Structure
Base and Lid-like Structure
Inspired by the "Paper Fortune Teller", we thrived to think of a structure that can satisfy our main goal: to control the revealing of one surface originally hidden; while simultaneously hide the surface that is originally exposed.
We eventually come up with a structure consists of three components: Base, Left lid, and right lid. The combination of these three is what we called "NANO-FACEOFF", for it can "change its face" when we give different DNA single strands signals. To understand how it works, see mechanism.
Base
The base is a 54.0nm x 15.9nm x 10.2nm E-shaped structure, which serves as the foundation for the two lids. It makes sure that the lids can properly attach to the pillars on the base.
Figure 1
Figure 2&3&4
In Figure 1, we can see that the base looks like a plate with eight stretching hexagonal columns. The thickness of the plate and the pillars are about 10.2nm and 25.5nm respectively. On the top of some pillars, there are different modifications which can attach to lids, hinges and blockers. In Figure 2, 3 and 4, we can see the pillars No.11, 13, 15, 17, 107 and 121, have 3’ single strand DNAs modification while No. 60, 74, 160, 162, 164 and 174 have 5’ ssDNA modification. (Arrows in the figure mean 3’ end, while squares mean 5’ end.)
Lids
The lids are 24.0nm x 15.9nm x 10.5nm L-shaped structure. Both lids are pretty much identical in appearance. They can rotate when given specific signals.
Right lid
Pillars No. 13, 15, 41 and 51 have 5’ single strand DNAs modification stretching downward, while No. 59 and 69 have 3’ single strand DNAs stretching upward (Rotate the staple and scaffold figure 90 degrees to left).
Left lid
Pillars No. 13, 15, 41 and 50 have 3’ single strand DNAs modification stretching downward, while No. 59 and 69 have 5’ single strand DNAs stretching upward(Rotate the staple and scaffold figure 90 degrees to right).
Sequence Design
3’ single strand DNAs on the lids can stick to the 5’ single strand DNAs on the base, and vice versa. Table 1 will illustrate the linkage sequences between base and lids. Note that those ssDNAs having 3’ modification will have a poly-A section on their 5’ end, and those having 5’ modification will have a poly-A section on their 3’ end. This design allows the single strand DNAs to move freely and be easier to connect with their designated pairings.
Table 1
3D structural model
3D structure made by Blender and Vectary is displayed below. It shows the design of our base and lids in 360 degree. You can rotate it at will, as well as zoom in to observe specific part of the structure.