BME100 f2013:W900 Group17 L4: Difference between revisions
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'''The Original Design'''<br> | '''The Original Design of the PCR machine'''<br> | ||
[[Image:OpenPCR17.jpg]] | [[Image:OpenPCR17.jpg]] | ||
The device displayed in this image is an Open PCR machine which is a machine that conducts a polymerase chain reaction which in turn is a reaction that amplifies a given piece of DNA, or in other words makes many more copies of it. This is done inside the machine through a multi-step heating and cooling process the first of which is to heat the DNA in order to have it split apart from the two helix form into individual chains. Here primers, small strands of nucleotides, inside the reaction mixture attach to the ends of the individual DNA chain. Then when cooling begins to happen the polymerase, an enzyme, in the reaction mixture attaches to the ends of the primers and begins replicating the individual chains of DNA that it's attached to using floating nucleotides in the reaction mixture. Finally, the new DNA chains made as copies fuse together as do all the DNA chains present. This represents just one cycle of many taken to produce a multitude of copies of the DNA that is being amplified. This whole process takes place inside an area called the thermal block that holds tubes with the reaction mixtures which are heated and cooled according to the process. A lid on top of this area prevents condensation of the water of the reaction mixture. Another feature of this machine is its ability to interface with a computer via a USB cable which allows the monitoring of the machine's progress through cycles like the aforementioned one on the computer. However, if one wishes to view this information directly on the machine this is also possible due to the attached | The device displayed in this image is an Open PCR machine which is a machine that conducts a polymerase chain reaction which in turn is a reaction that amplifies a given piece of DNA, or in other words makes many more copies of it. This is done inside the machine through a multi-step heating and cooling process the first of which is to heat the DNA in order to have it split apart from the two helix form into individual chains. Here primers, small strands of nucleotides, inside the reaction mixture attach to the ends of the individual DNA chain. Then when cooling begins to happen the polymerase, an enzyme, in the reaction mixture attaches to the ends of the primers and begins replicating the individual chains of DNA that it's attached to using floating nucleotides in the reaction mixture. Finally, the new DNA chains made as copies fuse together as do all the DNA chains present. This represents just one cycle of many taken to produce a multitude of copies of the DNA that is being amplified. This whole process takes place inside an area called the thermal block that holds tubes with the reaction mixtures which are heated and cooled according to the process. A lid on top of this area prevents condensation of the water of the reaction mixture. Another feature of this machine is its ability to interface with a computer via a USB cable which allows the monitoring of the machine's progress through cycles like the aforementioned one on the computer. However, if one wishes to view this information directly on the machine this is also possible due to the attached LCD screen. <br> | ||
'''Experimenting With the Connections'''<br> | '''Experimenting With the Connections on the machine'''<br> | ||
[[Image:OpenPCRModel.jpg]] | [[Image:OpenPCRModel.jpg]] | ||
When | When part three, or the screen, was unplugged from part 6, the control circuit, the screen ceased to function and would not turn on until the connection was restored because without the conncection the screen was not receiving a signal from the control circuit. It is important for the screen to continue to function since it displays the number of cycles performed by the achine and the temperature. | ||
When | When the white wire connecting part 6, the control circuit, to part 2, the thermometer, was disconnected the temperature measurement changed suddenly from 23.6 degrees Celsius to -40 degrees Celsius. Essentially, the temperature readout began to be extremely inaccurate. | ||
'''The Test Run''' | |||
'''Test Run''' | |||
The PCR machine was first used to run through a test cycle on October 23, 2013 at 9:56 am | The PCR machine was first used to run through a test cycle on October 23, 2013 at 9:56 am | ||
Revision as of 03:12, 30 October 2013
 BME 100 Fall 2013
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OUR TEAM
LAB 1 WRITE-UPInitial Machine TestingThe Original Design of the PCR machine The device displayed in this image is an Open PCR machine which is a machine that conducts a polymerase chain reaction which in turn is a reaction that amplifies a given piece of DNA, or in other words makes many more copies of it. This is done inside the machine through a multi-step heating and cooling process the first of which is to heat the DNA in order to have it split apart from the two helix form into individual chains. Here primers, small strands of nucleotides, inside the reaction mixture attach to the ends of the individual DNA chain. Then when cooling begins to happen the polymerase, an enzyme, in the reaction mixture attaches to the ends of the primers and begins replicating the individual chains of DNA that it's attached to using floating nucleotides in the reaction mixture. Finally, the new DNA chains made as copies fuse together as do all the DNA chains present. This represents just one cycle of many taken to produce a multitude of copies of the DNA that is being amplified. This whole process takes place inside an area called the thermal block that holds tubes with the reaction mixtures which are heated and cooled according to the process. A lid on top of this area prevents condensation of the water of the reaction mixture. Another feature of this machine is its ability to interface with a computer via a USB cable which allows the monitoring of the machine's progress through cycles like the aforementioned one on the computer. However, if one wishes to view this information directly on the machine this is also possible due to the attached LCD screen.
When part three, or the screen, was unplugged from part 6, the control circuit, the screen ceased to function and would not turn on until the connection was restored because without the conncection the screen was not receiving a signal from the control circuit. It is important for the screen to continue to function since it displays the number of cycles performed by the achine and the temperature. When the white wire connecting part 6, the control circuit, to part 2, the thermometer, was disconnected the temperature measurement changed suddenly from 23.6 degrees Celsius to -40 degrees Celsius. Essentially, the temperature readout began to be extremely inaccurate. The Test Run The PCR machine was first used to run through a test cycle on October 23, 2013 at 9:56 am
and stopped at 11:16 am for a total run of one hour and twenty minutes. During this
time the machine ran without any major problems and in fact was very quiet throughout
the cycles it went through. Also, the time to completion displayed on the computer
monitor through the program was always within reasonable parameters given the
average time it takes for the PCR machine to complete its ideal number of cycles. Given the
time that the PCR machine in this experiment was allowed to operate, one hour and
twenty minutes, it was able to complete 25 cycles in total with thirty six minutes being
left of operation time as inficated by the timer.
ProtocolsThermal Cycler Program
Research and DevelopmentPCR - The Underlying Technology (Add a write-up, essay-style, organized into paragrpahs with descriptive headers, based on the Q&A's from Section three of your worksheet)
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