BME103:T930 Group 1 l2

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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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Nick Hool: Machine Engineer
Joseph Heath: Machine Engineer, R&D Scientist
Jessica Kemper: Protocol Planner
Maile Ravenkamp: Protocol Planner
Christian Boden: R&D Scientist


Thermal Cycler Engineering

Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.

System Design

Key Features




Supplied in the Kit Amount
PCR Machine 1
Positive Control DNA Sample 27282151
Negative Control DNA Sample 35526894
Patient 1 DNA Sample 19073943
Patient 2 DNA Sample 29391013
PCR: Patient 2 ID 11260 , rep 1 1903450
PCR: Patient 2 ID 11260, rep 2 5214727
PCR: Patient 2 ID 11260, rep 3 5099077

PCR Protocol

1. You will need a PCR machine and computer.

2. Download the PCR software onto the computer.

3.Thaw the GoTaq Colorless Master Mix at room temperature. Vortex the Master Mix, then spin it briefly in a microcentrifuge to collect the material at the bottom of the tube.
4 . Prepare the following reaction mix on ice:

Reagent Volume
Template DNA (20 ng) 0.2 µL
10 µM forward primer 1.0 µL
10 µM reverse primer 1.0 µL
GoTaq master mix 50.0 µL
dH2O 47.8 µL
Total Volume 100.0 µL

5. If using a cycler without a heated lid, overlay the reaction mix with 1-2 drops of mineral oil to prevent evaporation during thermal cycling. Centrifuge the reaction mix in a microcentrifuge for 5 seconds.

6. Place the reactions in a thermal cycler that has been preheated to 95 degrees Celsius. Perform PCR.

What Occurs In the PCR Machine
1. Denaturation: a 2-minute denaturation at 95 degrees celsius.

2. Annealing: perform the reaction about 5 degrees Celsius below the calculated melting temperature of the primers and increasing the temperature in increments of 1°C to the annealing temperature; this should occur anywhere between 30 seconds and 1 minute.

3. Extension: performed between 72-74 degrees Celsius, extension allows 1 minute for every 1 kb of DNA to be amplified; the suggested time for extension is 5 minutes.

4. Refrigeration: refrigerate the tubes at 4 degrees Celsius for several hours; this will minimize the opportunity for DNA polymerase to continue to be active at higher temperatures.

5. Cycle Number: the optimal amplification is 25-30 cycles, but up to 40 may be performed.

DNA Measurement Protocol

Research and Development

Background on Disease Markers

Primer Design



"GoTaq® Colorless Master Mix (M714) Product Information." GoTaq® Colorless Master Mix Protocol. Promega, 2012. Web. 15 Nov. 2012. <>.

Hunt, Margaret. "Real Time PCR Tutorial." Real Time PCR Tutorial. University of South Carolina, 10 July 2010. Web. 15 Nov. 2012. <>.