BME103:T130 Group 14

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Initial Machine Testing

The Original Design

The Open PCR machine is fairly easy to use. Simply plug it in to the USB port on your computer and turn it on. From your computer, you can adjust the temperature, add or remove steps to the process, and adjust the number of cycles.

Experimenting With the Connections

When we unplugged the LCD from the Circuit Board, the LCD turned off.

When we unplugged the white wire that connects the circuit board to heat block, the LCD was unable to accurately read the temperature.

Test Run

The very first time that our group used the Open PCR machine was October 28, 2012. The process went fairly smoothly, which was unexpected. All we did was put the samples into the machine, set the peak temperature and number of cycles, then let it run for an hour and forty-nine minutes.


Polymerase Chain Reaction

The polymerase chain reaction (PCR) is a biochemical machine used in biological chemistry to produce numerous copies of a particular piece of DNA, generating multiple duplicates of DNA sequences. The PCR machine works similar the cycle of DNA replication at the cellular level. The machine consists of four individual steps, initiation, denaturation, annealing, and extension. The initiation step is solely to prepare the DNA samples to be put through the thermal cycler program. During the denaturation step, the DNA strand is split into two separate strands. After, the annealing step is where the DNA primer attaches to the targeted DNA sequence. The primer only attached to a specific site on the strand, not necessarily the entire strand. The purpose of the primer is to mark the beginning and the end of the targeted DNA sequence. Lastly, in the extension step, the DNA polymerase is first activated, which begins to synthesize the DNA primer. This results in two double stranded target DNA sequences. The PCR machine cycles numerous times to amplify the specific sequence. 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. The stages of the PCR machine are listed below:

  1. Acquire the DNA samples that have been submitted for testing
  2. Run the DNA samples through the thermal cycler program (see Stage 1)
    1. Stage 1 (Initiation): 1 cycle at 95°C for 3 minutes, to separate the DNA strand.
    2. Stage 2 (Denaturation): 35 cycles: first at 95°C for 30 seconds, and then gradually decrease the temperature to approximately 57°C for 30 seconds, and then raise the temperature to approximately 72°C for 30 seconds, so the DNA polymerase can be activated. This is also an example of heat shock, and is effective to initiate the addition of complementary nucleotides onto the DNA strand, which the DNA polymerase does.
    3. Stage 3 (Elongation) : At this step, hold the DNA at 72°C for 3 minutes.The temperature is held here so that the DNA polymerase can copy the strand. Also, this is where the two desired fragments begin to appear- two strands that begin with primer one and end with primer two- and these are the DNA copies of the segment of DNA you began with.
    4. Stage 4: Final hold until the DNA stabilizes at 4°C. At the end of this cycle you will have 8 fragments of the DNA (see Table 2)
  3. After the DNA has been through the numerous cycles, you will have over thousands of fragments of the same DNA sequences. 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-contamination into 8 separate tubes (see Table 2).

Reagent Volume
Template DNA ( 20 nanograms) 0.2 microliters
10 micrometers forward primer 1.0 microliters
10 micrometers reverse primer 1.0 microliters
GoTaq Master Mix 50.0 microliters
Distilled Water 47.8 microliters
Total Volume 100.0 microliters

Table 1

Sample Descriptions (8 Samples)
Positive Control: Cancer DNA Template Patient 1: 44231 Patient 1: 44231 Patient 1: 44231
Negative Control: No DNA Template Patient 2: 57447 Patient 2: 57447 Patient 2: 57447

Table 2

Flourimeter Measurements
In this lab, we used SYBR Green I, which is used to detect a particular DNA strand. In this lab, our fluorimeter was created using optical caustic because it eliminated the need for lasers, mirrors, and lenses. A fluorimeter is a device used to measure parameters of fluorescence: it's intensity and and wavelength distribution. The quality is related to the amount of florescent material and indirectly proportional to the molecule being detected. The objective of this part is to determine if you have actually amplified the target DNA in your PCR experiment. Through this you will be able to visually observe the fragments and calculate the relative amount of DNA. During the first procedure, you amplified your DNA, so now that you are going dye it with the following procedure:

  1. You will have 8 sample from the OpenPCR instrument and 1 DNA(calf thymus standard at 2 micrograms/mL) sample and water from the scintillation vial to analyze.
  2. With a permanent marker, number the transfer pipettes at the bulb so that you limit cross-contamination and only use ONE per solution, and number your Eppendrof tubes at the top. At the end, you should have 10 Eppendorf tubes and 10 pipettes clearly labeled. (See Table 3)
  3. Transfer each sample separately ( using one pipette per sample) into an Eppendorf tube containing 400 mL of buffer. Label this tube with the number of your sample. Make sure to transfer all of the sample into the Eppendorf tube. Use the same pipette to place ONLY this sample's drop onto the fluorescent measuring device.
  4. Take the specially labeled Eppendorf tube containing the SYBR GREEN I and using it's assigned pipette, place two drops on the first two centered drops.
  5. Now take the diluted sample and place two drops on top of the SYBR GREEN I solution drops.
  6. Align the light going through the drop.
  7. Take pictures with the smartphone, as many as desired.
  8. If you are not satisfied with that sample, you may rerun that sample again or move on to the next sample.
  9. Be sure to only run 5 samples per slide.
  10. Before completing the lab, run the water from the scintillation vial as a BLANK using the same procedure listed above.

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.)


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