I am a biochemist working with a bunch of physicists, and an interesting point came up the other day while discussing PCR in plasmids.
At the end of the extension, you are left with a nicked piece of DNA. The nick appears between the beginning of the primer, and the last nucleotide added to the circle. During the next cycle, heating the dsDNA to 95 degrees melts the two strands apart. Why does the nicked strand not linearize? How is it that you end up with circular product?
The next round of PCR should start by adding a primer and extending the chain over the nick to form circular product. How is the polymerase able to reconcile this nick, possibly linear at this point? How does it find where to start replicating the chain?
I would never have thought about this without them asking me, and tech consultants from Stratagene have been unable to answer this question... I am hoping someone on here can lend insight.
Is it due to DNA persistence length? Stacking energies? I have no idea.