Biomod/2011/TeamJapan/Tokyo/Achievements/DNA Devices: Difference between revisions
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[[Image:Deoxyribozyme2.png|thumb|center|Simplified image of deoxyribozyme|280px]]</td> | [[Image:Deoxyribozyme2.png|thumb|center|Simplified image of deoxyribozyme|280px]]</td> | ||
<td> | <td> | ||
*5' -(NH2)-TTATTATTAT CTCTTCTCCGAGCCGGTCGAAATAGTGAAAA-3' | *5' -(NH2)-TTATTATTAT <font color="#dc143c">CTCTTCTCCGAGCCGGTCGAAATAGTGAAAA</font>-3' | ||
*Size: 41bases | *Size: 41bases | ||
**This DNA is the only DNA which is attached to DNA ciliate body. This has enzyme activity for substrate. The 31bases from 3' end of the strand1 are act as a deoxyribozyme when it hybridizes with the substrate. Those 31bases are same to the DNA spider's leg(CTCTTCTCCGAGCCGGTCGAAATAGTGAAAA). | **This DNA is the only DNA which is attached to DNA ciliate body. This has enzyme activity for substrate. The 31bases from 3' end of the strand1 are act as a deoxyribozyme when it hybridizes with the substrate. Those 31bases are same to the DNA spider's leg(CTCTTCTCCGAGCCGGTCGAAATAGTGAAAA). | ||
**We designed by ourselves the first 10 bases from 5’ end as a linker between a substrate and a polystyrene bead (TTATTATTAT). Thanks to this linker, the space between DNA ciliate body and deoxyribozyme’s enzyme activity area is appeared, so deoxyribozyme can easily hybridize with other DNAs. The linker shouldn’t hybridize with other DNAs and make unexpected structure, so we also took care of these things. We designed linker which doesn’t make dimer and unexpected inner structure. In addition, we don’t use guanine and cytosine because these bases are easy to make nonspecific dimer. We select some strands as the candidates for linkers. As a result, we decide to use “TTATTATTAT” as a linker. | **We designed by ourselves the first 10 bases from 5’ end as a linker between a substrate and a polystyrene bead (TTATTATTAT). Thanks to this linker, the space between DNA ciliate body and deoxyribozyme’s enzyme activity area is appeared, so deoxyribozyme can easily hybridize with other DNAs. The linker shouldn’t hybridize with other DNAs and make unexpected structure, so we also took care of these things. We designed linker which doesn’t make dimer and unexpected inner structure. In addition, we don’t use guanine and cytosine because these bases are easy to make nonspecific dimer. We select some strands as the candidates for linkers. As a result, we decide to use “TTATTATTAT” as a linker. | ||
<!--**The 31bases from 3' end of the strand1 are act as a deoxyribozyme when it hybridizes with the strand2. Those 31bases are same to the DNA spider's leg(CTCTTCTCCGAGCCGGTCGAAATAGTGAAAA). | <!--**The 31bases from 3' end of the strand1 are act as a deoxyribozyme when it hybridizes with the strand2. Those 31bases are same to the DNA spider's leg(<font color="#dc143c">CTCTTCTCCGAGCCGGTCGAAATAGTGAAAA</font>). | ||
**We designed the first 10 bases from 5’ end as a linker between a substrate and a polystyrene bead (TTATTATTAT). Thanks to this linker, strand1 can easily hybridize with its counterpart DNA. We also took care that the linker didn't make unexpected structures. | **We designed the first 10 bases from 5’ end as a linker between a substrate and a polystyrene bead (TTATTATTAT). Thanks to this linker, strand1 can easily hybridize with its counterpart DNA. We also took care that the linker didn't make unexpected structures. | ||
**The 5' end is aminated to be fixed on polystyrene beads. | **The 5' end is aminated to be fixed on polystyrene beads. |
Revision as of 18:15, 31 October 2011
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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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DNA designs
Abstract
- To achieve three mode of DNA ciliate, we designed five types of DNA arrangements.
- Five types of DNA are followings. First is "deoxyribozyme" which is attached to DNA ciliate body. Second is "substrate" which is attached to a glass plate as a scaffold of the track walking mode. Third is "UV-switching DNA" which is used for UV-switching system. Forth is "blocking DNA" which is also used for UV-switching system. Fifth is "complementary strand for deoxyribozyme". Especially, the third DNA, "UV-switching DNA" is the DNA strand which we designed only by ourselves.
- We could check that all these five types of DNA strand work as we expected. This is worthy of special mention.
- In this page, we explain five types of DNA strands which we designed.The results of checking DNA’s work by experimentation are [here].
Deoxyribozyme
|
Substrate
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UV-switching DNA
- 5' -(NH2)-TTTTTT TTTTCACTATTTCGACCGGCTCGGAGAAGAG TTTTT CT X CT X TC-3' (X means azobenzene. )
- Size: 48bases + 2azobenzenes
- UV-switching DNA is used for the scaffold in light-irradiated gathering mode. We designed this DNA by ourselves. UV-switching DNA has a five bases’ loop (TTTTT) and there are two azobenzenes (X) in the one side of the stem (CTXCTXCT).
- By spotting UV, azobenzenes are isomerized (trans to cis), so the part which contains azobenzenes becomes hard to form double strand. It is known that UV-switching can be realized by using this principle. (ref)
- To achieve this switching, it is necessary to design the stem which forms the loop firmly in the room temperature and opens the loop by isomerizing of two azobenzenes. We didn’t find the precedent which succeeded in opening and closing at a single molecular by azobenzenes which are inserted into a stem, so the designing is very difficult. After trial and error, we designed to use “GAAGAG” and “CTXCTXCT” as the stem and “TTTTT” as the loop.
- The 7th to 37th bases from 5' end (TTTTCACTATTTCGACCGGCTCGGAGAAGAG) is a complete complementary part for the deoxyribozyme. In addition, the 7th to 31th bases from 5’ end (TTTTCACTATTTCGACCGGCTCGGA) are a complementary part for blocking DNA. Consequently, the 32th to 37th bases from 5’ end (GAAGAG) are a complementary part for deoxyriboyme and not a complementary part for blocking DNA, so branch migration is started from this part and blocking DNA is released. Moreover, these 6 bases are a part which makes stem, so this part is blocked when the loop is closed. By this structure, branch migration doesn’t happen when the loop is formed.
- We designed the first 6 bases from 5' end as a linker (TTTTTT). This is also designed not to make unexpected structures. As a result, we decide using this linker
- The 5' end is aminated to be fixed on a glass plate.
Blocking DNA
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Complementary DNA for deoxyribozyme
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