Simulation
Simulations were performed using the cando software based on the caDNAno designs discussed in the Design section. The examined models are 1. Neutral, 2.Closed, 3.Open, 4. Free (control).
- Neutral: Latch and Bridge are single-stranded.
- Closed: Latch forms double-strands with complementary DNA while Bridge is single- stranded.
- Open: Bridge and Open form double strands, while Latch is single-stranded.
- Free: Latch and Bridge are not attached.
Here, the color bar under the figure reflects the calculated values for the stability of the DNA Origami, and the smaller the value, the more stable the structure is.
1. Neutral
The results are shown in Fig1. It can be told that one unit is composed of four parallelogram panels. In addition, Bridge was seen to be slightly bent in a V shape due to entropy effect.
/simulation/neutral1-optimize.gif)
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Fig.1 Neutral
2. Closed
The results are shown in Fig1. It can be told that one unit is composed of four parallelogram panels. In addition, Bridge was seen to be slightly bent in a V shape due to entropy effect.
/simulation/close1-optimize.gif)
/simulation/close2-optimize.gif)
Fig.2 Closed
3. Open
The results are shown in Fig. 3. The double-stranded DNA shown in the center area of the DNA Origami is the hybridized Actuator and Open. Due to the rigid double strands, the DNA Origami is not as bent as Neutral, and the Origami takes a flatter structure.
/simulation/open1-optimize.gif)
/simulation/open2-optimize.gif)
Fig.3 Open
4. Free
The results of are shown in Fig.4. In this state, only the DNA constructing the DNA Origami panels to compose one Miura-Folding unit exists. The structure was confirmed to take the flattest form out of all the states.
/simulation/free1-optimize.gif)
/simulation/free2-optimize.gif)
Fig.4 Free
Cando simulates what figure the unit structure takes when the DNA are forming double strands according to the design in caDNAno. Here, it should be noted that the stability is simply calculated from the location of the crossover in the DNA scaffold. The simulation does not take into account the other possible elements affecting the structure, such as the negative charge of the DNA. Thus, the DNA is shown to occasionally overlap or penetrate each other. Generally, DNA strands maintain a certain distance among each other due to repulsion from their negative charges. For the project, we took into account this repulsive force and the DNA Origami of our designed structure is designed to bend constantly in a single direction. For the results in 2. Closed, the structure is thought to have taken an unexpected form due to the simulation being incomplete in fully taking account the actual factors in play, instead of an error in our design.