Team:Warwick/modelling3
Binding E.coli to a DNA Structure
Concept and Use
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Cube Construction
This shows how the DNA strands come together. Three double stranded strings of DNA are denatured and then when slowly cooled will come together to form the Y shape. However after the denaturing each strand of DNA has an equal chance of bonding to the original piece of DNA as it does to the correct origami side. Therefore the more complex the structure the less likely it is that that structure will fully form.
Tetrahedron Construction
The aim of this model is to design a 3D, self-assembling structure which forms a shape which allows E-coli cells to be bonded to the outside. One of the shapes we decided to use is a geodesic sphere made up of multiple tetrahedron ‘bricks’. Tetrahedrons are the strongest 3D structure and would allow any sized scaffold to be made. A sphere is the best 3D structure as it has the largest surface area to volume ratio which will allow the largest number of E.coli cells to bond to it.
The first two images are how the tetrahedrons are made, using DNA origami. Our sequences will be designed so that each side will have DNA hairpins which bond to another side of a different tetrahedron. The last image is what the DNA origami structure will look like once it has been made.
Each side of the tetrahedrons will have the binding sequences needed to bind the E.coli cells to the outside of the structure, so that it doesn’t matter where each tetrahedron goes.
These images show how each side of the tetrahedron will have different hairpins. The red side will bond to the yellow side, and as you can see they can form many shapes.
Optimising the size of the tetrahedrons
The smaller the tetrahedrons the stronger they are and hence the stronger the resulting formed 3D structure will be. However by decreasing their size you increase the amount of DNA you need to construct it which adds complexity, takes more time and is more expensive. Therefore it is important to find a compromise between size and amount of DNA used.
From reading various papers, such as this one we determined the maximum size you could make was a tetrahedron with side lengths of 75nm. This size maximised stiffness and strength while minimising the amount of DNA.
This graph shows the exponential increase of the number of tetrahedrons needed to bond various amounts of E.coli cells to the surface of the formed structure. Due to our time period and budget it would seem a lot better to use a smaller value of E.coli cells to be bonded (<50) to minimise the DNA sequencing.
If we wanted to bond different zinc fingers to the outside of the structure we would add different binding sites to the tetrahedrons. So each tetrahedron would have, for example 4 different types of zinc finger binding site, each repeated to increase the number of bonded cells. You would also need to change the proportion of binding sites if they have different binding constants. For example if a zinc finger had a binding constant half that of another then you would have to double the number of binding sites for that zinc finger (if you wanted the same number of zinc fingers for each type).
And finally the image shows how the more tetrahedrons are used to construct the structure, the smoother the resulting sphere will be.
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