Biomod/2013/Komaba/Project

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== Background of Project ==
 
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There were many previous studies related to the spontaneous activities of biomolecules like kinesin, which is a class of motor proteins, or walking DNA robots. But genuine nano-scale rotating DNA motors were not yet created. In our project, we are aiming at creating the DNA screw system to achieve this goal. The DNA screw was name after the rotary motion which is similar to that of screws. The rotation system is used to create the complex motion with any devices, such as drills, screws and clocks. Therefore we have thought that the nano-scale rotation system enables us to extend the future of DNA engineering. By this particular rotation move, the DNA screw is not just an other molecular motor, but a scalable and potential new feature for more complex molecular devicesIn addition, DNA is a stable material than protein and can be used in various environments (ex. Temperature, pH and salt-density).
 
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== Vision for the future ==
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==<br/>Background of Project ==
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One of our project’s applications is a suspension rod. 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.  
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Many kinds of active biomolecules such a kinesin and DNA walkers which are a class of motor proteins and artificial chemical devices have been 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 to create 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.
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==Process of the making DNA screw==
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By using suspending movement, our DNA screw can measure kinetic properties. In detail, the DNA screw has FRET and emits fluorescence when the relative distance between the ring and cylinder changes in preparation. Then, the DNA screw is attached to an object such as a protein. The kinetic force is detectable by observing FRET's emission. Compared to AFM, this method can observe one protein's elastic force.
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Furthermore, this DNA suspension rod can provide a dynamical creating methodology for large micro-scale structures from nano-scale objects. We assume that tensegrity can be used to obtain these objects. Our DNA cylinders can function as cables 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.
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[[Image:biomod-2.jpg]]
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utting connections between DNA cylinders and nano rods and discomposing a large tensegrity structure.
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The key components of DNA screw are three; A cylinder, a ring, and DNA spider. In addition, to visually see how the spider actually move, simulation is also an important factor of our project.
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==Vision for the future ==
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[[Image:FigureP1.jpg|frame|Figure P2]]
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First of all, our DNA screw is designed to be appled to phage-like functional structure(Figure P2). Phages make pores on the cellular surface and inject DNA or RNA genome inside cells. It has to be researched on what way the structure attaches to the surface and makes pores
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[[Image:FigureP2.jpg|frame|Figure P3]]
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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. The rod stretching 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.
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By using suspending movement, our DNA screw can act as a biophysical sensor which measures kinetic properties. For example, DNA screw can be applied to unfolding proteins. The cylinder is attached to a protein, the ring stretches protein’s one end.
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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.
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Reference:
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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.

Current revision



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 have been 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 to create 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-2.jpg

The key components of DNA screw are three; A cylinder, a ring, and DNA spider. In addition, to visually see how the spider actually move, simulation is also an important factor of our project.

Vision for the future

Figure P2
Figure P2

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

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. The rod stretching 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 which measures kinetic properties. For example, DNA screw can be applied to unfolding proteins. The cylinder is attached 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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