BME103 s2013:T900 Group2
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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LAB 1 WRITE-UP
Initial Machine Testing
The Original Design
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)
(Write the date you first tested Open PCR and your experience(s) with the machine)
Thermal Cycler Program
DNA Sample Set-up
DNA Sample Set-up Procedure
PCR Reaction Mix
DNA/ primer mix
Research and Development
Specific Cancer Marker Detection - The Underlying Technology
Polymerase Chain Reaction (PCR) is a scientific method that utilizes DNA Polymerase to create a complimentary base strand from a template strand of DNA. Triphosphate nucleotides align with open DNA strands and DNA polymerase works to link the complementary nucleotide bases together growing strands through both condensation and hydroysis reactions. One major issue with DNA polymerase is that DNA strands are anti parallel, and polymerase is only able to add nucleotides to the free 3'OH group hence it can only build new strands in the 5'-3' direction (Sadava 279). Therefore, to correct for this issue the presence of a primer is required so that polymerase can proceed with directing the new nucleotides in place. Through these mechanisms it is possible to target specific positions on the template DNA sequence that a scientist intends to amplify(PCR 1). When the PCR process is completed the targeted DNA sequence containing the single-nucleotide polymorphism (SNP) will have manufactured over a billion copies (amplicons).
The SNP included in the amplicon for this experiment was denoted as rs17879961. This polymorphism is a variant of the CHEK2 gene which if present in a person's genome may increase the risk of developing breast cancer (Brennan et al 1795). This SNP is signified by a single base change from a Thymine (T) to a Cytosine (C) located on chromosome 22. With the PCR system, forward and reverse primers can be designed to target the cancer gene abnormality and amplify/multiply it. The normal DNA strands may multiply, but not as exponentially as the abnormal cancer DNA strands.
(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.)
Brennan, Paul et al. Uncommon CHEK2 Mis-sense Variant and Reduced Risk of Tobacco-related Cancers: Case-control Study. Rep. 15th ed. Vol. 16. Oxford: Advance Access, 2007. Human Molecular Genetics. Oxford University Press, 21 May 2007. Web. 25 Mar. 2013. PDF. <http://hmg.oxfordjournals.org/content/16/15/1794.full.pdf>.
"PCR Introduction." NCBI. U.S. National Library of Medicine, n.d. Web. 25 Mar. 2013. <http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechPCR.shtml>.
Sadava, David E. Life: The Science of Biology. Sunderland, MA: Sinauer Associates, 2011. Print.