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Team:IIT Madras/Dry lab/Tools
From 2011.igem.org
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<h1> <u>Site directed Mutagenesis-Primer Design</u></h1> | <h1> <u>Site directed Mutagenesis-Primer Design</u></h1> | ||
| - | <p>We received proteorhodopsin sequence from Kwang-Hwan "Kevin" Jung, Ph.D., Associate Professor, Department of Life Science and Institute of Biological Interfaces, Sogang University with three restriction sites EcoRI, SpeI and PstI. Hence the plasmid had to be mutated for iGEM compatibility. Hence we had to design primers for site directed mutagenesis at each of these sites. So we have come up with a Primer design tool for SDM as a | + | <p>We received proteorhodopsin sequence from Kwang-Hwan "Kevin" Jung, Ph.D., Associate Professor, Department of Life Science and Institute of Biological Interfaces, Sogang University with three restriction sites EcoRI, SpeI and PstI. Hence the plasmid had to be mutated for iGEM compatibility. Hence we had to design primers for site directed mutagenesis at each of these sites. So we have come up with a Primer design tool for SDM as a Criteria: |
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<ol> <li>Mutations in the middle of primer</li> | <ol> <li>Mutations in the middle of primer</li> | ||
<li> Tm difference should be less than 5</li> | <li> Tm difference should be less than 5</li> | ||
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<p align="center"><img src="https://static.igem.org/mediawiki/2011/e/e1/Tool-1.jpg" width="800" height="600"/></p> | <p align="center"><img src="https://static.igem.org/mediawiki/2011/e/e1/Tool-1.jpg" width="800" height="600"/></p> | ||
| - | <p align="center"><b> <u>Fig(1): Showing The Command Prompt </u></b><br/><br/> | + | <p align="center"><b> <u>Fig(1): Showing The Command Prompt </u></b><br/><br/><br/> |
<p align="center"><img src="https://static.igem.org/mediawiki/2011/d/d9/Tool-2.jpg" width="800" height="600"/></p> | <p align="center"><img src="https://static.igem.org/mediawiki/2011/d/d9/Tool-2.jpg" width="800" height="600"/></p> | ||
| - | <p align="center"><b> <u>Fig(2): Showing The Output of the toolbox </u></b><br/><br/> | + | <p align="center"><b> <u>Fig(2): Showing The Output of the toolbox </u></b><br/><br/><br/> |
<p align="center"><img src="https://static.igem.org/mediawiki/2011/1/17/Tool-3.jpg" width="800" height="600"/></p><br/> | <p align="center"><img src="https://static.igem.org/mediawiki/2011/1/17/Tool-3.jpg" width="800" height="600"/></p><br/> | ||
| + | <p align="center"><b> <u>Fig(3): Showing The Output of the toolbox </u></b><br/><br/><br/> | ||
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</html> | </html> | ||
Revision as of 03:04, 6 October 2011
Site directed Mutagenesis-Primer Design
We received proteorhodopsin sequence from Kwang-Hwan "Kevin" Jung, Ph.D., Associate Professor, Department of Life Science and Institute of Biological Interfaces, Sogang University with three restriction sites EcoRI, SpeI and PstI. Hence the plasmid had to be mutated for iGEM compatibility. Hence we had to design primers for site directed mutagenesis at each of these sites. So we have come up with a Primer design tool for SDM as a Criteria:
- Mutations in the middle of primer
- Tm difference should be less than 5
- No 3' Breathing should be ensured by keeping G or C at the end
- GC content:40-60%
Fig(1): Showing The Command Prompt
Fig(2): Showing The Output of the toolbox
Fig(3): Showing The Output of the toolbox
