Apart from wet lab confirmation of annealing temperature of a primer by gradiant pcr;Is there have any mathematical equation to find it?
One can deduce the annealing temperature of primers from its tm
tm= 4 (A+T) + 2 (G+C), once the Tm is calculated, Ta is 2 to 10 0c less than tm. If we deduct on an avg 6 0c from tm then it will give approximate range of annealing temperature and most of the time it will work. Please do check it by doing pcr.
Suppose Tm=65 then Ta=Tm-6= 65 - 6 = 59 so Ta will be around 57 to 59
2 common calculations are the simple GCx4 +ATx2 which is only any good for oligos less than 13 bases long.
also for oligos longer than 13 bases there is
Tm (°C) = 81.5 + 0.41(%GC) - (675/N)
where %GC is the percentage of G and C nucleotides in the oligo and N is the length of the oligo given in nucleotides.
Both equations assume that the annealing occurs under the standard conditions of 50 nM primer, 50 mM Na+, and pH 7.0.
The more complex and accurate nearest neighboar calculations are used by companies making oligos and can be found on most of their websites
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