M W F; 10:10 - 11:00 pm

 Molecular Biology

 Douglas W. Smith
York 2722

 BIMM 100

 5254 Muir Biology Building
Fall, 2000  

 x42620; dsmith@ucsd.edu

 

PCR Calculations

 

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Extent of Amplification per DNA molecule for N cycles of PCR
in a basic DNA experiment:

1. With each cycle, all of the DNA nucleotides found between the two primers are duplicated for all of the DNA molecules currently present in the reaction.
Thus, the number of these DNA nucleotides doubles with each cycle ...
and the overall increase of these nucleotides is an exponential increase ...
Hence, after N cycles, each of these nucleotides will be present in 2N DNA molecules.

2. Some of these nucleotides will be present in DNA molecules that contain ONLY these nucleotides found between the two primers. Others, however, will be present in DNA molecules that also contain nucleotides present on the original DNA molecules but not found between the two primers. ... see Lodish, Fig 7-37 and the CD-ROM video

3. With each PCR cycle, the number of DNA molecules that contain nucleotides present on the original DNA molecules but not found between the two primers will only increase arithmetically, since, with each cycle, only the two original DNA strands can be used as templates to produce new DNA strands containing nucleotides not found between the two primers. Hence, after N cycles, the number of DNA molecules containing nucleotides not found between the two primers will be 2 x N DNA molecules.

4. Thus, with each PCR cycle, the number of DNA molecules that contain ONLY nucleotides between the two primers will be: 2N - 2 x N DNA molecules.

 

Numbers of DNA Molecules per PCR Cycle:

 PCR Cycle Num:
N

 Total DNA:
2N

Non-Target DNA:
2 x N

Target DNA:
2N - 2 x N

% Target DNA
1 2 2 0 0
2 4 4 0 0
3 8 6 2 25%
4 16 8 8 50%
5 32 10 22 68.8%
... ... ... ... ...
10 1024 20 1004 98.0%
11 2048 22 2026 98.9%
12 4096 24 4072 99.4%
... ... ... ... ...
30 1,073,741,824 60 1,073,741,764 99.999994%

 

DNA Molecules Synthesized per PCR Cycle:

 

 






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If you have problems or comments, send email to Doug Smith