Since our primer TM is lower than the extension temperature by design, (and often by a significant amount) shouldn't the primers be released from the template at extension temperatures?

Now, I have done PCR experiments and know they work. I just want to justify what's actually going on molecularly to be at peace. The only thing I can think of is that as the temperature ramps up to the extension temp, the polymerase has already begun adding nucleotides, thus raising the effective TM, preventing dissociation.

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    $\begingroup$ That will happen in some cases, but by the time you are ready to extend, the annealing step will have mean that primers formed double helix stretches with you template, and the polymerase will have bound to both, stabilising it, thus it isn't free to be released from the strand. $\endgroup$ – Joe Healey Jul 3 '17 at 7:41

Note that 'melting temperature' is actually about POPULATIONS--it's generally the temperature at which 1/2 of all of the millions of copies of 2 things will be stuck together and 1/2 apart. Once stuck, not all primers will leap off the template simultaneously even at much higher temperature... As you indicate, there's nothing to stop the polymerase from starting its work (extending the primer) before the extension temperature.

And, as in another answer, polymerase can add stability to the pairing.


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