Mechanism
Assembly
A single DNA strand will pair itself with the most complementary strand under suitable circumstances. Utilizing this characteristic, we designated several single strands onto the sides of the base and the lids.
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These stands are illustrated as follows, protruding from itselves. With their help, the monomers are able to connect to each other, and can even react to signals added afterwards.
Before mixing all the monomers together, two process has to be conducted, let's take a look at the right side of the device. (The mechanism on the other side is virtually the same, only the sequences were changed.)
Adding the Blockers
"Blocking staple" (D'CF'B) is added to the base monomer to avoid staple DEF from interacting with staple XE' on the lid. (Figure 1 & 2)
Figure 1 & 2
Adding the Hinges
"Hinge" (J'YK') is added to the lids, which partly pairs with the J on the lid. This is an important step because this very "hinge" serves as a direction guide. (Will discuss in the next section)
Figure 3 & 4
Combinig the Components
Now that we complete the blocker and hinge adding, we can mix the components together. As shown in (Figure 5, 6) , A' on the base will partly pair with AB on the lid. At the same time, J'YK', now partly pairs with the J on the lid, will partly pairs with the K on the base, and the unpaired Y added flexibility to the rotating hinge, guiding the monomers to assemble in the correct direction. Without the hinges’ help, the mixing of monomers may lead to undesirable forms. (see Figure 8) If done right, the device should look like the picture below. (Figure 7)
Figure 5
Figure 7
Figure 6
Figure 8
(Undesirable Form)
Starting to Flip
When both sides are properly anchored, it is time that we made it rotate! As shown in Figure 9, DC'FB'A' serves as the signal that initiates the rotation. When added, it will compete with the binding of DEF and D'CF'B. Since DC'FB'A' is better matched with D'CF'B (the blocker), they will drop off the base together; thus, the blocker is removed (Figure 10). In addition, DC'FB'A' will also compete with A' , and the AB will be taken away (Figure 11).
Now that the pairing on the side no longer exists, the lid is free to rotate within 180 degrees, for the hinge is still holding it on the base. Then, by Brownian motion, XE' can meet DEF within reaction range. They will be paired since this is the most thermodynamically favorable reaction (Figure 12).
Hence, the flipping is complete, resulting in an opening form on one side. If another set of signal is introduced, the other side may flip as well using the same principle.
Figure 9
Figure 10
The lid rotates 90°
counterclockwise