The Original Design
(Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is)
Experimenting With the Connections
When we unplugged (part 3) from (part 6), the machine ... (did what? fill in your answer)
When we unplugged the white wire that connects (part 6) to (part 2), the machine ... (did what? fill in your answer)
Test Run
(Write the date you first tested Open PCR and your experience(s) with the machine)
Protocols
Thermal Cycler Program
Heated Lid: 100°C
Initial Step: 95°C for 3 minutes
Next Step: 35 cycles, denature at 95°C for 30 seconds, anneal at 57°C for 30 seconds, extend at 72°C for 30 seconds
Final Step: 72°C for 3 minutes
Final hold: 4°C
DNA Sample Set-up
PCC= Positive control: Cancer DNA
NCC= Negative control: Non-cancer DNA
P11,P12,P13= Patient 1's DNA samples
P21,P22,P23= Patient 2's DNA samples
Patient 1 ID: 54174
Patient 2 ID: 43184
PCC
P11
P12
P13
NCC
P21
P22
P23
DNA Sample Set-up Procedure
1. Label 6 50 μL disposable pipette tips with the labels given below corresponding to each patient.
2. Label the remaining 2 50 μL pipette tips, one as the positive control cancer DNA (PCC) and one as the negative control non-cancer DNA (NCC).
3. Pipette the PCR reaction mix into each reaction tube.
4. Using a different disposable pipette tip for each sample, pipette the DNA sample primer mix into each reaction tube.
5. Place the reaction tubes in the thermal cycler.
6. Run the PCR software that follows the protocol below.
PCR Reaction Mix
The PCR reaction mix contains:
-Tag DNA Polymerase
-MgCl2
-dNTP's
DNA/ primer mix
The DNA primer mix contains:
-Different template DNAs
-Forward primer
-Reverse primer
Research and Development
Polymerase Chain Reaction (PCR) - The Underlying Technology
Polymerase chain reaction occurs when DNA is heated and cooled at exact temperatures for exact intervals of time. However, there are five components required for the reaction to work successfully; template DNA, primers, TAQ polymerase, Magnesium Chloride (MgCl2), and dNTPs (****).
(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the PCR video/ tutorial might be useful. Be sure to credit the sources if you borrow images.)