Biomod/2011/TeamJapan/Tokyo/Achievements/DNA Devices
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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 design
- To achieve the DNA ciliate and its three modes, we constructed five types of DNA sequences: (1) "deoxyribozyme", attached to the body of the DNA ciliate; (2) "substrate DNA", attached to a glass plate as a DNA track for the track walking mode; (3) "UV-switching DNA", used for the UV-switching device and originally designed by ourselves; (4) "blocking DNA", used for the UV-switching device; (5) "complementary strand for deoxyribozyme", used for constantly-gathering of the DNA ciliate. All these five types of DNA strands worked as we expected (see Experimental Results). Here, we explain the sequence information and the functions of the five types of DNA strands in detail.
1.Deoxyribozyme
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2.Substrate
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3.UV-switching DNA
- 5' -(NH2)-TTTTTT TTTTCACTATTTCGACCGGCTCGGAGAAGAG TTTTT CT X CT X TC-3'(X = azobenzene)
- Size: 48 bases + 2 azobenzenes
- The UV-switching DNA was used for an anchoring-DNA spot in the light-irradiated gathering mode. The UV-switching DNA forms a stem-loop structure. The loop consists of five bases (TTTTT), and the stem (CT X CT X TC) has two trans-formed azobenzenes (X ). By UV irradiation, the azobenzenes are isomerized from the trans-form to the cis-form. As a result, the stem with the azobenzenes becomes hard to form the double strand [2].
To achieve this switching, it is necessary to design the stem sequence that firmly forms the stem-loop structure at the room temperature but opens the stem-loop structure by isomerization of the two azobenzenes from trans- to cis-form. There are no reports on the opening-and-closing transition of a single molecular by azobenzenes inserted into a stem. Here, we designed the sequences “GAAGAG” and "CT X CT X TC" as the stem and "TTTTT" as the loop by thermodynamic calculations[3]. - The 7th to 37th bases from 5' end (TTTTCACTATTTCGACCGGCTCGGAGAAGAG) is a complementary sequence for the deoxyribozyme (1). In addition, the 7th to 31th bases from 5’ end (TTTTCACTATTTCGACCGGCTCGGA) are a complementary part for blocking DNA (4) below.
Before UV irradiation, the stem-loop structure of the UV-switching DNA forms, and the blocking DNA is hybridizing with the UV-switching DNA. Thus, the deoxyribozyme cannot hybridize with the UV-switching DNA. After UV irradiation, the branch migration of the deoxyribozyme for the UV-switching DNA starts from the stem part and the blocking DNA is released. As a result, the deoxyribozyme and the UV-switching DNA form a double strand. - We designed the first 6 bases from 5' end as a linker (TTTTTT). This is also designed not to make unexpected structures.
- The 5' end is modified by an amino group (-NH2) to be fixed on a glass plate by a silane coupling reaction.
- The UV-switching DNA was used for an anchoring-DNA spot in the light-irradiated gathering mode. The UV-switching DNA forms a stem-loop structure. The loop consists of five bases (TTTTT), and the stem (CT X CT X TC) has two trans-formed azobenzenes (X ). By UV irradiation, the azobenzenes are isomerized from the trans-form to the cis-form. As a result, the stem with the azobenzenes becomes hard to form the double strand [2].
4.Blocking DNA
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5.Complementary DNA for deoxyribozyme
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References
- [1] Kyle Lund et al.: Molecular robots guided by prescriptive landscapes, Nature, 465, 206/210(2010)
- [2] Xingguo Liang et al.: Molecular Design for Reversing the Photoswitching Mode of Turning ON and OFF DNA Hybridization, Chem. Asian J., 3, 553/560(2008)
- [3] J.N. Zadeh,et al.: NUPACK: analysis and design of nucleic acid systems, J Comput Chem, 32, 170/173(2011)