Biomod/2011/Harvard/HarvarDNAnos:Designs: Difference between revisions

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{{Template:Biomod/2011/Harvard/HarvardDNAnos}}
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=Rectangular Box Container Design=
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[[Image:Screen Shot 2011-10-20 at 1.19.58 AM.png|thumb|right|Figure 1. A [http://cando.dna-origami.org/ CanDo] model of a component of our rectangular box.]]
 
[http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html Andersen's box] impressed us with its ability to open and close, but we worried about its robustness and tightness as a container.  
=Rectangular Box Container Design Summary=
*Cryo-EM imaging performed by Andersen revealed that the faces are either bent inward or outward.  
[[Image:Screen Shot 2011-10-20 at 1.19.58 AM.png|thumb|right|Figure 1. A model of a component of our rectangular box.]]
*Furthermore, the Andersen box is formed from a one-layer DNA sheet and, as such, is held together by five potentially weak seams.  
*Andersen's box impressed us with its ability to open and close, but we worried about its robustness and tightness as a container.  
'''Therefore, with the help of [http://yin.hms.harvard.edu/people/sun.wei/index.html Wei Sun], we have designed our own box, which we feel stands a much better chance of keeping cargo inside and which is more straightforward to fold and to characterize.'''
**Cryo-EM imaging performed by Andersen revealed that the faces are either bent inward or outward.  
**Furthermore, the Andersen box is formed from a one-layer DNA sheet and, as such, is held together by five potentially weak seams.  
*Therefore, with the help of Wei Sun, we have designed our own box, which we feel stands a much better chance of keeping cargo inside and which is more straightforward to fold and to characterize.


''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Box | Continue reading...]]''
''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Box | Continue reading...]]''
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See also: ''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Box_Container | Rectangular Box Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Methods#Rectangular Box Methods | Rectangular Box Methods]]''
See also: ''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Box_Container | Rectangular Box Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Methods#Rectangular Box Methods | Rectangular Box Methods]]''


=Spherical Container Design Summary=
=Spherical Container Design=
[[Image:Sphere_Han_model.png |thumb|right|Figure 2. A three-dimensional model of the Han sphere (Han et al. 2011).]]
[[Image:Sphere_Han_model.png |thumb|right|Figure 2. A three-dimensional model of the Han sphere (Han et al. 2011).]]
*In our search for a robust and elegant design, we were inspired by the origami sphere that Dongran Han demonstrated in his 2011 Science paper [http://www.sciencemag.org/content/332/6027/342.full "DNA Origami with Complex Curvatures in Three-Dimensional Space"].
In our search for a robust and elegant design, we were inspired by the origami sphere that Dongran Han demonstrated in his 2011 Science paper [http://www.sciencemag.org/content/332/6027/342.full "DNA Origami with Complex Curvatures in Three-Dimensional Space"] (Figure 2).
*The design principles for an origami sphere (and other 3D origami with complex curvatures) employed by Han are the following (see Figure 1):
 
**Multi-planar arrangement of parallel double helices with in-plane curvature of helices into  rings, and
The spherical design appealed to us because of its efficient use of DNA and lack of weak points--that is, instead of having edges, it only has two holes at each pole, minimizing spots where cargo can leak out.
**Curvature across planes caused by different ring sizes and greater distance between crossovers in larger rings than in smaller rings.
 
'''We changed the design of the Han sphere to make it an openable and closable container. To open the sphere, we removed all staple strands holding its two hemispheres together; to close the sphere, we designed a system of locks; and to re-open the sphere, we designed strand displacement and photocleavage mechanisms.'''


''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Sphere | Continue reading...]]''
''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Sphere | Continue reading...]]''
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See also:''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Sphere_Container | Sphere Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Methods#Sphere Methods | Sphere Methods]]''
See also:''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Sphere_Container | Sphere Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Methods#Sphere Methods | Sphere Methods]]''


=Cargo=
[[Image:Screen_Shot_2011-10-23_at_1.17.21_PM.png |thumb|right|Figure 4. Strand Displacement Mechanism for Displacing Cargo]]
[[Image:Screen_Shot_2011-10-23_at_1.45.54_PM.png |thumb|right|Figure 5. Photo-cleavable SpacerMechanism for Displacing Cargo]]


*With a few container designs in mind, our next goal was to provide them with functionality.   
 
