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:We designed five DNA strands.  
:We designed five DNA strands.  
*Three DNA strands relate to "amino modified DNA and polystyrene conjugation".  
: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.
*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.
:On the other hand, Two DNA strands relate "SAM".
: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.
: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.  
:We designed these DNA strands using NUPACK*1.  

Revision as of 03:26, 19 September 2012


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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

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.
On the other hand, 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.)

Reference

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