1. A technique to make a lot of DNA from only a little!
PCR
A technique to make a lot of DNA from only a little!

2. PCR Full name of the process is Polymerase Chain Reaction
Invented in 1983 by Dr. Kary Mullis
Allows scientists to make unlimited copies of specific DNA fragments
Can amplify DNA fragments of up to approximately 10,000 bp

3. PCR
Two problems exist for scientists to make a visual analysis of a specific DNA locus (site or location):
Must first isolate the specific locus from all the other millions of sites in chromosomes
Must amplify (duplicate) the locus so that you can see it on the gel

4. PCR Requirements Template DNA (what you extract) Primers
DNA polymerase
DNTP (deoxyribonucleoside triphosphates) or the A’s, T’s, C’s, and G’s
Thermal Cycler

5. PCR Requirements Primers
Short segments of DNA bp long which “bracket” the desired DNA segment
One primer is a complement “forward” primer to produce DNA strand from left to right while one is a “reverse” primer that is for right to left strand
A T T C G C G A A A T G T T G G G C A A C A G G T A C T C T A
G C G C T T T A C
C A G G T A C T C
T A A G C G C T T T A C A A C C C G T T G T C C A T G A G A T

6. PCR Requirements
If primers are carefully chosen they can select a unique sequence in the genome

7. PCR Requirements Heat stable DNA polymerase
Most commonly use Taq polymerase –
Thermus aquaticus (a bacteria found around hot springs)
Is an enzyme that helps form new bonds between the nucleotides in new strands of bacteria
A T T C G C G A A A T G T T G G G C A A C A G G T A C T C T A
G C G C T T T A C
C A G G T A C T C
T A A G C G C T T T A C A A C C C G T T G T C C A T G A G A T

8. PCR Requirements DNTP’s Deoxyribonucleoside triphosphates –
Nitrogen bases: adenine, thymine, cytosine, and guanine
These DNTP’s attach to the exposed complementary bases of the original DNA
A T T C G C G A A A T G T T G G G C A A C A G G T A C T C T A
G C G C T T T A C
A A C C C G T T G T C C A T G A G A T
A T T C G C G A A A T G T T G G G C A A
C A G G T A C T C
T A A G C G C T T T A C A A C C C G T T G T C C A T G A G A T

9. PCR Requirements **Note** Ready to go PCR Beads
For convenience, we use PCR beads which contain freeze-dried DNTP’s and Taq polymerase enzyme
All we add to them are the primer mix and template DNA
**Note**
These beads are very expensive – Almost $2.00 per bead!!! So don’t mess it up!!

10. PCR: The Steps of the Process
3 phases for each cycle (these vary slightly from one protocol to another)
Denaturing: (94-95°C) DNA strands separate into single strands
Annealing: (58°C) Primers anneal (attach) to the separated DNA strands
Extending: (72°C) New complementary strands are made as the Taq enzyme helps to form bonds with the DNTP’s

11. PCR: The Steps of the Process
Approximately 30 cycles of these 3 phases are used
Each cycle produces twice as many targeted DNA segments as existed before
After 30 cycles approximately 1 billion copies are produced
Takes approximately 2 hours

14. PCR Equipment: Thermal Cycler
$2,600

15. PCR Equipment: Thermal Cycler
It is possible to substitute 3 water baths at the 3 different temperatures for a thermal cycler, but…
DNA samples would have to be moved from water bath to water bath to water bath for 30 cycles!

16. PCR Activity: Paper PCR
Use strips of paper to create 4 cycles of a PCR reaction.
Color code the reactions as follows:
Red: Template DNA strand (40 bp)
Write the following sequence on one red strip:
A C G A T T G G G C C A A T A T A C G C G T G A T G T T C G A A G A G A C T

17. PCR Activity: Paper PCR
Yellow: 1st copied strand
Blue: 2nd copied strands
Green: 3rd copied strands
Forward primers are white
Reverse primers are gray
G A T T C C A T A

18. Steps of DNA Isolation:
10 mL of saline, swish, spit, use 1mL of this.
Centrifuged
Poured off saline & then resuspended
Removed 30 uL and added to 100 uL of Chelex to absorb cell debris and ions.
Boiled for 10 minutes.
Withdrew 30 uL & stored in new tube.

19. Day 2: Amplification Added 22.5 uL of Primer Mix into PCR bead.
Added 2.5 uL of DNA.
Quick spin to put everything together.
Thermal cycler
DAY 3: Ran gels