I recently enquired a program for Tm calculation in oligonucleotide
hybridization experiments, and received pointers to the "Primer" by
Whitehead and "Oligo" from a commercial source.
Naturally, Tm is DNA concentration dependent. But ......., in washing,
the DNA concentration is negligible, and the situation is not an
equilibrium condition. It is only a transient state. Equilibrium
may require days or years to attend. Thus the Tm predicted by both
programs cannot be applied to the real washing step.
So, is there any better solution to this (excluding emperical determination)?