calculate the Tm based only on the 
matching parts of the primer (without your added tags).  In later cycles, 
you are priming off the molecules synthesised during the earlier cycles, 
and the primer will thus match all the way along, including the tags.

This means that if you want, you can do something similar to a touchdown 
PCR: use a lower Tm for the first few cycles, and then raise it.  This 
may help if you are getting a lot of background / non-specific bands. 
However, I've never found this to be necessary, so I'd advise you to just 
calculate the lower Tm (i.e. without tags) and use that.


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