Biomod/2012/Titech/Nano-Jugglers/Methods/DNA Design
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} </style> </head> <BODY> <div id="biomodlink"> <<a href="http://openwetware.org/wiki/Biomod">BIOMOD</a>|<a href="http://openwetware.org/wiki/Biomod/2012">2012</a>|Titech Nano-Jugglers </div> <div id="header"> <div id="navigation"> <div id="menu"> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers"><br>Home<br><br></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Team/Students"><br>Team<br><br></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Project"><br>Project<br><br></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Results">Results<br>&<br>Methods</a></font></li> <li class="ach"><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Achievements"><br>Achievements<br><br></a> <li class="sup"><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Protocols"><br>Suppl. Info.<br><br></a></li> <li class="none"><a href="http://openwetware.org/wiki/Biomod/2012/Titech/Nano-Jugglers/Acknowledgement"><br>Acknowledgements<br><br></a></li> </ul> </div> </div> </div> </BODY> </html>
0.2. Design of linker DNA strands
- We use DNA strands for bonding between a body of Biomolecular Rocket and platinum particles. DNA strands must be designed 4 DNA strands to hybridize at room temperature stably. DNA strands are categorize into two types, one type is a DNA strand for conjugation to polystyrene surface and its cDNA, and another type is a DNA strand for conjugation to gold surface and its cDNA. Each cDNA conjugated to platinum particles.
- In this section, we explain how we design DNA strands. There are three steps to design DNA strands, first step is selection of DNA strands , second step is adjustment of the number of bases and final step is design of cDNA strand. We use NUPACK[1] for these processes of DNA design. NUPACK is a software for the analysis and design of nucleic acid systems.
- First, we chose DNA strands from a treatise[2]. In this step, we analyze whether DNA can easily hybridize at room temperature stably. Then we select two DNA strands. Secondly, we adjust number of bases in order to make easily dissociate when they introduced photo-switching systems. Finally, we design c of each cDNA strands, and modify amino group and thiol group as necessary.
- [1] NUPACK nucleic acid package. http://www.nupack.org/
- [2] Tetsuro Kitajima, Masahiro Takinoue, Ko-ichiroh Shohda, Akira Suyama. LNCS 4848, 119-129 (2008)
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