Team:USTC/Tool
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- | == | + | {|valign = "top" align = "center" border = "0" width = "800px" |
- | '''Problem 1:''' | + | = Problem & Solution = |
- | How to distinguish the different biobricks in a biobrick | + | [[Image:barcode.jpg|thumb|right|200px|Barcode & its Scanner]] |
- | + | *'''Problem 1:''' How to distinguish the different biobricks in a biobrick pool in experiment? | |
- | To take a DNA sequencing?---it's costly and time-consuming. | + | **To take a DNA sequencing?---it's costly and time-consuming. |
- | + | **We are faced with such a problem to identify the final outputs of [https://2009.igem.org/Team:USTC/Project E.ADEM]. An inspiration comes from the supermarket checkout system where thousands of commodities are tagged by barcodes. This universal commercial ID both shortens the check-out time and adds the accuracy. By comparing our problem with this system, what we need to do can be concluded as to design barcodes for biobricks, '''BioBrick-Barcode''', as we call it. | |
- | We are faced with such a problem to | + | *'''Problem 2:''' Where is the scanner? |
- | + | **PCR (Polymerase Chain Reaction)[http://en.wikipedia.org/wiki/PCR], which is so conveniently conducted, can serve as the scanner while the primers it needs are the analogue of barcode sequences. | |
- | '''Problem 2:''' | + | |
- | Where is the scanner? | + | |
- | + | ||
- | PCR (Polymerase Chain Reaction)[http://en.wikipedia.org/wiki/PCR], which is so conveniently conducted, can serve as the scanner while the primers it needs are the analogue of barcode sequences. | + | |
---- | ---- | ||
- | '''Solution:''' | + | '''Solution: '''To check the final outputs in the system of E.ADEM, we need to design a set of DNA oligo-sequences primers as the barcodes to go through the scanner of PCR and help identify the final evolutionary products. |
- | To check the final outputs in the system of E.ADEM | + | |
- | + | = Design = | |
- | A set of barcodes under a certain kind of barcode reader has to satisfy its conditions in order to be picked out respectively. For BioBrick-Barcodes, the oligo-sequences must meet several conditions as we considered: | + | *A set of barcodes under a certain kind of barcode reader has to satisfy its conditions in order to be picked out respectively. For BioBrick-Barcodes, the oligo-sequences must meet several conditions as we considered: |
1. Since the BioBrick-Barcodes function as PCR primers, they must satisfy the basic conditions as high-quality primers: | 1. Since the BioBrick-Barcodes function as PCR primers, they must satisfy the basic conditions as high-quality primers: | ||
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b. All of the primers should be specific for the target sequence without combining with other sites. | b. All of the primers should be specific for the target sequence without combining with other sites. | ||
- | '''Software''' | + | *'''Software''' |
+ | |||
+ | Primer3[http://primer3.sourceforge.net/releases.php] is an open-source primer-design software, and we modified its C codes in parts to design the BioBrick-Barcodes. Since Primer3 is mainly used to pick primers from a DNA template while the BioBrick-Barcodes are supposed to be randomly produced, and a set of BioBrick-Barcodes should be diverse to avoid overlapping PCR, we changed three functions and structure of Primers. | ||
+ | 1. Add a function to randomly produce the DNA oligo-sequences which replaced the previous function used to pick | ||
+ | segments from the template. | ||
+ | 2. Modified the structure used to store information of each primer. | ||
+ | 3. Use the Libray_Mispriming to choose diverse primers. | ||
+ | |||
+ | *'''Experiment''' | ||
+ | |||
+ | We design a set of ten diverse primers by using the modified software. Apparently, we need to conduct experiments to test its feasibility. | ||
+ | |||
+ | 1.Synthesize the DNA oligo-sequence; | ||
+ | 2.Construct plasmids; | ||
+ | 3.Conduct a 10*10 cross experiment: Each primer reacts with all the plasmids; | ||
+ | |||
+ | Expectation: only complementary couple leads to PCR results. | ||
+ | |||
+ | = Results = | ||
+ | {|- | ||
+ | |align="right"| | ||
+ | [[Image:tool_result.png|450x450px|thumb|left|cross experiment result]] | ||
+ | |<p> In the electrophoretogram, only the combination of primer 5 & plasmid 5, primer 6 & plasmid 6, primer 7 & plasmid 7 lead to PCR results. Along with other electrophoretograms we conclude that this set of primers can be used as a set of barcodes.</p> | ||
+ | |} | ||
- | |||
- | |||
+ | <!--[[Image:tool_result.png|500px|left|thumb|cross experiment result]] | ||
+ | --> | ||
+ | = Application = | ||
+ | *'''In Synthetic Biology: '''BioBrick barcodes are a set of artifical DNA parts designed for PCR. They can be used alone as a high-quality PCR primer. Also, they can be used in a group as a convenient tool to identify the biobrick parts just as we do. | ||
- | ''' | + | *'''Beyond Synthetic Biology: '''We create a new software to design PCR primers without a template. The primers chosen from a random oligo-sequences can enlarge the application scope of PCR. |
- | + | <!-- | |
- | + | *Jiayi Dou is responsible for this subproject. If you have any problem or any suggestion, please contact her by e-mail: cherrytrees_dot@hotmail.com | |
- | + | --> |
Latest revision as of 17:19, 21 October 2009
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In the electrophoretogram, only the combination of primer 5 & plasmid 5, primer 6 & plasmid 6, primer 7 & plasmid 7 lead to PCR results. Along with other electrophoretograms we conclude that this set of primers can be used as a set of barcodes. |
Application
- In Synthetic Biology: BioBrick barcodes are a set of artifical DNA parts designed for PCR. They can be used alone as a high-quality PCR primer. Also, they can be used in a group as a convenient tool to identify the biobrick parts just as we do.
- Beyond Synthetic Biology: We create a new software to design PCR primers without a template. The primers chosen from a random oligo-sequences can enlarge the application scope of PCR.