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=Rectangular Box Container Design=
[[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.
*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 [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.'''


<div style="padding: 10px; width: 800px; border: 5px solid #333333;">
''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Box | Continue reading...]]''


=Rectangular Box Container Design Summary=
See also: ''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Box_Container | Rectangular Box Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Methods#Rectangular Box Methods | Rectangular Box Methods]]''
[[Image:Screen Shot 2011-10-20 at 1.19.58 AM.png|thumb|right| Figure 1.]]
*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, a box which we feel stands a much better chance of keeping cargo inside and which is more straightforward to fold and to characterize.


=Spherical Container Design=
[[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"] (Figure 2).


''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Box | Continue reading...]]''
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.
<br>See also:
''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Box_Container | Box Results]]''


=Spherical Container Design Summary=
'''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.'''
[[Image:Sphere_Han_model.png |thumb|right|Figure 2. A three-dimensional model of the Han sphere (Han et al. 2011).]]
[[Image:2011-06-13_figure1.png |thumb|right|Figure 3. A two-dimensional, caDNAno representation of the Han sphere.]]
*In our search for a robust and elegant design, we were inspired by the origami sphere that Dongran Han demonstrated in their 2011 Science paper [http://www.sciencemag.org/content/332/6027/342.full "DNA Origami with Complex Curvatures in Three-Dimensional Space"].
**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 imagined that we would be able to change the design of the Han sphere to make it an openable and closable container.


*The design principles for an origami sphere (and other 3D origami with complex curvatures) employed by Han are the following (see Figure 1):
''[[Biomod/2011/Harvard/HarvarDNAnos:Design_Sphere | Continue reading...]]''
**Multi-planar arrangement of parallel double helices with in-plane curvature of helices into  rings, and
**Curvature across planes caused by different ring sizes and greater distance between crossovers in larger rings than in smaller rings.
*Ultimately, the Han sphere is comprised of 24 parallel rings of helices (12 rings in each hemisphere) and is 6626 bases long. Its largest ring is 42 nm in diameter and the hole at each pole is 4 nm.


*To adapt the Han sphere to our purposes, we first had to generate a caDNAno file from diagrams provided in Han's supplementary materials. We succeeded in reconstructing the Han sphere down to the base and matched all staple strands generated by caDNAno to staple strands used by Han et al.
See also:''[[Biomod/2011/Harvard/HarvarDNAnos:Results#Sphere_Container | Sphere Results]]'', ''[[Biomod/2011/Harvard/HarvarDNAnos:Methods#Sphere Methods | Sphere Methods]]''
**The final caDNAno file can be found here: [[Media:Sphere_match.json]] (see Figure 2).




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


=Cargo=
=Cargo Design=
[[Image:Screen_Shot_2011-10-23_at_1.17.21_PM.png |thumb|right|Figure 4. Strand Displacement Mechanism for Displacing Cargo]]
[[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.]]
[[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 <b>provide them with functionality</b>. 
*We use 5-nm gold nanoparticle cargo as a test platform for our ability to <b>capture, contain, and controllably release cargo</b>.
*We chose 5-nm gold nanoparticles because the sharp contrast they provide under TEM helps us to classify our results easily.


*With a few container designs in mind, our next goal was to provide them with functionality. 
**We decided to use 5nm gold particle cargo as a test platform for our ability to capture, contain, and controllably release cargo. 
**We decided to use 5nm gold particles because the sharp contrast they provide under TEM would help us to classify our results easily.
*Our primary mechanism for attaching cargo involved conjugating 5nm gold particles to DNA strands complementary to staple strands extending into the the inside of our containers. 
*We then designed two processes to release our cargo within our containers:  strand displacement and photo-cleavage. 
**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 | Photo-cleavage 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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Latest revision as of 16:15, 2 November 2011

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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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