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It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 grams of DNA. This is clearly absurd and not the case.

Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an upper bound - but even so, a very uninformative one), and in practice, yields will fall far short of it because:

  • Every single duplex of DNA does not denature at each cycle
  • Primers do not bind to every single molecule of DNA at each cycle
  • Not every DNA strand gets bound by a polymerase at every cycle
  • Not every polymerase that binds manages to complete the entire product in time in every cycle
  • The reaction inhibits itself by depleting dNTPs
  • The heat denatures the reaction by degrading enzyme

In fact, cursory examination of qPCR output often follows saturation kinetics:

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Mathematical methods for modeling qPCR are obviously well developed.

My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?

For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).

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The equation is correct, but there's an additional asymptotic limit to a maximum concentration of product depending on the starting concentration of NTPs, template and primer pairs in solution too.

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