BME103 s2013:T900 Group9

BME 103 Fall 2012	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: student Role(s) Name: student Role(s) Name: student Role(s) Name: student Role(s) Name: student Role(s) 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) 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 Set-up row 1 cell 1 row 1 cell 2 row 1 cell 3 row 1 cell 4 row 2 cell 1 row 2 cell 2 row 2 cell 3 row 2 cell 4 DNA Sample Set-up Procedure Step 1 Step 2 Step 3... PCR Reaction Mix What is in the PCR reaction mix? DNA/ primer mix What is in the DNA/ primer mix? 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.) DNA replication is a biochemical process that highlights the importance of making and breaking bonds. DNA is composed of a sugar-phosphate backbone and bases. A phosphate group, a ribose, and a base bonded together create a nucleotide. The chemical attraction between complementary nucleotides results in the double-helix structure of DNA. The base adenine is complementary to thymine, and similarly guanine is complementary to cytosine. The chemical structures of these nucleotides make them ideal for hydrogen bonding to their complementary base pairs. DNA contains the genetic information of a cell, and is unique to every organism. In some cases, a mutation in DNA can cause serious diseases, such as cancer. A gene mutation is typically an error in the complementary base pair rules, an adenine being bonded to a cytosine for example. Polymerase chain reaction, or PCR, is a procedure that is used to detect these mutations early on so action can be taken to prevent the disease before it increases in severity. PCR amplifies small segments of DNA to allow doctors to pinpoint any mutations with more ease. The procedure for this relies heavily on using temperature to either break bonds or encourage binding. The extracted segment of DNA, called the template DNA, is placed in an aqueous solution also consisting of dNTP’s, or extra bases. The temperature of the mixture is raised to 95°C, causing the hydrogen bonds between bases to break, consequently unzipping the double helix. A primer, which is a short fragment of artificially synthesized DNA, is added once there are two separate strands. Typically, primers consist of 20 base pairs that are complementary to the DNA strands. There are two kinds of primers, a forward primer and a reverse primer. Once they are added, the temperature of the solution is reduced to 57°C, encouraging primer annealing to occur with the template DNA strands. The forward primer binds from left to rich, while the reverse primer binds from right to left. This process results in segments of DNA that are double stranded. In order to create a complete double strand, the temperature is increased again, this time to 72°C. This activates tag polymerase, an enzyme that seeks areas with primers and continues down the DNA strand grabbing base pairs from the surrounding solution and binding them to the template strand. Magnesium chloride is a small molecule that serves as a cofactor for tag polymerase, helping the protein efficiently do it's job. This procedure as a whole is usually repeated 30 times. In this way, a small portion of DNA can be replicated repeatedly. Polymerase chain reaction can be used in two ways to detect cancer genes. One way is to use a healthy DNA primer, which will consequently not bind to a gene mutation. This will cause one of the DNA strands to not replicate, indicating a problem. The other way is to design a primer so that it binds to the cancer mutation. In this case, if a positive result occurs, it will signify the presence of a cancerous gene. These two methods can be combined as well, in order to make sure the experiment did not fail.