Difference between revisions of "Team:Warwick/Modelling4"

 
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<h4>DNA Origami Glue</h4>
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<h4>DNA Beading</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><img src="https://static.igem.org/mediawiki/2015/2/29/Warwickbubbles2.png" height="120px" width="800px" border="1px"></p>
 
<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.
 
<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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<h5 class="sidebartitle">Minimum E.coli for Image</h5>
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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>
 
<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>
 
<p style="float: left;"><img src="https://static.igem.org/mediawiki/2015/8/88/Pixelsnumber.png" height="200px" width="200px" border="1px"></p>
 
<p style="float: left;"><img src="https://static.igem.org/mediawiki/2015/8/88/Pixelsnumber.png" height="200px" width="200px" border="1px"></p>
 
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.
 
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 E.coli 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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<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                                                                               
  
 
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.
 
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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<h5 class="sidebartitle">DNA Beading</h5>
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<p>_______________________________________________________________________________________________________________________________________</p><h5>DNA Beading</h5>
 
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<img src="https://static.igem.org/mediawiki/2015/b/ba/WarwickE.coli_Beads.png" class="pics" alt="">  
 
<img src="https://static.igem.org/mediawiki/2015/b/ba/WarwickE.coli_Beads.png" class="pics" alt="">  
 
<p style="float: left;"><img src="https://static.igem.org/mediawiki/2015/a/a0/WarwickBead_Drawing.png" height="200px" width="200px" border="1px"></p>  
 
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One option we came up with is to create a string of DNA (by adapting an E.coli plasmid) which has Zinc finger binding sites at certain spots so that you could create a pattern of different E.coli cells which could be used to study microbial communities.
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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 E.coli cells along them to create something like the image to the left.
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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 E.coli 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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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.
  
 
<br>This shows how numerous strings of DNA could come together to make an image in a 2D plane.
 
<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 E.coli plasmid.
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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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<h5 class="sidebartitle">Primer Sequences for Beads</h5>
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<p>_______________________________________________________________________________________________________________________________________</p><h5>Primer Sequences for Beads</h5>
 
<p><p style="float: left;"><img src="https://static.igem.org/mediawiki/2015/5/55/WarwickPrimersequences.png" height="300px" width="300px" border="1px"></p>
 
<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 E.coli 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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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).   
 
<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.
 
<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 E.coli cells across the DNA string with approximately half an E.coli cell between each one.
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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.
 
<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>
 
<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>
 
The patterns to the right are created by the following, respective primer/ binding sequences:   
 
The patterns to the right are created by the following, respective primer/ binding sequences:   
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Latest revision as of 20:35, 17 September 2015

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