Name: Renee Tran Role: Research and Development Scientist
LAB 1 WRITE-UP
Initial Machine Testing
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
DNA Sample Set-up
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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
Specific Cancer Marker Detection - The Underlying Technology
These “3 steps” are repeated for 30 cycles, each step taking about 30 seconds.
Step 1:Heat up the Template DNA, Primers, Taq Polymerase, and Magnesium Chloride (MgCl2) to 95 degrees Celsius
• What happens?
o The bases need to me detected, in order to do so “melting” or unzipping needs to DNA will expose those base pairs.
o When the base pairs are exposed the primers will create a forward and reverse strand appropriately
Step 2:The mixture is cooled down to 57 degrees Celsius
• What happens?
o The primers “anneal,” or in other words the bond.
Step 3:Heat the mixture back up to 72 degrees Celsius.
• What happens?
o The Taq Polymerase detect where the template DNA and primer and uses the template DNA strand and primer to build a new copy of DNA
Remember: The cancer gene will produce a positive result, while the non-cancer gene will give a negative result, because the primers are designed to amplify cancerous DNA. Therefore, the cancerous mutation cannot bind to normal DNA, ultimately meaning that amplification cannot occur. *
Cancer Associated with the gene: Chromosome: Gene being analyzed: SNP #: SNP's Surrounding DNA: Cancer-Sequence Primer: "Partner Primer": Description of Gene:
(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 OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)
BME 103 Fall 2012
