Introduction
To achieve our project, we designed various DNA structures with caDNAno. As mentioned in “Project” page, helical structure is a very efficient structure to move at nano scale. However, when we designed that structure, we faced two major obstacles. One was the stability of the structure, and the other was the size.
1st Obstacle
First, we discuss about the size. Just like most machines, measuring devices, such as AFM, are vulnerable to the magnetic field. Thus we want to observe the structures with optical microscope which is not broken by the magnetic field. However, the resolution of the optical microscope is only 200nm. So we proposed to make a structure with a size of more than 300nm. In addition, there is another advantage by increasing the size. The advantage is that we can definitely perform sputtering. If the structure is small, nickel may get into the gap of the helical structure and bury the gap. However, there are also disadvantages by increasing the size. One of them is that the structures become unstable and the cost also becomes expensive.
2nd Obstacle
Next, we refer on the stability.
If the structure is not stable enough, it is probably broken when sputtering is performed or it moves in the solution.
So we had difficulties in balancing the size, stability and cost-wise.
Design
Fig2.size description of a helix
Each number in Fig2. represents ①length, ②outside diameter, ③pitch, ④width and ⑤thickness. Furthermore, we add ⑥winding number to them, and express the size of a helix.
First of all, we designed a simple helical structure.
Fig3.simple helix
Its size is
①length：95nm
②outside diameter：30nm
③pitch：32nm
④width：10nm
⑤thickness：6nm
⑥winding number：2
However, as seen from the animation of Fig3, this structure is very unstable. Additionally, the size is too small to observe with the optical microscope. We made it large and thick, but it did not become stable very much.
So we enhanced its stability by reinforcing the structure of Fig3.
Fig4.helix surrounded by a cylinder
We succeeded in enhancing its stability greatly by surrounding it by a cylinder.
Its size is
①length：230nm
②outside diameter：36nm
③pitch：40nm
④width：10nm
⑤thickness：6nm
⑥winding number：4
Length of this structure is more than 200nm. So this structure can be operated with the optical microscope. However, this structure is too expensive to make in reality. It costs about 20,000$.
We perceived that its cost became expensive because of its cylinder. Therefore, we thought of another idea.
Fig5.helix supported by six poles
By supporting the helix by six poles instead of the cylinder, we made the structure cheap and stable.
Its size is
①length：100nm
②outside diameter：30nm
③pitch：30nm
④width：10nm
⑤thickness：6nm
⑥winding number：2
This structure is not long enough, but we think it will be able to be developed by devising from now on.
Furthermore, we came up with the idea to make the similar structure of Fig4. cheaper.
We thought of the way to make a structure with an optional length by connecting same structures. We called unit structure of this structure “car”, and connected structure “tram”.
Fig6.car
The size of "car" is
①length：30nm
②outside diameter：30nm
④width：7nm
⑤thickness：6nm
⑥winding number：2/3
In this research, we connect nine “cars” to make a “tram”.
Fig7.tram
So the size of "tram" is ①length：300nm
③pitch：40nm
⑥winding number：6
The advantages of this structure is to be able to change its length and cheap.
Fig8.mechanism of connecting cars
Next, we discuss mechanism of connecting cars. One combination uses two staple as adapter. (Fig8.) In this research, we combine at three places and connect nine cars. Thus, we have to prepare 48 kinds of base sequence. In addition, we also have to cover the end with staple. Each “car” connects specific car.We must pay attention to base sequences in order not to happen unexpected combination.
From the above results, we decided to experiment the structure of Fig5 and Fig7.