Biomod/2011/TeamJapan/Tokyo/Project/Model of the DNA ciliate body
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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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Model of the DNA ciliate body
Introduction
- To create DNA ciliate, a micrometer-sized body and its motor are indispensable. We chose DNA as a material for the motor because DNA is the most suitable material that is nanometer-sized and easy to be attached to micrometer-sized objects by various surface modifications. The micrometer-sized body is required to be micrometer-sized, homogeneous, and easy to attach DNA. We use micrometer-sized polystyrene beads as the micrometer-sized bodies because their forms are homogeneous and their carboxylic acid is useful for attaching molecular.
- We use two methods to attach DNA to polystyrene beads. In both methods, we bind polystyrene beads' carboxylic acid to amino group of aminated DNA. In first method, we apply reference [1]. In this method, we used linker between polystyrene beads and aminated DNAs. The linker has amino group and carboxylic acid. The linker’s amino group combines with carboxylic acid of polystyrene beads and the linker’s carboxyric acid combines with amino group of aminated DNA, so polystyrene beads combine DNA through the linker. In second method, we use NHS and EDC to alter carboxylic acid to NHS. NHS has very high reactivity, and DNA's amino group reacts with NHS of porystyrene beads. The DNA ciliate body is developed in this process. :
As a motor of DNA ciliate, we used deoxyribozyme which is the enzyme comprised of DNA. Deoxyribozyme cleaves its substrate at an RNA base, if there are 2+ metal ions. Using this reaction, DNA ciliate can move.
Principle and methods
- Two experiments were needed to complete developing DNA ciliate body.
First experiment was creating DNA ciliate by attaching DNAs to polystyrene beads. This process is used the reaction of connecting aminated DNAs’ amino group and polystyrene beads’ carboxylic acid. We took two methods to react. Both methods are used the common reaction, but chemical materials are different. First method is used EDC and NHS. This induces transforming carboxylic acid to succinimide which is been able to react with aminated DNAs and connect.
- Second method is used EDAC. EDAC reacts with both aminated DNAs and polystyrene beads’ carboxylic acid.
Second experiment is confirming whether deoxyribozyme is attached to polystyrene beads and able to cleave substrate. We confirm deoxyribozyme activity by urea-PAGE. Making mixture of DNA ciliate and substrate and Zn2+ ions. If DNA ciliate has deoxyribozyme activity, substrate is cleaved and the band of cleaved substrate appears as a band.
Sequence design
[Deoxyribozyme]
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