Biomod/2013/Komaba/Project

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(DNA Clocks)
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== Background of Project ==
 
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: There were many previous studies related to the spontaneous activities of biomolecules about Kinesin, which is a class of motor proteins, and walking DNA robots. But genuine nano-scale DNA motors which rotate at the stable speed were not yet created.
 
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: We are aiming at creating the DNA screw system to overcome these issues in the present studies.
 
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: 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.
 
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: The DNA screw has many strong points. DNA screw is able to embed in any other DNA structures and to be assembled into more complex structures easily, because we can take engineering approaches to make DNA structures. And, the size of the structure can be easily scaled. In 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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== Project Overview ==
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==<br/>Background of Project ==
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:    The motor made in this project comprises three parts; the cylinder as an axis, the DNA Spiders as a source of power, and the rotating ring. In the first phase in the project, we design each part and confirm if each part is actually formed as we design by an Atomic Force Microscope. Then, in the second phase, we develop a method to combine those three parts, which results in construction of the DNA screw.
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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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:    If you need details of each experiment, please click ">>read more" link and jump to Design page.
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==Process of the making DNA screw==
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===== (Phase 1) =====
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[[Image:biomod-2.jpg]]
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=== Cylinder ===
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:    The cylinder is put in the center of the motor as an axis supporting the rotation. The material DNA is formed into a cylindrical shape using DNA Origami technology. [[Biomod/2013/Komaba/Design#Cylinder|>>read more]]
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=== DNA Walker ===
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:   The sources of power in rotational motion is DNA Spiders. DNA Spider consists of three DNA Walker which moves on footing by taking strands after another with DNAzyme. As they orbit the cylinder, their rotational movement is transmitted to DNA Ring. [[Biomod/2013/Komaba/Design#DNA_Walker|>>read more]]
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=== Rotary Ring ===
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:    It is the DNA ring part that actually rotates. It has shape like the side surface of a disk, and is also composed with DNA Origami technology. [[Biomod/2013/Komaba/Design#Rotary_Ring|>>read more]]
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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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===== (Phase 2) =====
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==Vision for the future ==
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=== Motor ===
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[[Image:FigureP1.jpg|frame|Figure P2]]
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:   The motor is realized by assembling above thee parts: Cylinder, Spider, Ring. Unlike motors in electrical work, rotary parts of our motor is outer ones and the central cylinder are fixed. [[Biomod/2013/Komaba/Design#Cylinder_Motor_(Combination_of_above_parts)|>>read more]]
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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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=== Another Structure ===
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:    The motor made in this project rotates by DNA spider and round footings. In this system, the cylinder becomes too long if motor make many revolutions. However, we have an idea which makes it possible to make lasting rotation by using long straight footing and DNA spiders positioned circularly.
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== Vision for the future(Phase ∞) ==
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[[Image:FigureP2.jpg|frame|Figure P3]]
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=== DNA submarine ===
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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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DNA submarine is a structure which move in a solution and transport materials. In addition, in combination with sensors made by DNA Origami technology, this DNA submarine would be able to develop into autonomous DNA robots which have the function of chemotaxis.
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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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=== DNA pore-forming ===
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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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If this DNA screw is realized, it would be possible to make a hole on the surface of a vesicle like rotating a screw by connecting the ring to a vesicle with cholesterol.
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=== DNA Clocks ===
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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.
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Rotations of DNA screw can be stabilized by raising the number of DNA spiders, and then DNA screw will become a time counting machine like a clock. It would contribute to DNA computing technology by using it as a clock of CPU.
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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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