BME100 s2014:W Group2 L4

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Owwnotebook icon.png BME 100 Spring 2014 Home
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
Course Logistics For Instructors
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Name: Marianne Alnimri
Name: Carilee Farrell
Name: Joel Larson
Name: Roger Rose
Name: Marshall Treleven


Initial Machine Testing

The Original Design


Essentially, this apparatus performs Polymerase Chain Reaction (PCR). PCR is a reaction that is used to copy DNA segments. PCR is used every day to diagnose diseases, identify bacteria and viruses, and match criminals to crime scenes. Using a heater, it splits the DNA into two segments and allows the PCR reaction to take place. The apparatus raises and lowers temperatures over specific time sequences to control the rate of the reaction. Because of this, the apparatus can be set to perform a specific amount of cycles of PCR.

Experimenting With the Connections

When we unplugged (part 3) from (part 6), the machine's screen turned off.

When we unplugged the white wire that connects (part 6) to (part 2), the machine displayed the incorrect temperature.

Test Run

Machine was first tested on 3/19/14. It appeared to be fully functional. The screen is working and it reached cycle 19 of 35 before we shut it off. After watching the temperature readout change on the screen it appeared that the temperature was fluctuating properly and everything seemed to be working.


Thermal Cycler Program

DNA Sample Set-up

disease DNA Tube label:DD ID:51225 Tube label:11 ID:51225 Tube label:12 ID:51225 Tube label:13
non-disease DNA Tube label:NDD ID:60779 Tube label:21 ID:60779 Tube label:22 ID:60779 Tube label:23

DNA Sample Set-up Procedure

  1. Step 1: Get patient ID's
  2. Step 2: Set up 8 total reactions. Decide how each PCR reaction tube will be labeled and enter this information in the blank spaces above. Each Tube Label should be unique and have no more than 3 characters.
  3. Step 3: Enter the information into lab report.

PCR Reaction Mix

  • What is in the PCR reaction mix?

- Taq DNA polymerase, MgCl2, and dNTP's

DNA/ primer mix

  • What is in the DNA/ primer mix?

- Each mix contains a different template DNA. All tubes have the same forward primer and reverse primer.

Research and Development

PCR - The Underlying Technology
Q1. What is the function of each component of a PCR reaction?

  During a PCR reaction the template DNA is the strand of DNA that will be used as a template to transcribe the
messenger RNA for protein synthesis. Primers are used to prime the nucleic acid template for the attachment of
the polymerase. This is the first step towards duplicating that template. The primer directs the polymerase to
move in a 5' to 3' direction (drawn left-to-right) because of the 'direction' of DNA. Taq DNA Polymerase from
Thermus aquaticus is a thermostable DNA polymerase that is used for the polymerase chain reaction (PCR) in order
to amplify DNA sequences. Nucleotides (dNTPs or deoxynucleotide triphosphates) are single units of the bases A,
T, G, and C, which are essentially "building blocks" for new DNA strands.

Q2. What happens to the components (listed above) during each step of thermal cycling?

  The first step in PCR is to heat the mixture to a high temperature, usually 94 to 95 °C, for about five 
minutes. The hydrogen bonds that hold together the two strands of a double helix are broken at
these temperatures, and the DNA separates into single strands. This process is termed denaturation. In the second step,
the PCR mixture is cooled to a lower temperature, typically between about 50 °C and 65 °C. This allows the primers
to anneal to their specific complementary sequences in the template DNA. The temperature for this
step is chosen carefully to be just low enough to allow the primers to bind, but no cooler. In the third
step, the reaction is heated again, usually to about 72 °C, the temperature at which the DNA polymerase
is most active. At 72 °C, Taq DNA polymerase adds nucleotides to the 3′ ends of annealed primers at the rate of
about two thousand nucleotides per minute. Therefore, to amplify a sequence that is one thousand nucleotides
long, the primer extension step must last about thirty seconds at 72 °C. By the end of this step, each
template strand has a new complementary strand. This completes the first cycle of the PCR reaction.

Q3.Which base anneals to each base listed below?
Adenine(A): Thymine
Thymine(T): Adenine
Cytosine(C): Guanine
Guanine(G): Cytosine

Read more:

Read more:

Read more:

Read more:

(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 PCR video/ tutorial might be useful. Be sure to credit the sources if you borrow images.)