BME103:T130 Group 14

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Lab Write-Up 1
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Contents

OUR TEAM

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LAB 1 WRITE-UP

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 ... (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

Polymerase Chain Reaction

The polymerase chain reaction (PCR) is biochemical machinery in biological chemistry to produce numerous copies of a particular piece of DNA, generating multiple duplicates of DNA sequences. In order to complete the reaction several components are required such as:
-DNA template
- A PCR reaction mix that contains: Taq DNA polymerase, MgCl2, dNTP’s, and a forward and reverse primer
Most PCR methods use thermal cycling, alternating heating and cooling steps. These thermal cycling steps are necessary to separate the two strands in a DNA double helix at a high temperature in a process called DNA melting. At the lower temperature, the DNA polymerase to amplify a particular target DNA uses each DNA strand as a template in DNA synthesis. The primers aid discrimination of the DNA to target the specific region for amplification under specific thermal conditions.


1. Acquire the DNA samples that have been submitted for testing
2. Run the DNA samples through the thermal cycler program.
1. Stage one (Initiation): 1 cycle, 95 C for 3 minutes.
2. Stage 2 (Denaturation): 35 cycles, 95C for 30 seconds, 57 C for 30 seconds, 72C for 30 seconds.
3. Stage 3 (Elongation) : 72 * C for 3 minutes.
4. Stage 4: Final hold for 4*C.
3. After the DNA has been through the thermal cycle, mix each DNA sample with the PCR reaction mix (Taq DNA polymerase, MgCl2, dNTP’s, and a forward and reverse primer), using a separate pipette each time to reduce cross-contaminatio into 8 separate tubes.



Flourimeter Measurements

(Add your work from Week 3, Part 2 here)




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.)




Results

(Your group will add the results of your Fluorimeter measurements from Week 4 here)


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