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>
DNA Design
Purpose of Design
Principle of Design
Methods of Design
- We designed five DNA strands.
- Three DNA strands relate to "amino modified DNA and polystyrene conjugation".
- One DNA strand is modified amino group to conjugate polystyrene-beads. The other one is a complementary strand, which is modified thiol group to conjugate platinum. Another DNA strand also is a complementary strand, which is modified FAM.
- Two DNA strands relate "SAM".
- One DNA strand includes azobenzene to photo-control. Another DNA is a complementary strand, which is modified thiol group to conjugate gold.
- We designed these DNA strands using NUPACK*1.
- And we selected orthonormal sequence, referring to a paper*2.
- When we designed DNA strands, we fixed the temperature at 25.0℃ and the Na+ concentration at 0.195M.
- And we selected DNA strands, which didn't form secondary structure.
- 1) NUPACK nucleic acid package. http://www.nupack.org/
- 2) Tetsuro Kitajima, Masahiro Takinoue, Ko-ichiroh Shohda, and Akira Suyama.: Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics. LNCS 4848, 119-129 (2008)
Result of Design
- We designed five DNA strands.
- The DNA strands
seqA_azo4_5thiol [ThiSS]AATXACXCCXAGXCC (X=Azobenzene) seqAc_5thiol [ThiSS]GGCTGGGTATT seqB_5thiol [ThiSS]CGTCTATTGCTTGTCACTTCCCC seqBc_5amino [AminoC6]GGGGAAGTGACAAGCAATAGACG seqBc_5FAM [6-FAM]GGGGAAGTGACAAGCAATAGACG
- (The DNA strands selected by us.)