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
Is an affordable tool that is used to focus on a specific segment of DNA and produces about a billion copies. It is used in numerous ways such as for medical research, identifying a marker gene, diagnosing a disorder, identifying bacteria, and crime scenes. The thermal cycler program work by gathering desirable DNA and placing it in the PCR tubes. The tubes then are lowered into the temperature chamber using the top part of the PCR machine. Then the cycler raises and lowers temperature according to the pre-set program. The program contains thirty cycles and takes about two hours to complete. In the first cycle, the thermal cycler heats up to 95 degree Celsius which is almost boiling point. During this time, the DNA double helix spates forming two single strand DNA. Then the thermal cycler cools to about 50 degree Celsius. At this time the single stranded DNA would want to match up with its original pair. However, the primer sequences lock on to the single stranded DNA before it can join. The thermal cycler then changes temperature to 72 degree Celsius which activates the DNA polymerase. DNA polymerase then finds the primers and starts attaching complimentary nucleotides to the DNA strand until it reaches the end. This marks the end of cycle one and start of cycle two. In the second cycle, the same steps repeat. In cycle three, the desired product appears: two strands that begin with primer one and end with primer two. Even though it is only two strands during this time, the strands makes more and more copies further down the cycles. By the end of cycle four there will be eight fragments and twenty two by cycle five etc. After thirty cycles there will be over a billion fragments.
DNA Sample Set-up
DNA Sample Set-up Procedure
Step 1
Step 2
Step 3...
PCR Reaction Mix
What is in the PCR reaction mix?
DNA/ primer mix
What is in the DNA/ primer mix?
Research and Development
PCR - The Underlying Technology
(Add a write-up, essay-style, organized into paragrpahs with descriptive headers, based on the Q&A's from Section three of your worksheet)
(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.)