Biomod/2011/TeamJapan/Tokyo/Project: Difference between revisions
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===UV-switching DNA device and the mechanism of light-irradiated gathering=== | ===UV-switching DNA device and the mechanism of light-irradiated gathering=== | ||
The UV-switching DNA device is composed of a UV-switching DNA and a blocking DNA. The UV-switching DNA includes a complementary sequence of the deoxyribozyme on the DNA ciliate. However, the deoxyribozyme cannot hybridize with the UV-switching DNA before UV irradiation because the UV-switching DNA has a stem-loop structure and the blocking DNA at the complementary sequence of the deoxyribozyme (the “closed” state in the right figure). After UV irradiation, the stem-loop structure of the UV-switching DNA open, caused by the UV-responsive structural transition of azobenzenes in the UV-switching DNA. When the UV-switching DNA is open state, the deoxyribozyme can partly hybridizes with the UV-switching DNA and finally wholly hybridizes with the UV-switching DNA as a result of the branch migration of them. | :The UV-switching DNA device is composed of a UV-switching DNA and a blocking DNA. The UV-switching DNA includes a complementary sequence of the deoxyribozyme on the DNA ciliate. However, the deoxyribozyme cannot hybridize with the UV-switching DNA before UV irradiation because the UV-switching DNA has a stem-loop structure and the blocking DNA at the complementary sequence of the deoxyribozyme (the “closed” state in the right figure). After UV irradiation, the stem-loop structure of the UV-switching DNA open, caused by the UV-responsive structural transition of azobenzenes in the UV-switching DNA. When the UV-switching DNA is open state, the deoxyribozyme can partly hybridizes with the UV-switching DNA and finally wholly hybridizes with the UV-switching DNA as a result of the branch migration of them. | ||
|width="450px"|[[Image:Tokyo-gathering2.png|450px|center]] | |width="450px"|[[Image:Tokyo-gathering2.png|450px|center]] | ||
|} | |} | ||
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<div id="navigation"> <div id="menu" style="position:static"> <ul> <li><a class="aMain" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo">Home</a></li> <li><a class="aTeam" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Team/Students">Team</a></li> <li><a class="aProject" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Project</a> <!-- <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Overview</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/introduction">Introduction</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Model">Model</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Devices">Devices</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Modes">Modes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Results</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> </ul> --> <li><font color="#ffffff">Results</font> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Experiments</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Design</a></li> </ul></li> <!-- <li><a class="Simulation" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a class="DNA design" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Designs</a></li> --> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Protocols">Protocols</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Lab.notebook">Notes</a></li> <li><a class="aNotebook" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sponsors/">Sponsors</a></li> <li><a class="aSitemap" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sitemap">Sitemap</a></li>
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Project
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The aim of our project is the construction of an autonomous micrometer-sized molecular robot. We designed and constructed a micrometer-sized molecular robot, “DNA ciliate”, named after water microorganisms, ciliate. The DNA ciliate has three independent functional modes (see the left figure): free moving mode, track walking mode, and light-irradiated gathering mode. The DNA ciliate consists of a micrometer-sized body and cilia. The micrometer-sized body is made of a microsphere such as a polystyrene microbead, a glass microbead, etc. The cilia are made of deoxyribozymes (single-stranded DNAs with cleaving activity). In the free moving mode, the DNA ciliate move around in a broad space based on the Brownian motion. In addition, the DNA ciliate can walk along a single-stranded DNA track using the deoxyribozyme activity. The DNA ciliate can be gathered up at a UV-irradiated area. The construction of the DNA ciliate is shown in detail below. |
The body of the DNA ciliate
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Three independent modes of the DNA ciliate
1. Free moving mode
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The principle of free moving
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2. Track walking mode
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The mechanism of track walking
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Construction of DNA tracks
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3. Light-irradiated gathering mode
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In the light-irradiated gathering mode, DNA ciliates gather at a specific UV-irradiated UV area; i.e., the DNA ciliate can be controlled by UV irradiation. This mode is achieved by a UV-switching DNA device with UV-responsive bases, azobenzenes. Before UV-irradiattion, this DNA device does not hybridize with deoxyribozyme of the DNA ciliate. After UV irradiation, azobenzenes are isomerized and the DNA device can hybridize with the deoxyribozyme of DNA ciliate. By this reaction, the hybridization of DNA ciliates with arrayed DNAs on a glass plate is controlled. |
UV-switching DNA device and the mechanism of light-irradiated gathering
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