Biomod/2013/Komaba/Project

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Background of Project

Many kinds of active biomolecules such a kinesin and DNA walkers which are a class of motor proteins and artificial chemical devices are studied, and their features inspired biomimetics, a large research area aiming at mimicking organism to design novel materials. One of the aims of biomimetics is creating motors by using recent DNA synthesis technologies. We challenged to design a DNA-based rotational structure, named “DNA screw.” Because genuine nano-scale rotating DNA motors are not yet demonstrated, designing such motors is a challenging subject. This structure consists of a small cylinder inside a large ring, which are connected by DNA strands. Since our structure is made of DNA, combining other existing DNA structures is feasible.

Process of the making DNA screw

Image:biomod-1.png

Vision for the future

Figure P2
Figure P2

First of all, our DNA screw is designed to apply phage-like functional structure(Figure P2). Phages make pores on the cellular surface and inject DNA or RNA genome inside cells. On what way the structure attaches to the surface and makes pores has to be researched.

Figure P3
Figure P3

In addition, one of our project’s applications is a suspension rod(Figure P3). Let’s imagine a pointer used in class lectures. The rod contains many cylinders and can extend and shrink by changing a relative distance of each cylinder. Inner cylinder corresponds to the DNA cylinder and outer one does to the DNA ring in our project. In addition, how the rod stretch can be controlled by ordering DNA strands. For example, the rod, which has zigzag-placed strands in parallel to the cylinder's axis, can shrink and suspend spontaneously.

By using suspending movement, our DNA screw can act as a biophysical sensor measures kinetic properties. For example, DNA screw can be applied to unfolding proteins. Attaching the cylinder to a protein, the ring stretches protein’s one end.

Furthermore, this DNA suspension rod can provide a dynamical creating methodology for large micro-scale structures from nano-scale objects such as DNA tensegrity by Liedl et al. (2010). We assume that our DNA cylinders can function as strings and rod-shape structures such as carbon nanotube can work as rods. This method contains three steps. First, combining DNA cylinders and nano rods. Second, starting DNA spiders' movements and reaching a maximum-strength state. Third, cutting connections between DNA cylinders and nano rods and discomposing a large tensegrity structure.

Reference: Tim Liedl, Björn Högberg, Jessica Tytell, Donald E. Ingber, and William M. Shih, Self-assembly of 3D prestressed tensegrity structures from DNA. Nat Nanotechnol. 2010 July ; 5(7): 520–524.

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