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Team:Davidson-Missouri Western/Online Tools that Support Design of New Biobrick Parts
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How do you choose the right percent gel for separating any two DNA bands? Rather than guessing, there should be a more reliable method, especially since so many iGEM students are new to the lab. Therefore, we produced a Gel Optimizer to help you choose the right percent agarose gel. When you submit the MW of your band, you will get the optimal percent agarose (between 2% and 0.4%) as well as a photo showing molecular weight markers at this percent gel and the equation that helped us determine the migration of the nearest MW marker fragment at the different gel concentration. <br> | How do you choose the right percent gel for separating any two DNA bands? Rather than guessing, there should be a more reliable method, especially since so many iGEM students are new to the lab. Therefore, we produced a Gel Optimizer to help you choose the right percent agarose gel. When you submit the MW of your band, you will get the optimal percent agarose (between 2% and 0.4%) as well as a photo showing molecular weight markers at this percent gel and the equation that helped us determine the migration of the nearest MW marker fragment at the different gel concentration. <br> | ||
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Revision as of 18:20, 29 October 2008
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During the summer of 2008, we realize two substantial shortcomings in the iGEM world.
1. Optimal Percent Agarose Gel
How do you choose the right percent gel for separating any two DNA bands? Rather than guessing, there should be a more reliable method, especially since so many iGEM students are new to the lab. Therefore, we produced a Gel Optimizer to help you choose the right percent agarose gel. When you submit the MW of your band, you will get the optimal percent agarose (between 2% and 0.4%) as well as a photo showing molecular weight markers at this percent gel and the equation that helped us determine the migration of the nearest MW marker fragment at the different gel concentration.
2. PCR Primers with Digestable BioBrick Ends
Can we design PCR primers that include BioBrick ends automatically? We decided to generate a web page that allows users to submit the fragment of DNA they want amplified and then produce synthesis-ready PCR primers that not only amplify the fragment, but append the BBa prefix and suffix nucleotides as well as 4 additional bases (GCAT) so you can digest the PCR product with EcoRI and PstI and generate sticky ends. The primers appear in blue with the four BBa restriction sites underlined. The additional GCAT bases appear red.
In previous iGEM competitions, we produced two other online tools that might be helpful to others.
3. Splitting genes for Hin/Hix flipping (iGEM 2007)
This page is designed to tell you what 4 PCR primers can be used to split a gene such that hixC can be inserted within the gene's coding sequence and not alter the reading frame.
Target Site
PCR Primers and Split Target Site
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