Difference between revisions of "Team:Warwick/Modelling4"

Revision as of 12:39, 7 August 2015

Warwick iGEM 2015

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DNA Beading

Minimum E.coli for Image

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 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 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.

DNA Beading

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.
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.
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.
This shows how numerous strings of DNA could come together to make an image in a 2D plane.
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.

Primer Sequences for Beads

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).
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. 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.

The patterns to the right are created by the following, respective primer/ binding sequences:

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