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<h2>Abstract</h2>
<li><a href="http://openwetware.org/wiki/Biomod/2014/VCCRI">Home</a></li>
<li class="active"><a href="http://openwetware.org/wiki/Biomod/2014/VCCRI/Project">Project</a></li>
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<p class="text-justify"><img src="http://openwetware.org/images/f/ff/2014-EchiDNA-PROJECT-ABSTRACT-IMAGE-1.png" align="right" style="padding-left:10px; padding-bottom: 10px;"/>What is the difference between a few undergraduates and a BIOMOD team? Or between a single ant and a colony of social insects? What about a population of individual cells and a multicellular organism? Between monodispersed proteins and a multi-protein complex like the bacterial flagella motor? What is the difference between a set of oligos and a DNA nanomachine?</p>
<p class="text-justify">It is believed that cooperativity between staples expedites the assembly of folding DNA origami <span style="color:#f7941e; font-weight: bold;">structures</span>. We aim to design, build and characterise a DNA nanomachine that exhibits cooperativity in its <span style="color:#f7941e; font-weight: bold;">function</span>. We have drawn inspiration primarily from two sources in the design of our DNA biosensor - the molecular beacons used routinely to identify trace amounts of DNA and the switching mechanism of the bacterial flagella motor. Here we construct a circular ring of DNA switches which are tethered together such that they essentially 'vote' whether to undergo a conformational change. This project has the potential to inform realistic models of the molecular mechanics of bionanomachines, but also to provide a cheap, robust alternative to existing DNA biosensors. Our design is modular, so that the DNA targeted by our biosensor might be anything - an HIV virus, a mutation associated with cancer, a gene causing antibiotic resistance. Furthermore, our biosensor is accompanied by an extensive mathematical model of its dynamics and thus we hope it will be tuneable to specific outputs.</p>
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What is the difference between a single ant and a colony of social insects? What about a population of individual cells and a multicellular organism? Between monodispersed proteins and a multi-protein complex like the bacterial flagella motor?
<br><br>
We have drawn inspiration primarily from two sources in the design of our DNA biosensor - the molecular beacons used to identify trace amounts of DNA and the switching mechanism of the flagella motor used by bacteria. By taking inspiration from the design of the bacterial flagella motor, we are not only capitalising on millions of years of evolutionary optimisation of this natural switching mechanism but also building a unique experimental system in which to explore the phenomenon of cooperativity. Our team has designed a circular ring of DNA switches that are tethered together so that they ‘vote’ to undergo a conformational change. This conformational change is triggered by the increasing concentration of a specific DNA strand, which we anticipate will convert a continuous environmental signal into a discrete binary output. Our design is modular - therefore the DNA targeted by our biosensor might be anything; an ebola virus, a mutation associated with cancer, a gene causing antibiotic resistance. Furthermore, our biosensor is accompanied by an extensive mathematical model of its dynamics and thus we hope it will be tunable to specific outputs. This project lays the groundwork for a cheap, robust alternative to existing DNA biosensors, while simultaneously exploring a key component of all biological systems - cooperativity.
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<div style="width: 85%; margin-left: auto; margin-right: auto;"> Click here to see some background for our work, and to see why our project is <orange>relevant</orange>.</div>
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<a id="APPROACH" href="http://openwetware.org/wiki/Biomod/2014/VCCRI/Project/Approach"></a>
<br>
<div style="width: 85%; margin-left: auto; margin-right: auto;"> Click here to see how we tackled the project, including <orange>specification</orange> of our goals, and <orange>feasibility</orange> of our project.</div>
</div>
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<a id="SOLUTION" href="http://openwetware.org/wiki/Biomod/2014/VCCRI/Project/Solution"></a>
<br>
<div style="width: 85%; margin-left: auto; margin-right: auto;"> Click here to see the <orange>merits</orange> of our innovative and elegant solution.</div>
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Latest revision as of 05:21, 25 October 2014

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What is the difference between a single ant and a colony of social insects? What about a population of individual cells and a multicellular organism? Between monodispersed proteins and a multi-protein complex like the bacterial flagella motor? <br><br> We have drawn inspiration primarily from two sources in the design of our DNA biosensor - the molecular beacons used to identify trace amounts of DNA and the switching mechanism of the flagella motor used by bacteria. By taking inspiration from the design of the bacterial flagella motor, we are not only capitalising on millions of years of evolutionary optimisation of this natural switching mechanism but also building a unique experimental system in which to explore the phenomenon of cooperativity. Our team has designed a circular ring of DNA switches that are tethered together so that they ‘vote’ to undergo a conformational change. This conformational change is triggered by the increasing concentration of a specific DNA strand, which we anticipate will convert a continuous environmental signal into a discrete binary output. Our design is modular - therefore the DNA targeted by our biosensor might be anything; an ebola virus, a mutation associated with cancer, a gene causing antibiotic resistance. Furthermore, our biosensor is accompanied by an extensive mathematical model of its dynamics and thus we hope it will be tunable to specific outputs. This project lays the groundwork for a cheap, robust alternative to existing DNA biosensors, while simultaneously exploring a key component of all biological systems - cooperativity.

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<div class="row" style="width: 750px; margin-left: auto; margin-right: auto;"> <div class = "col-md-4"> <a id="PROBLEM" href="http://openwetware.org/wiki/Biomod/2014/VCCRI/Project/Problem"></a> <br> <div style="width: 85%; margin-left: auto; margin-right: auto;"> Click here to see some background for our work, and to see why our project is <orange>relevant</orange>.</div> </div> <div class = "col-md-4"> <a id="APPROACH" href="http://openwetware.org/wiki/Biomod/2014/VCCRI/Project/Approach"></a> <br> <div style="width: 85%; margin-left: auto; margin-right: auto;"> Click here to see how we tackled the project, including <orange>specification</orange> of our goals, and <orange>feasibility</orange> of our project.</div> </div> <div class = "col-md-4"> <a id="SOLUTION" href="http://openwetware.org/wiki/Biomod/2014/VCCRI/Project/Solution"></a> <br> <div style="width: 85%; margin-left: auto; margin-right: auto;"> Click here to see the <orange>merits</orange> of our innovative and elegant solution.</div> </div> </div>


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Contact: <a href="mailto:BIOMODaustralia@gmail.com">BIOMODaustralia@gmail.com</a> | ©2014 Team EchiDNA. All rights reserved. This team is supported by the <a id="vccri" href="http://www.victorchang.edu.au">Victor Chang Cardiac Research Institute</a>. | <a id="edit-link" href="">Edit</a>

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