Re: How to calculate the theoretical yield in moles in a PCR?

Dear Kanwaljit,

We are typically not allowed to answer homework problems, so I will just
give you some hints and try to lead you in the right direction. Hopefully
this will be helpful, and you can have the satisfaction of figuring out the
final answer on your own :)

Okay. The idea behind PCR is amplification. In every cycle, the amount of
the PCR product theoretically doubles. So, for example, if you start with 1
fmole of template: after 1 cycle, there will be (1 fmole)*(2^1) = 2 fmoles
of product; after 2 cycles, there will be (1 fmole)*(2^2) = 4 fmoles; after
3 cycles, there will be (1 fmole)*(2^3) = 8 fmoles of product, etc. But be
careful! This is assuming that you don't run out of any of the other
ingredients necessary for the reaction! The key to your problem is figuring
out which ingredient runs out first (i.e., what is the limiting reagent).
To begin thinking about this, let's take a look at what is necessary in a
PCR reaction.

So in a standard PCR, there is:
- Template DNA
- Forward and reverse primers
- dNTPs
- DNA polymerase
- Buffer containing Mg2+ to keep the polymerase happy

In your case specifically, we have:
- 0.10ng of a 3000bp template
	-> can be converted to moles using the
           approximation of 650g/mole per bp
- 1.20uM of each primer
	-> can be converted to moles using the
           fact that the total volume is 100uL
- 100uM of each dNTP (means 400uM dNTPs total)
	-> can be converted to moles using the
           fact that the total volume is 100uL

Now think about how much of each reactant gets used up in each cycle. Don't
forget that the amount of template doubles in each cycle, and so the amount
of reactant used up doubles for each cycle as well! This will allow you to
figure out what the limiting reagent is. How many moles of product is
synthesized for each mole of that reagent? Do you run out of reagent before
or after the 30 cycles is complete?

Your initial answer will probably be in MOLES of product. To convert this
back into grams (or MICROGRAMS, as the problem indicates), remember that
your product is 600bp, and that each bp is 650g/mole.

If you need a review of how PCR works, look in your textbook, or see the
"Procedure" section here: http://en.wikipedia.org/wiki/Polymerase_chain_reaction

This is a very clever problem in that it requires you to think carefully
about exactly what happens in each PCR cycle, so thanks for sending it in
:) Good luck!

-Kathy Xie