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a problem about the Tm of the BSP primer - (Apr/04/2008 )

hi everyone ,
i have a problem about the Tm of the BSP primer.

the sequence contain so many CG sites and my primer have to contain 1 CG.
so the C in the forward primer was replaced by degeneracy Y, the G was replaced by degeneracy R.

i want to do some change on the primer, but the Methyl Primer Express can not edit the primer; the Primer 5.0 can , but if you use the degeneracy, it will not show the Tm.

what should i do?

thanks a lot ,everyone.


I would just calculate the Tm by using the "lower" base, meaning T or A in place of Y or R bearing in mind when you synthesising the primer it should be an Y or R depending on which primer you are talking about.


thank u Nick!
I will try.