Biomod/2011/Harvard/HarvarDNAnos:Design Box

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Rectangular Box Container Design

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Specifications and Schematics

Figure 1. Summary of general design principles of box.
Figure 1. Summary of general design principles of box.
  • Our box consists of two separately-folded scaffolded origami structures: a barrel and a lid.
    • The barrel is two DNA layers thick, and the lid is three DNA layers thick.
    • The lid is designed to cover an end of the barrel, an interaction achieved through DNA base-pairing interactions between "lock strands" that protrude from the barrel and the lid.
    • The box is in its closed state when the barrel has associated with two lids, one lid covering the top, and one covering the bottom.
    • Both the lid and barrel can be folded with protruding ssDNA "handles" capable of binding ("loading") a ssDNA-conjugated 5-nm gold nanoparticle such that closing of the box places the nanoparticle inside the box.
    • These nanoparticles can be subsequently solubilized via photocleavage of a photocleavable spacer that can be internalized onto the handle.
    • The box can be opened from its closed state via introduction of a ssDNA "key" signal that performs strand-displacement of the lid.
  • Figure 1, in two dimensions only, summarizes the general design principles governing this box, omitting the second lid for clarity.
  • Figure 2 provides a more detailed three-dimensional schematic analysis of the barrel and lid, including dimensions, positioning and complementarity of protrusions such as lock strands and handles, and the character of possible additional inputs into the system, such as our AuNP-DNA conjugates and key strands. Note that the barrel handle is not depicted for purposes of clarity.
Figure 2. Schematic of barrel and lid. Note that the barrel handle is not depicted for purposes of clarity.
Figure 2. Schematic of barrel and lid. Note that the barrel handle is not depicted for purposes of clarity.

Closing/Opening Mechanism

Figure 3. NUPACK analysis of closing/opening mechanism.
Figure 3. NUPACK analysis of closing/opening mechanism.
  • To close the box, simply introduce at least a two-fold excess of lids to barrels. Base-pairing interactions between lock strands on the lid and their complementary lock strands on the barrel should fit each barrel with two lids, one to cover each of its openings. (See Figure 2.)
  • To open the box, simply introduce an excess of the key strands to the closed boxes. These key strands will bind to the toeholds on the lid lock strands and subsequently strand-displace the barrel off of both of its lids.
  • Figure 3 is NUPACK's analysis of our closing/opening mechanism's base-pairing interactions.

Loading and Solubilization of Nanocargo

  • Both the lid and barrel can be folded with protruding ssDNA "handles" capable of binding ("loading") a ssDNA-conjugated 5-nm gold nanoparticle such that closing of the box places the nanoparticle inside the box. (See Figure 2.) There are three handles inside our barrels whereas only one handle on our lids.
  • These nanoparticles can be subsequently solubilized via photocleavage of an photocleavable spacer that can be internalized onto the handle. When used, the PC spacer for both the lid and the handle is located exactly in between the origami structure and the beginning of the handle. (See Figure 2.)

CanDo Visualizations

The three embedded videos below are CanDo visualizations of our barrel (one view) and our lid (both top view and side view). The animation and coloration shows estimates of positional fluctuations in thermal equilibrium at room temperature.

3D Viewer

Here are 3D views of the barrel and lid. To zoom out in order to see the full barrel and lid, select "zoom" from the menu bar and drag the mouse downwards.

Source Files

  • Here are the caDNAno files we created to generate staple sequences for our origami structures. Figures 4 and 5 below are caDNAno-generated SVG files of the barrel and lid, respectively.
  • Here is an Excel file of the DNA sequences for both our origami structures, the protrusions from our origami structures, and the possible additional inputs. It should help you understand the caDNAno files better.
Figure 4. Strand diagram for barrel.
Figure 4. Strand diagram for barrel.
Figure 5. Strand diagram for lid.
Figure 5. Strand diagram for lid.

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