Difference between revisions of "Team:Alverno CA/Design"

Revision as of 23:34, 18 October 2016

Alverno iGEM 2016

Design

The goal of of our project is to counteract a problem in synthetic biology known as supercoiling. Supercoiling is a possible consequence that can occur in the construction of a multi-genetic circuit. When the two genes transcribe, the double helix is opened in order to allow for the expression for the genes, however, the dna in between the two genes receive extraordinary amounts of tension when both genes try to transcribe at the same time, which can lead to the over transcription of one gene, and the under expression of the other gene. This can greatly affect the predictability of gene expression.

To test if we could reduce the supercoiling between these two genes, we proposed several different strategies that we felt may alleviate the problem. The first method we tried was adding random base pair sequences in between the two genes, with lengths of 500bp or 1000bp. We created this in the hope that the spacer in between the two genes would alleviate the tension that creates the supercoiling. Another one of our methods was to use a dCas9 clamp between the RFP and GFP to clamp down between the two genes and stop the supercoiling. In order to see whether or not the problem of supercoiling was reduced, we had to first construct the plasmid circuits used for our experiment by using Golden Gate Assembly. First, we designed primers to amplify our parts off current iGEM parts using the online DNA design editor, Benchling (for parts designs: https://benchling.com/sclamons/f_/fBGWWXin-parts/?sort=name). For our experiment we have used RFP and GFP and parts from the iGEM inventory: BBa_J04450 (insert hyperlink on wiki: http://parts.igem.org/Part:BBa_J04450) and BBa_I13522 (insert hyperlink on wiki: http://parts.igem.org/Part:BBa_I13522), respectively. These parts were amplified off and ligated together in varying orientations (see picture designs) with a spacer part between them (either 500bp spacer, 1000bp spacer, or a dcas9 clamp site spacer) and finally a vector, or backbone piece, with Chloramphenicol or Kanamycin resistance.

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-<h5> In order to solve this problem, we have assembled a circuit in which RFP and GFP are constructed in the same plasmid. To test if we could reduce the supercoiling between these two genes, we designed several different strategies that we felt may alleviate the problem. The first method we tried was adding random base pair sequences in between the two genes, with lengths ranging between fifty and one thousand and five hundred base pairs. We created this in the hope that the space in between the two genes would alleviate the tension that causes the supercoils. Another of our methods was to use a dCas9 clamp on the space between the RFP and GFP to hopefully clamp down on the supercoiling. We utilized Golden Gate Assembly in order easily build several variations of these plasmids by cloning with  several different parts. <h5>
+<h5> To test if we could reduce the supercoiling between these two genes, we proposed several different strategies that we felt may alleviate the problem. The first method we tried was adding random base pair sequences in between the two genes, with lengths of 500bp or 1000bp. We created this in the hope that the spacer in between the two genes would alleviate the tension that creates the supercoiling. Another one of our methods was to use a dCas9 clamp between the RFP and GFP to clamp down between the two genes and stop the supercoiling.
+In order to see whether or not the problem of supercoiling was reduced, we had to first construct the plasmid circuits used for our experiment by using Golden Gate Assembly. First, we designed primers to amplify our parts off current iGEM parts using the online DNA design editor, Benchling (for parts designs: https://benchling.com/sclamons/f_/fBGWWXin-parts/?sort=name). For our experiment we have used RFP and GFP and parts from the iGEM inventory: BBa_J04450 (insert hyperlink on wiki: http://parts.igem.org/Part:BBa_J04450) and BBa_I13522 (insert hyperlink on wiki: http://parts.igem.org/Part:BBa_I13522), respectively. These parts were amplified off and ligated together in varying orientations (see picture designs) with a spacer part between them (either 500bp spacer, 1000bp spacer, or a dcas9 clamp site spacer) and finally a vector, or backbone piece, with Chloramphenicol or Kanamycin resistance. <h5>
+#put pictures of Katie's plasmid designs!!
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