Biomod/2013/Komaba3

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            <a href="http://openwetware.org/wiki/Biomod/2013/Komaba/"><span class="element brand"><img class="place-left" src="./js/logo32.png" style="height: 20px">Komaba-Team <small>Biomod 2013</small></span></a>
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                <h1>Abstract</h1>
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                        <img src="http://openwetware.org/images/d/d1/Biomod-2013-Komaba-Home-Top.png"><p class="indent">The Komaba team will develop a new molecular motor based on DNA origami, and the particularity of this motor is that the circular movement involved a cylinder and a ring. Rotation move is exploited from DNA walker which advance in a certain one direction by cutting a DNA footing with DNAzyme. The ring is connected with DNA walker, and on the surface of the cylinder DNA footings are set out with a spiral line. DNA Screw will greatly contribute to the practical realization of tricky movement of the Biomolecular - machine, because its circular movement has many applications. We are, for example, aiming to make a DNA structure with this screw moving like a submarine, which swim by rotating on the principle of the propeller. Alternatively, DNA screw will be able to make a pore on a vesicle like a drill. Moreover, these functions will develop into an autonomous DNA robot in combination with DNA sensors. As described above, DNA screw will be a giant step toward creating surprising DNA machines. </p></div>
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                <a name="#project"><h1>Project</h1></a>
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                      <h2>Background of Project</h2>
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                        <p class="indent">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. We are aiming at creating the DNA screw system to overcome these issues in the present studies. 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. 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). </p>
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                      <h2>Project Overview</h2>
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                      <p class="indent">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. If you need details of each experiment, please click ">>read more" link and jump to Design page. </p>
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                        <h2 class="fg-color-white">&nbsp;Cylinder</h2>
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                        <h2 class="fg-color-white">&nbsp;DNA Spider</h2>
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                        <h2 class="fg-color-white">&nbsp;Rotary Ring</h2>
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                      <h2>Vision for the future(Phase ∞)</h2>
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                      <h3>DNA submarine</h3>
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                        <p class="indent">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. </p>
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                      <h3>DNA structure with the function of Phage</h3>
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                        <p class="indent">By using the rotary motion of this DNA screw, the motion of a phage that makes a hole on a cell wall of bacteria could be imitated artifically. And in the end, it would be possible to make an artificial phage that is entirely consisted of DNA and controlled artificially.</p>
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                      <h3>DNA Clocks</h3>
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                        <p class="indent">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. </p>
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                <a name="#design"><h1>Design</h1></a>
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                      <h3>(Phase 1)</h3>
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                      <h2>Cylinder</h2>
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                      <p class="indent">The cylinder is put in the center of the motor as an axis supporting the rotation. DNA strands of staples and a scafold are formed into a cylindrical shape using DNA Origami technology. It was designed with cadnano software, which "simplifies and enhances the process of designing three-dimensional DNA origami nanostructures".(Figure 1) In order to bind footing DNAs on its surface spirally, 10mer long DNA strands which we call footings of footings come up from the cylinder's surface. After the cylinder with the footing of footings are formed, one of the three legs of DNA spiders is connected to a specific strand at the start point on the cylinder's surface. Then the footings get connected to the footing of footings. The footing tracks, each of which consists of three lanes of the footings, enable DNA Spiders to orbit the cylinder. In detail, there are two tracks of DNA footings and two spiders can walk on each track. In addition, in order to make it easy to observe the direction of spiders' walk, a small sub-cylinder is attached at the end of the footing tracks. The diameter of the cylinder is 25.4 nm and height is 43.5 nm. This is calculated considering that the cylinder can be observed with an Atomic Force Microscope and that the interval between the two tracks are wide enough for spiders not to jump to next footing track. </p>
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                      <h2>DNA Spider</h2>
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                      <p class="indent">Our DNA screw rotates by using DNA spiders produced by Lund, et al.. DNA Spider consists of a core and three legs. These legs move on the footing by cutting strands with DNAzyme. Since legs orbit the cylinder, they rotate the DNA Ring. In this paragraph, how to create DNA spiders is described. This method is the same as the way Lund, et al. did. First, Streptavidin(STV) and capture leg [5’ - GCC GAG AAC CTG ACG CAA GT/iSp18//iSp18//3Bio/ - 3] are connected in a solution. To create one-to-one product (“STV-(C)1” ), ion exchange is used. Second, deoxyribozyme legs [5’ - /5BioTEG//iSp18//iSp18//TCT CTT CTC CGA GCC GGT CGA AAT AGT GAA AA – 3’ ] are attached to the STV-(C) i.e. NICK3.4A+1. Third, Cy3 MONO NHS ester dissolved in DMSO is added in the solution containing NICK3.4A+1. By increasing the number of DNA spiders and DNA tracks, it would be possible to stabilize the rotating speed of the ring.  </p>
