Biomod/2011/TeamJapan/Tokyo/Project/Summery and outlooks

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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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Summery and outlooks

We summarize this project’s results. In this project, we developed three devices and tried to confirm DNA ciliate’s three modes.
To make devices, we made DNA devices: deoxyribozyne for DNA ciliate, complimentary DNA for deoxyribozyme, substrate for this deoxyribozyme, UV-switching-DNA, and blocking DNA. We made these devices to be the best for experimentation.

We developed three devices: DNA ciliate, DNA tracks, and DNA devices.
<html><body><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/DNA_ciliate's_body"><img src="http://openwetware.org/images/8/8c/DNA_ciliate_body.jpg" border=0 width=200 height=200></a></body></html>
First, we made DNA ciliate. To make DNA ciliate, we had to attach DNA to polystyrene beads before carboxylic acid of polystyrene beads is hydrolyzed. We used the protocol(Direct link) to attach DNA quickly after putting beads into the solution.
<html><body> <a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/DNA_tracks"><img src="http://openwetware.org/images/f/f6/Micrometer_sized_track.jpg" border=0 width=200 height=200></a></body></html>
Second, we made DNA tracks. To make DNA track, we had to make fine path. We devised method of fine tuning machine. At last, we made fine path which the width is 50 um. After making path, we attached DNA on the path.
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<a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/UV_switch"><img src="http://openwetware.org/images/b/b5/DNA_devices.jpg" border=0 width=200 height=200></a>

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Third, we made UV-switching DNA and its system. To make UV-switching system, we had to make UV-switching DNA. We decided using azobenzenes, but the traditional azobenzenes DNA use two DNAs needs many azobenzenes, so the cost is high and the swicthing is slow. (not finished)



We tried to confirm three modes: free moving mode, track walking mode, UV-switching mode.
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<a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Free_moving_mode"><img src="http://openwetware.org/images/f/f8/Biomod2011_Team_Tokyo111028FreeMovingMode.png" border=0 height=200></a>

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First mode is free moving mode. We observed DNA ciliate’s movement in solution.(Link:Free Moving Mode)We devised the solution’s composition to prevent DNA ciliates from sticking nonspecific fast to glass plate and cover glass. By this observation, we confirmed DNA ciliate moves at random and drastic. In conclusion, we checked DNA ciliate can take this mode.
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<a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Track_walking_mode"><img src="http://openwetware.org/images/b/bc/Biomod2011_Team_Tokyo111028TrackWalkingMode.png" border=0 height=200></a>

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Second mode is track walking mode. To achieve this mode,firstly we confirmed deoxyribozyme activity by electrophoresis. We devised the reaction solution composition and more reactive for deoxyribozyme. Secondary, we confirmed DNA tracks by using fluorescents. Fluorescents are very easy to attach glass plate by nonspecific adhesion, so we devised the protocol to prevent this adhesion.(Link:DNA attaching to glass beads protocol) Furthermore, we made complex DNA track and confirmed complex DNA track is prepared. Thirdly, we simulated DNA ciliate movement to confirm DNA ciliate moves directly and doesn’t move by Brownian motion. In simulation, we confirmed DNA ciliate moves directly. In conclusion, we created DNA track, confirmed DNA ciliate can walk on DNA track, and simulated DNA ciliate’s movement.



Third mode is light-irradiated gathering mode. To achieve this mode, we designed UV-switching system, confirmed UV-switching system, and confirmed DNA ciliates’ gathering. Firstly, we designed UV-switching system. In this system, UV-switching-DNA and complimentary DNA for deoxyribozyme are used. This UV-switching system is completely original. Secondary, we confirmed UV-switching system by electrophoresis. UV-switching-DNA’s loop is fragile, so . Thirdly, we confirmed DNA ciliates’ gathering by using ----
Through our experimentation, we made micrometer-sized DNA robot: DNA ciliate body, DNA tracks, and UV-switching system. We submit these three devices.

Followings experiments and expected results are our project’s outlook.
First is observing DNA ciliate’s movement on DNA track. By this observation, DNA ciliate’s real movement on DNA track will be confirmed.
Second is making narrow DNA track enough to DNA ciliate move directly. In our simulation, we supposed the width of DNA track was 5 um, but the width of DNA track we actual made was 50 um. The movement of DNA ciliate depends on the width of DNA track, so making much narrower microchannel to observe DNA ciliate’s directly movement is needed. By using photolithography, we would make narrower microchannel and DNA track, but we couldn’t it because we didn’t know about photolithography in detail.
If these two things are done, the track walking mode will be accomplished.
Third is observing the function of OFF state in UV-switching system (Link:UV-switching trap DNA ). To check whether UV-switching-DNA works as we thought, it’s necessary to not only check the function of ON state but also check the function of OFF state. We checked the function of ON state by using complimentary DNA for deoxyribozyme, but we didn’t check the function of OFF state. If we Attach OFF state UV-switching-DNA or complimentary DNA for blocking DNA on a glass plate, we will check whether OFF state UV-switching-DNA works as we thought.
If this thing is done, the UV-irradiated-gathering mode will be accomplished.
By these three things, three modes are all accomplished.
Forth is making UV-switching system which is able to switch ON state to OFF state. The UV-switching-DNA which we made is very reasonable and the switching is speedy because this DNA needs only two azobenzenes. However, this DNA can’t switch ON state to OFF state because this DNA hybridizes with deoxyribozyme in UV, but this DNA can’t hybridize blocking DNA by branch migration in no UV. This opened loop doesn’t close because the loop is fragile and the power to release deoxyribozyme is none.
If we could perfect UV-switching-DNA, we could change three modes.
Fifth is making system of mode changing. Free moving mode and track walking mode can be changed by temperature. If the temperature is lower than Tm, deoxyribozyme of DNA ciliate hybridizes with substrate and DNA ciliate becomes track walking mode. On the other hand, if the temperature is upper than Tm, deoxyribozyme of DNA ciliate release substrate and DNA ciliate becomes free moving mode. If UV-switching-system is changeable ON state to OFF state, light-irradiated-gathering mode and the other two modes can changed by switching on UV or switching off UV. If UV is spotted, UV-switching-gathering DNA hybridizes with deoxyribozyme of DNA ciliate, and DNA ciliate becomes light-irradiated-gathering mode. If UV is NOT spotted, UV-switching-gathering DNA hybridizes with blocking DNA, and DNA ciliate becomes one of the other two modes. By observing these changing modes, it’s confirmed that DNA ciliate is the mode changing molecular robot.
If these five experimentations and creating are successful, DNA ciliate becomes more perfectly switching modes in response to external environment.