Biomod/2011/Harvard/HarvarDNAnos:Results Sphere: Difference between revisions

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{{Template:Biomod/2011/Harvard/HarvardDNAnos}}
{{Template:Biomod/2011/Harvard/HarvardDNAnos}}
=Spherical Container=
=Spherical Container=
==Formation gel==
==Overview==
<br>
With our sphere design, we were able to:
[[Image:2011-07-06_Spheregel.jpg |600x600px| Figure 1.]]
*Fold and characterize through atomic force microscopy (AFM) the original Han et al. sphere, which we call the "closed" sphere.
<br>
*Fold and characterize through AFM our "open" sphere in which we removed all equator staple strands.
<br>
*Test various lock mechanisms to transition between the closed and open states of the sphere.
==AFM image of unpurified closed sphere sample==
 
<br>
Note that due to the sphere being a single-layer DNA structure and a popular shape for water droplets, it was hard to characterize via transmission electron microscopy.
[[Image:2011-07-06_Sphereunpurifiedclosed_AFM1.jpg |700x700px| Figure 2. Closed spheres]]
 
<br>
==Folding Origami==
<br>
===Gel===
==AFM image of gel-purified open sphere band==
{|
<br>
| At right we have a 2% agarose gel of spheres in the closed and open states. The circled bands indicate possible locations of desired origami in the gel. We expect the closed and open state spheres to run faster than scaffold, as they are more compact. Indeed, closed spheres can be found in the band boxed in the "Closed Sphere" lane and open spheres can be found in the middle box of the "Open Sphere" lane. AFM imaging of the top band proved inconclusive, but we theorize that the higher band is an aggregated form of the open sphere, perhaps two open spheres bound together.
[[Image:2011-08-10_spheregelpur8bp_bottom1.jpg|700x700px| Figure 3. Open spheres (8bp lock)]]
 
<br>
| [[Image:2011-07-06_Spheregel.jpg |350px]]  
<br>
|}
==AFM zoom-in image of open spheres==
 
<br>
===Closed Sphere===
[[Image:2011-08-03_sphere8bplock4.jpg |700x700px| Figure 4. Open spheres (8bp lock)]]
{|
<br>
| We successfully recreated the Han et al. sphere down to the base, and were able to characterize the structure under AFM. The AFM image at right shows an unpurified sample of closed sphere. We find circles consistently around 50 nm in diameter. Han et al. designed the closed sphere to be 42 nm in diameter; considering flattening that may occur when the sphere is AFMed and the width of the AFM cantilever, these circles are what we expect closed spheres to look like under AFM.
<br>
 
| [[Image:2011-07-06_Sphereunpurifiedclosed_AFM1.jpg |350px]]
|}
 
==Opening the Sphere==
===Open Sphere===
{|
| We removed the equator staples that hold the two halves of Han's sphere together to create an open state held together only by a scaffold crossover. To make this open state close-able, we designed equator staples with extensions that can bind to a "lock" strand that closes the sphere.
 
To the right is an AFM image of gel-purified open spheres with equator staples compatible with such a closing mechanism. We see that each structure is comprised of two circles of diameter ~50 nm, which is what we expect to see of open spheres when their two halves are splayed open along the plane of the AFM image.
 
| [[Image:2011-08-10_spheregelpur8bp_bottom1.jpg|350px]]
|}
{|
| Here is a zoomed-in version of open spheres. In this image we see rings in addition to circles, indicating an orientation of open spheres where the edges of each hemisphere point up (imagine the AFM image two bowls side by side on a table would create).
 
| [[Image:2011-08-03_sphere8bplock4.jpg |350px]]
|}
 
 
</div>
</div>

Revision as of 02:47, 2 November 2011

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Home              Mission              Process              Designs              Results              Resources              Team

Spherical Container

Overview

With our sphere design, we were able to:

  • Fold and characterize through atomic force microscopy (AFM) the original Han et al. sphere, which we call the "closed" sphere.
  • Fold and characterize through AFM our "open" sphere in which we removed all equator staple strands.
  • Test various lock mechanisms to transition between the closed and open states of the sphere.

Note that due to the sphere being a single-layer DNA structure and a popular shape for water droplets, it was hard to characterize via transmission electron microscopy.

Folding Origami

Gel

At right we have a 2% agarose gel of spheres in the closed and open states. The circled bands indicate possible locations of desired origami in the gel. We expect the closed and open state spheres to run faster than scaffold, as they are more compact. Indeed, closed spheres can be found in the band boxed in the "Closed Sphere" lane and open spheres can be found in the middle box of the "Open Sphere" lane. AFM imaging of the top band proved inconclusive, but we theorize that the higher band is an aggregated form of the open sphere, perhaps two open spheres bound together.

Closed Sphere

We successfully recreated the Han et al. sphere down to the base, and were able to characterize the structure under AFM. The AFM image at right shows an unpurified sample of closed sphere. We find circles consistently around 50 nm in diameter. Han et al. designed the closed sphere to be 42 nm in diameter; considering flattening that may occur when the sphere is AFMed and the width of the AFM cantilever, these circles are what we expect closed spheres to look like under AFM.

Opening the Sphere

Open Sphere

We removed the equator staples that hold the two halves of Han's sphere together to create an open state held together only by a scaffold crossover. To make this open state close-able, we designed equator staples with extensions that can bind to a "lock" strand that closes the sphere.

To the right is an AFM image of gel-purified open spheres with equator staples compatible with such a closing mechanism. We see that each structure is comprised of two circles of diameter ~50 nm, which is what we expect to see of open spheres when their two halves are splayed open along the plane of the AFM image.

Here is a zoomed-in version of open spheres. In this image we see rings in addition to circles, indicating an orientation of open spheres where the edges of each hemisphere point up (imagine the AFM image two bowls side by side on a table would create).


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