BME103 s2013:T900 Group4

BME 103 Spring 2013	Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help
OUR TEAM Name: Kinjal Ahir Role:Experimental Protocol Planner Name: Zach Young, Role:Initial Machine Testing Name: Amelia Lax Research and Development Name: Anna Essex Role:Initial Machine Testing Name: student Tuan Phan Role:Research and Development Name: student Role(s) LAB 1 WRITE-UP Initial Machine Testing The Original Design (Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is) Here's the OpenPCR machine. Made up of thin pieces of wood, the case contains the hardware of the machine. With another smaller wood case on top of the main case containing the loading bay which acts as a lid. Small test vials can be placed into holders here in the bay to be heated by PCR machine. Inside the main body of the machine sits the hardware similar to a personal computer. A processor unit connects to the heating hardware as well as the power supply and led display board. Above the power supply lies the heatsink with a fan attached facing vents in the case allowing for efficient thermal control inside the machine to prevent overheating. 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 Thermal Cycler Program DNA Sample, 50 μL each: patient ID's from the UnderGrad Teaching Assistant(UGTA). Positive control Patient 1 Patient 1 Patient1 cancer DNA template ID:85158 ID: 85158 ID: 85158 Replicate 1 Replicate 2 Replicate 3 Tube label: A+ Tube label: B1 Tube label: C1 Tube label: D1 Negative Control: no Patient 2 Patient 2 Patient 2 DNA template ID: 17818 ID: 17818 ID: 17818 Replicate 1 Replicate 2 Replicate 3 Tube label: A- Tube label: B2 Tube label: C2 Tube label: D2 DNA Sample Set-up Procedure Step 1: Student were Provided with 8 tubes of 50 μL PCR reaction mix, 8 tubes of 50 μL diluted template + primers, and disposable transfer pipettes. Step 2: Protocol planner labeled the test tube that is provided above. Step 3: 50μL of each DNA sample Mix in to test tube. Step 4: Protocol planner set up the DNA and ran the PCR reactions. PCR Reaction Mix In the PCR reaction mix there is Mix contains Taq DNA polymerase, MgCl2, dNTP's, forward primer, reverse primer. DNA/ primer mix In the DNA/ primer mix there is patient's DNA. Research and Development Basic DNA components: DNA Template DNA Polymerase DNA Primers Nucleotides Procedure: First, the components are combined and heated. Once the reaction is heated to a temperature of 95 degrees Celsius, the hydrogen bonds between the DNA strands break and create two separate DNA sequences. After that, leave it to cool down to a temperature of around 55 degrees Celsius. This allow the DNA polymerase is going the bind the DNA sequence with the DNA Primer with hydrogen bonding. Once, the DNA polymerase is bound, it is going to take some of the free nucleotides from the surrounding area and complete the DNA strand. The result is a two separate DNA sequences, with two DNA strand identical to the first one. Repeatedly doing the steps multiple times and the result will give a total of 4 double DNA strands, and so on... 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.)