Difference between revisions of "Team:Warwick/Modelling4"

 
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<h4>DNA Origami Glue</h4>
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<p><img src="https://static.igem.org/mediawiki/2015/2/29/Warwickbubbles2.png" height="120px" width="800px" border="1px"></p>
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<p>Once we  had a method of calculating the concentration of cells needed we had to model the number of cells required to make a certain shape. We also needed to invent a novel approach to creating 2D shapes using cells, this page discusses bonding them to a longer string of DNA to form a pattern.
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<p>_______________________________________________________________________________________________________________________________________</p><h5>Minimum <i>E.coli</i> for Image</h5>
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<p style="float: right;"><img src="https://static.igem.org/mediawiki/2015/5/5f/WarwickCellnumber.png" align="right" height="380px" width="380px" border="1px"></p>
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<p style="float: left;"><img src="https://static.igem.org/mediawiki/2015/8/88/Pixelsnumber.png" height="200px" width="200px" border="1px"></p>
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The image on the left shows the minimum number of cells needed to produce a clear image with a discernible shape. For this we looked at simple shapes to see how complexity increased the number of cells or pixels needed.
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<br> The image on the right shows the increase of <i>E.coli</i> cells needed to make a shape. The number of cells per shape follows a linear progression, proportional to the number of sides that the shape has. A basic first order, linear differntial equation would be                                                                             
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C=13(S-2)+12, where C is the approximate number of cells needed to make that shape and S is the number of sides of the shape.
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<p>_______________________________________________________________________________________________________________________________________</p><h5>DNA Beading</h5>
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One option we came up with is to create a string of DNA (by adapting an <i>E.coli</i> plasmid) which has Zinc finger binding sites at certain spots so that you could create a pattern of different <i>E.coli</i> cells which could be used to study microbial communities.
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This could potentially then be used to create 2D shapes and images, by combing strings of DNA with the bonded <i>E.coli</i> cells along them to create something like the image to the left.
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To make the DNA beads we will use an <i>E.coli</i> genome and then denature the double stranded DNA and then add in primers at different locations with the zinc finger binding sequence attached to the end.
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<br>This shows how numerous strings of DNA could come together to make an image in a 2D plane.
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<br> The benefit of this idea is that you could create very complex patterns with relatively few zinc fingers by just using a longer section of the original <i>E.coli</i> plasmid.
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<p>_______________________________________________________________________________________________________________________________________</p><h5>Primer Sequences for Beads</h5>
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<p><p style="float: left;"><img src="https://static.igem.org/mediawiki/2015/5/55/WarwickPrimersequences.png" height="300px" width="300px" border="1px"></p>
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The way we created the strings of DNA was by using a plasmid from <i>E.coli</i> MG1655.To begin with we only wanted about 20 cells in one length of DNA so we decided to cut the plasmid down into a smaller section so that it is easier to handle. We used I-Ceui to cut at the 227920 base pair (down from 4644640 base pairs). 
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<br>To add the zinc finger binding sites we chose to find primer sequences along the string of DNA which we would then attach a primer to which had the corresponding zinc finger on the end.
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The table to the left shows the attachment sequences we used. These 20 sites evenly distribute the <i>E.coli</i> cells across the DNA string with approximately half an <i>E.coli</i> cell between each one.
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<p style="float: right;"><img src="https://static.igem.org/mediawiki/2015/6/67/WarwickBeadpatterns.png" align="right" height="380px" width="340px" border="1px"></p>
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The patterns to the right are created by the following, respective primer/ binding sequences: 
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<p style="float: right;"><img src="https://static.igem.org/mediawiki/2015/2/29/WarwickBindingsequences.png" align="right" height="540px" width="540px" border="1px"></p>
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Latest revision as of 20:35, 17 September 2015

Warwick iGEM 2015

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