Biomod/2013/StJohns/introduction: Difference between revisions

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====Abstract====
===Motivation===
 
There are many ways to detect viruses, but they rely on detecting small pieces of the virus rather than the whole structure. If we could reliably detect the entire virus rather than just a part, this could be applied to the rapid diagnosis of viral diseases as well as rapid detection of infectious agents in the environment.
 
===Project Overview===
The goal of this project is to design and characterize a DNA origami<sup>[[Biomod/2013/StJohns/References|[1]]]</sup> (DO) structure that undergoes significant conformational changes when bound to objects ranging in size from 10-100 nm.
The goal of this project is to design and characterize a DNA origami<sup>[[Biomod/2013/StJohns/References|[1]]]</sup> (DO) structure that undergoes significant conformational changes when bound to objects ranging in size from 10-100 nm.


Since binding-specifc conformational change can be transduced into a signal, this should enable the design of nanometre-scale sensors for viruses.
Since binding-specific conformational change can be transduced into a signal, this should enable the design of nanometre-scale sensors for viruses.
 
In our [[Biomod/2013/StJohns/Approaches#claw|proof-of-principle approach]], the origami structure is a three-pronged  DO ‘claw’<sup>[[Biomod/2013/StJohns/References|[2]]]</sup> with sticky-ended DNA strands complementary to the surface of a modified<sup>[[Biomod/2013/StJohns/References|[3]]]</sup> bacteriophage MS2 capsid substrate.
 
In parallel, we will investigate several other aspects of the design:
* [[Biomod/2013/StJohns/Approaches#selection|We will make ‘libraries’ of claws that have different geometries of virus-binding sites and select the most avid claw(s) for further study and optimization.]]
* [[Biomod/2013/StJohns/Approaches#antibodies|We will investigate immunoglobulins as potential binding elements for use in future claw designs.]]
* [[Biomod/2013/StJohns/Approaches#triangles|We will investigate methods of controlling the vertex angles of DO structures using computer-aided design.]]


In our proof-of-principle approach, [[Biomod/2013/StJohns/design#Virus-Binding Claw|the origami structure]] is a three-pronged  DO ‘claw’<sup>[[Biomod/2013/StJohns/References|[2]]]</sup> with sticky-ended DNA strands complementary to the surface of a modified<sup>[[Biomod/2013/StJohns/References|[3]]]</sup> [[Biomod/2013/StJohns/design#Model Virus Capsid|bacteriophage MS2 capsid substrate]].


To characterize the conformational changes and binding interactions of this system, we will use four primary methods:
To characterize the conformational changes and binding interactions of this system, we will use four primary methods:
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*[http://en.wikipedia.org/wiki/Dynamic_light_scattering Dynamic Light Scattering]
*[http://en.wikipedia.org/wiki/Dynamic_light_scattering Dynamic Light Scattering]


====Youtube video====
====Near-Term Goals====
* [[Biomod/2013/StJohns/approaches#Claw|The basic claw design itself:]]
**Synthesis of the claw with (‘sticky’) and without (‘blunt’) single-stranded binding elements.
**Synthesis of the claw with and without fluorescent tags for FRET analysis.
**Show that these claws fold into single structures (by testing for single band formation on electrophoresis gel).
**Visualize these claws on AFM to show that they take the desired shape.
**Verify that different FRET-tagged claw versions can be visually distinguished on a gel.
**Demonstrate that FRET occurs when the claw is bound to the capsid substrate.
**Show that the binding interaction between the claw and the virus capsid produces a visible change in gel mobility.
**Show that the functional claw preferentially binds to the functionalized substrate, not other objects.
**Differentiate bound and unbound claw/capsid mixtures via DLS.
* [[Biomod/2013/StJohns/approaches#Selection|Methods of selecting the most avid claws from a ‘library’ of designs with different binding-site geometries:]]
**Provide proof of principle for the use of a selection model to optimize claw avidity in the next phase of the project.
* [[Biomod/2013/StJohns/approaches#Antibodies| The potential use of immunoglobulins as binding elements in future claw designs:]]
**Demonstrate that we can isolate anti-Flag FAB fragments reliably and effectively.
**Attach small model ketones to DNA strands as a preliminary to attaching FAB fragments.
* [[Biomod/2013/StJohns/approaches#Triangle Tiles|Methods of controlling the vertex angles of DO structures for precise hinge angles:]]
**Synthesize small DO triangle elements with precise geometries, and verify these geometries on AFM.
 
===Youtube Video===


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<html><center><iframe class="youtube-player" style="text-align:center" type="text/html" width="420" height="315" src="http://www.youtube.com/embed/pdfXxF9UCWk" frameborder="0" allowfullscreen></iframe></center></html>

Latest revision as of 19:57, 26 October 2013

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Motivation

There are many ways to detect viruses, but they rely on detecting small pieces of the virus rather than the whole structure. If we could reliably detect the entire virus rather than just a part, this could be applied to the rapid diagnosis of viral diseases as well as rapid detection of infectious agents in the environment.

Project Overview

The goal of this project is to design and characterize a DNA origami[1] (DO) structure that undergoes significant conformational changes when bound to objects ranging in size from 10-100 nm.

Since binding-specific conformational change can be transduced into a signal, this should enable the design of nanometre-scale sensors for viruses.

In our proof-of-principle approach, the origami structure is a three-pronged DO ‘claw’[2] with sticky-ended DNA strands complementary to the surface of a modified[3] bacteriophage MS2 capsid substrate.

To characterize the conformational changes and binding interactions of this system, we will use four primary methods:

Near-Term Goals

Youtube Video

<html><center><iframe class="youtube-player" style="text-align:center" type="text/html" width="420" height="315" src="http://www.youtube.com/embed/pdfXxF9UCWk" frameborder="0" allowfullscreen></iframe></center></html>

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