BME103:T930 Group 11

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Owwnotebook icon.png BME 103 Fall 2012 Home
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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Name: Tony Nguyen
Name: Ryelle Pattuinan
Research and Development
Name: Kenze Caulfield
ImageJ Technician
Name: Jackie Janssen
Name: Ben Hook
Role (s)
Name: student


Initial Machine Testing

The Original Design
(Add image of the full OpenPCR machine here, from the Week 3 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's display screen didn't turn on or show up.

When we unplugged the white wire that connects (part 6) to (part 2), the machine's temperature reading was altered compared to the accurate values from the computer.

Test Run

(Write the date you first tested Open PCR and your experience(s) with the machine)
October 25, 2012. The machine was accurate and precise but the cycling was slow.


Polymerase Chain Reaction

The Polymerase Chain Reaction works by attaching MgCl to taq enzyme in the solution and then pulling deoxy nucleotide diphosphates, binding them to the strand that is already present. This gives a base to the DNA that is already there.
DNA amplification contains three important steps: heat denauturation,primer annealing, and primer extension.
Step One: Heat Denauturation-Heat is applied to the DNA and the two strands separate.
Step Two:Primer Annealing-With excess dNTPs, oligonucleotides are added.
Step three: Primer Extension-DNA polymerase is added and new strands of DNA are synthesized. The DNA strands combine with the nucleotides to form completed, complimentary strands of DNA.
PCR master mix contains Magnesium Chloride, all four Nucleotides needed to create DNA, and reaction buffers.
Reagent volume
Template DNA(20 ng) .2uL
10 uM forward primer 1.0 uL
10 uM reverse primer 1.0 uL
GoTaq master mix 50.0 uL
DH2O 47.8 uL
Total Volume 100.0 uL
Patient one's ID number is 12123, male, and 61 years old. Patient two's ID is 21312, female, and 56 years old.

Flourimeter Measurements
The Flourimeter was assembled by taking the black box, flipping it upside down so that the rest of the materials can be placed inside the box with the flap blocking out excess light. The glass slide was then placed into the flourimeter so that the light of the flourimeter was on the first two rows of holes in the glass slide. The flourimeter was then placed inside the overturned black box, and the phone was placed on the stand. The camera on the phone is lined up with the middle row of holes in the glass slide. After the pictures of the droplets of DNA and SYBR green solution were taken, they were sent to a computer through e-mail and downloaded.

Research and Development

Specific Cancer Marker Detection - The Underlying Technology

(Add a write-up of the information discussed in Week 3's class)

(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.)


Sample Integrated Density DNA μg/mL Conclusion
PCR: Negative Control E6 F6 G6
PCR: Positive Control E7 F7 G7
PCR: Patient 1 ID 12123, rep 1 E8 F8 G8
PCR: Patient 1 ID 12123, rep 2 E9 F9 G9
PCR: Patient 1 ID 12123, rep 3 E10 F10 G10
PCR: Patient 2 ID 21312, rep 1 E11 F11 G11
PCR: Patient 2 ID 21312, rep 2 E12 F12 G12
PCR: Patient 2 ID 21312, rep 3 E13 F13 G13


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