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                      <h2>Rotary Ring </h2>
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                      <p class="indent">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. 10mer staple strand for connecting DNA Spider is attached on the inner side of the Ring. The diameter of the ring is 50.9 nm, and so it can hold the cylinder and spiders in the inside of the ring. The thickness of ring is 10.9 nm in consideration of AFM visibility. </p>
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                      <h3>(Phase 2)</h3>
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                      <h2>DNA Screw (Combination of above parts) </h2>
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                      <p class="indent">The DNA screw is realized by assembling the above four parts: the cylinder, footings, DNA Spiders, and the rotary ring. </p>
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                <a name="#experiment"><h1>Experiment</h1></a>
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                    <div class="span12"><em>This content is under construction. We have already ordered DNAs of some parts and they will arrive soon. On arrival, we will conduct experiments. </em></div>
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                <a name="#supplementation"><h1>Supplementation</h1></a>
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                    <div class="span12"><p>we referred to this article in designing the cylinder and the ring; http://pubs.acs.org/doi/abs/10.1021/ja3076692
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we referred to this article in designing the DNA spider and the footings; http://www.nature.com/nature/journal/v465/n7295/full/nature09012.html
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</p></div>
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                <a name="#team"><h1>Team</h1></a>
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                        <h2>Team Information</h2>
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                        <p>Team Name : <strong>Komaba-Team</strong></p><p>Institution : <strong>University of Tokyo</strong> </p>
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                        <h2>Members</h2>
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                        <p>Fukuhara Yusuke - Major in Applied Physics</p>
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                        <p>Kondo Toyoki - College of Arts and Sciences </p>
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                        <p>Miyazaki Yuki - Major in Material Science and Engineering </p>
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                        <p>Osamu Ishimura - College of Arts and Sciences </p>
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                        <p>Shoko Yokokawa - College of Arts and Sciences </p>
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                        <p>Shuhei Nakajma - College of Arts and Sciences </p>
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                        <p>Soejima Tomohiro </p>
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                        <p>Wang Shaoyu </p>
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                        <h2>Episode</h2>
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                        <p>coming soon...</p>
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                <a name="#sponsors"><h1>Sponsors</h1></a>
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                        <img src="http://openwetware.org/images/e/e3/JPK_logo2013.jpg" class="place-right" style="margin: 0px; height:160px;">
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                        <p><a href="http://japan.jpk.com/index.2.ja.html" class="fg-color-white">&nbsp;JPK Instruments AG. </a></p>
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                    </div>
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                    <div class="span3 bg-color-green">
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                        <img src="http://openwetware.org/images/c/c5/%E5%92%8C%E6%B3%89%E3%83%86%E3%83%83%E3%82%AF_logo2013.jpg" class="place-right" style="margin: 0px;height:160px;">
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                        <p><a href="http://www.izumi-tech.com/index.html" class="fg-color-white">&nbsp;株式会社和泉テック </a></p>
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                    </div>
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                    <div class="span3 bg-color-yellow">
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                        <img src="http://openwetware.org/images/1/13/Level5-logo2013.jpg" class="place-right" style="margin: 0px;height:160px;">
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                        <p><a href="http://www.level-five.jp/" class="fg-color-white">&nbsp;株式会社レベルファイブ </a></p>
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                    </div>
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                    <div class="span3 bg-color-red">
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                        <img src="http://openwetware.org/images/c/cc/RIBM_logo2013.jpg" class="place-right" style="margin: 0px;height:160px;">
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                        <p><a href="http://www.ribm.co.jp/" class="fg-color-white">&nbsp;株式会社 生体分子計測研究所</a></p>
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                    </div>
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                    2013, Biomod © by <a class="fg-color-white" href="mailto:sergey@pimenov.com.ua">Komaba-Team</a>
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