BME103:T130 Group 7
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the DNA , the with the . and
==Research and Development==
==Research and Development==
Revision as of 19:57, 12 November 2012
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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LAB 1 WRITE-UP
Initial Machine Testing
The Original Design
When the PCB board was unplugged from the Open PCR circuit board, the machine's LED display ceased to function.
When the white wire that connects the Open PCR circuit board to 16 tube PCR block was unplugged, the machine's LED display read -40 Celsius indicating that the temperature could not be read.
October 18,2012; The test program labeled "Simple Test", was performed to ensure proper function of the Open PCR machine. It ran through two cycles at a full range of temperatures, no DNA was present for the test run. The test performed without any flaws.
Polymerase Chain Reaction
To amplify samples of DNA, the OpenPCR machine was used to perform a Polymerase Chain Reaction (PCR). This technique worked by cycling a mixture of DNA Template, Primers, Taq Polymerase, Magnesium Chloride, and dNTP's through three specific temperatures to create more copies of the desired sequence. After assembling the PCR mixture, the PCR machine was programmed to perform three stages. In the first stage, the samples went through one cycle at 95⁰C for 3 minutes. The purpose of this stage was to initially denature the DNA and allow the primers to act on the DNA. The second stage put the samples through 35 cycles of 95⁰C, 57⁰C, and 72⁰C each for 30 seconds. The purpose of the first part of the second stage is to break apart the hydrogen bonds between the base pairs, denaturing the DNA sequence into two separate strands. The purpose of the low temperature is to allow primers to bind. The purpose of the middle temperature is to create an environment for Taq Polymerase to assemble a new strand that is the desired product of the entire polymerase chain reaction. The last stage, stage three, puts the samples through one cycle of 72⁰C for 3 minutes. There is a final hold of 4⁰C that preserves the DNA. The samples were then taken out of the PCR machine. The target sequence had been amplified a million times and could now be analyzed with less sensitive equipment! To analyze the sequence, see the Fluorimeter section.
To analyze the DNA samples after they've been amplified,
a smartphone with adjustable settings was used.
- Exposure to highest setting
The Fluorimeter aparatus consists of a hydrophobic Teflon surface on a glass slide. There is an array of 3x10 glass wells on the surface to anchor drops in position for photographing. First, two drops of the cybergreen solution were placed on row 2, column 1&2 (Figure 1). With a sterile pipet two drops of amplified sample DNA were added to the cybergreen solution. It was important to place the DNA on top of the cybergreen in order to achieve the best results and to avoid contamination of the DNA samples. A picture was taken using the settings listed above and the next sample was prepared by sucking the liquid off the slide using a 'waste' pipet. The slide was then moved back by two columns for the next sample.This procedure was replicated for each of the patient samples and two slides were used in their entirety.
The cybergreen soluiton allowed the amount of DNA in a sample to be determined by its luminosity. The cybergreen glowed green in the presence of DNA and while this glow was not visable to the naked eye, the smart phone in conjunction with image j was able to quantify the luminosity. The brighter samples contained more DNA and this indicated that the sample reacted with the primers and was cancerous.
Research and Development
Specific Cancer Marker Detection - The Underlying Technology
Polymerase Chain Reaction, or PCR, is used to ampllify a specific segment of DNA, in this case the segment known to code for cancer. A primer, which is an artifically synthesized piece of complementary DNA, binds to the desired DNA segment, and the enzyme taq polymerase catalyzes the replication of the DNA strand using dNTPs (free bases). This is repeated over and over to produce many copies of the DNA. Once the copies are made, a fluorescent dye that only bonds to DNA double strands is added to the solution. If a solution that shows fluorescence by using a fluorimeter, then that DNA sample contains the cancer-associated sequence.
The single nucleotide polymorphism, or SNP, that is linked to cancer is rs17879961. The DNA base sequence associated with cancer is ACT, while the non-cancer sequence is ATT. PCR works to identify ACT from ATT because the primers, which are complementary to DNA strands containing cancer-positive ACT, will not bind to DNA containing ATT, and instead of DNA double strands, the solution will only contain single strands. The fluorescent dye will only bind to double strands and will identify those.
These Images were taken using a HTC evo4G using the settings described under flourimeter measurements.
Water and SYBR green
SYBR green and Calf Thymus