BME100 f2013:W900 Group18 L4

BME 100 Fall 2013	Home People 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 Photos Wiki Editing Help
OUR TEAM Name: Daniel McDermand Name: Dylan DeBruin Name: Nick Vale Name: Kirstin Peters Name: Matt Hanson 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) Displayed above, the OpenPCR Machine is used to amplify DNA in a short amount of time. PCR, or polymerase chain reaction, is a process that essentially replicates a small amount of DNA until there is a substantial amount present for testing. The DNA in the machine is subject to dynamic environment changes, as the machine rapidly heats and cools the single stranded sample until multiple copies of the original DNA are created. The OpenPCR Machine is connected to a computer via a USB cable, which allows the replication process to be controlled entirely on the computer screen. In order to run an experiment, temperatures and a desired amount of cycles must be entered on the computer, info which is then transmitted to the machine in order to run the process. After the inputted information is received by the OpenPCR Machine, the DNA inside will be subject to the exact amount of cycles and temperature conditions that were set on the computer. The machine will then read results of the completed process which are clearly displayed on an LCD screen on the OpenPCR mechanism itself. Experimenting With the Connections When we unplugged (part 3) from (part 6), the machine failed to display any information on the LCD projector. This is evidence that part 3 and part 6 connect the circuit board to the LCD display, so when unplugged, the machine was unable to display any results. When we unplugged the white wire that connects (part 6) to (part 2), the machine displayed a temperature that was lower than the actual temperature inside the system. This is evidence that part 2 and part 6 connect the circuit board to the temperature pad, so when unplugged, the PCR machine failed to display accurate temperature readings. Test Run The first test run of OpenPCR Machine 1 was conducted at 10:00 a.m. on October 23, 2013. The machine ran silently for two hours, and no complications were present. Data displayed on the LCD screen corresponded with data displayed on the computer software program, and the data displayed a steady increase in temperature as time went by. This is because the DNA needed to be raised to a temperature of 95 degrees Celsius to begin the process of copying. However, even though our machine displayed data that was consistent on both the computer and the machine itself, our team realized that a substantial amount of time is needed to run multiple cycles and produce enough duplicates of the targeted section, as each cycle takes around three to four minutes to complete. Protocols Thermal Cycler Program DNA Sample Set-up Positive Control: cancer DNA template Tube Label: PC Patient 1 ID: 34902 Replicate 1 Tube Label: 1A Patient 1 ID: 34902 Replicate 2 Tube Label: 1B Patient 1 ID: 34902 Replicate 3 Tube Label: 1C Negative Control: non-cancer DNA template Tube Label: NC Patient 2 ID: 39905 Replicate 1 Tube Label: 2A Patient 2 ID: 39905 Replicate 2 Tube Label: 2B Patient 2 ID: 39905 Replicate 3 Tube Label: 2C DNA Sample Set-up Procedure Step 1 Step 2 Step 3... PCR Reaction Mix: The PCR reaction mix contains bacterially derived Taq DNA polymerase, MgCl2, dNTP's, and reaction buffers. DNA/ Primer Mix: Each of the DNA/primer mixes contains a different template DNA. All of the tubes have the same forward primer and reverse primer. Research and Development PCR - The Underlying Technology (Add a write-up, essay-style, organized into paragraphs with descriptive headers, based on the Q&A's from Section three of your worksheet) Component Function of a PCR Reaction A PCR reaction is composed of multiple components, each serving its own unique purpose. The building block of the reaction, the template DNA, is a sample that is replicated into multiple copies. Once replicated, there will appear to be many identical strands of the template DNA. The component that synthesizes the copies of template DNA is called the taq polymerase. Taq polymerase is an enzyme that is thermostable, so it won't denature when temperatures rise (as they do in PCR reactions). The polymerase begins synthesizing DNA strand once it receives signal from the primers, another component of a PCR reaction. Occurrences During Thermal Cycling sDSAFA Base-Pairing asda (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.)