**We decided to use 5 nm gold nanoparticle cargo as a test platform for our ability to capture, contain, and controllably release cargo.   
=Cargo Design=
**We decided to use 5 nm gold nanoparticles because the sharp contrast they provide under TEM would help us to classify our results easily.
[[Image:Bestdnanp.jpg |thumb|right|Figure 3. We conjugated ssDNA strands to 5 nm gold nanoparticles. We could attach a single ssDNA strand, or multiple ssDNA strands, per nanoparticle.]]
*Our primary mechanism for attaching cargo involved conjugating 5 nm gold nanoparticles to ssDNA strands complementary to staple strands extending into the the inside of our containers. 
With a few container designs in mind, our next goal was to <b>provide them with functionality</b>.   
*Conjugation of gold to ssDNA was made possible by ordering our ssDNA with thiolated 5' or 3' ends.
*We use 5-nm gold nanoparticle cargo as a test platform for our ability to <b>capture, contain, and controllably release cargo</b>.   
*We then designed two processes to release our cargo within our containers: strand displacement and photo-cleavage.
*We chose 5-nm gold nanoparticles because the sharp contrast they provide under TEM helps us to classify our results easily.
**For the strand displacement method we engineered a staple extension within each structure complementary to a region of the DNA strand conjugated to our gold nanoparticles. The gold nanoparticles would in turn be displaced by a key strand we engineered to be brought into the vicinity of our structure (most specifically for the sphere) by an exterior toehold, and then would bind to a single stranded region of the container's staple extension, and would then proceed by kinetic probability to displace the conjugated AuNP by preferentially binding to its complementary region with the container's staple extension.   (See Figure 3 for a depiction of this process in the sphere)
 
**For the photo-cleavage method, we designed a staple extension into the interior of our containers that contained a region complementary to the DNA bound to our conjugated gold nanoparticles, but also a photo-cleavable spacer prior to the binding site with the gold nanoparticle's DNA strand.  Thus, after binding of the AuNP and the subsequent introduction of UV light, the nanoparticle's attachment to the inside of the container would be severed, and the NP would move freely within until subsequent (or simultaneous) opening of the container.  (See Figure 4 for a depiction of this process in the sphere.)
 
''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Cargo | Continue reading...]]''


See also:
See also:
''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Sphere#Loading Cargo | Cargo in the Sphere]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Box | Cargo in the Box]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Nanoparticles | Nanoparticle Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Photocleavage | Photocleavage Results]]''
''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Sphere#Loading Cargo | Cargo in the Sphere]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Box | Cargo in the Box]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Nanoparticles | Nanoparticle Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Photocleavage | Photocleavage Results]]''
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Home              Mission              Process              Designs              Results              Resources              Team

Rectangular Box Container Design

Figure 1. A CanDo model of a component of our rectangular box.

Andersen's box impressed us with its ability to open and close, but we worried about its robustness and tightness as a container.

  • Cryo-EM imaging performed by Andersen revealed that the faces are either bent inward or outward.
  • Furthermore, the Andersen box is formed from a one-layer DNA sheet and, as such, is held together by five potentially weak seams.

Therefore, with the help of Wei Sun, we have designed our own box, which we feel stands a much better chance of keeping cargo inside and which is more straightforward to fold and to characterize.

Continue reading...

See also: Rectangular Box Results, Rectangular Box Methods

Spherical Container Design

Figure 2. A three-dimensional model of the Han sphere (Han et al. 2011).

In our search for a robust and elegant design, we were inspired by the origami sphere that Dongran Han demonstrated in his 2011 Science paper "DNA Origami with Complex Curvatures in Three-Dimensional Space" (Figure 2).

The spherical design appealed to us because of its efficient use of DNA and lack of weak points--that is, instead of having edges, it only has two holes at each pole, minimizing spots where cargo can leak out.

We changed the design of the Han sphere to make it an openable and closable container. To open the sphere, we removed all staple strands holding its two hemispheres together; to close the sphere, we designed a system of locks; and to re-open the sphere, we designed strand displacement and photocleavage mechanisms.

Continue reading...

See also: Sphere Results, Sphere Methods


Cargo Design

Figure 3. We conjugated ssDNA strands to 5 nm gold nanoparticles. We could attach a single ssDNA strand, or multiple ssDNA strands, per nanoparticle.

With a few container designs in mind, our next goal was to provide them with functionality.

  • We use 5-nm gold nanoparticle cargo as a test platform for our ability to capture, contain, and controllably release cargo.
  • We chose 5-nm gold nanoparticles because the sharp contrast they provide under TEM helps us to classify our results easily.


Continue reading...

See also: Cargo in the Sphere, Cargo in the Box, Nanoparticle Results, Photocleavage Results





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