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=Design of the DNA Sequence=
In this section, we will explain the design of our DNA Shell in detail.
The DNA Shell is constructed of DNA Origami. In this section, we explain about DNA Origami, and then describe about our design of the typical structure and added functions of DNA Shell. Also, we will describe the simulation techniques to calculate the melting temperature and the Gibbs free energy in hybridization.
===DNA origami===
[[Image:Biomod-2012-UTokyo-UT-Hongo-side.png|thumb|400px|Fig. 2.2.3.3.1]]
[[Image:Biomod-2012-UTokyo-UT-Hongo-sidebou.png|thumb|400px|Fig. 2.2.3.3.2]]
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[[Image:Biomod-2012-UTokyo-UT-Hongo-TMBHRPkei.jpg|500px|thumb|Fig 2.4.1.2 The idea for the experiment of supporting enzyme]]
If trypsin decomposes HRP, before the reaction happens between TMB and HRP, HRP does not oxidize TMB. Furthermore, we used streptavidin-labeld HRP and DNA Shell with biotin. DNA Shell protects HRP because of the combination between streptavidin and biotin. As HRP protected by Shell, trypsin does not decompose HRP and the oxidization of TMB goes on.
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===Experiment Condition===
We made four kinds of solution like below (Table 2.4.2) and measured the absorption spectra of each solution.
<center>
{| border="1" cellpadding="6" cellspacing="0" style="text-align: center;"
|+
! style="border-style: solid; border-width: 1px"|
! style="border-style: solid; border-width: 1px"|TMB
! style="border-style: solid; border-width: 1px"|HRP
! style="border-style: solid; border-width: 1px"|Trypsin
! style="border-style: solid; border-width: 1px"|DNA Shell
! style="border-style: solid; border-width: 1px"|Expected Peak Wavelength[nm]
|-
! scope="row" | No.1
| + || - || - || - || 285
|-
! scope="row" | No.2
| + || + || - || - || 450
|-
! scope="row" | No.3
| + || + || + || - || 285
|-
! scope="row" | No.4
| + || + || + || + || 450
|}
</center>
Table 2.5.2 Four kinds of solution for the experiments.
* (No.1) We only used 2μM TMB in acetate buffer.
* (No.2) We added 20nM streptavidin-labeled HRP in tris HCl to the solution of 2μM TMB in acetate buffer.
* (No.3) We added the solution in which we reacted trypsin and HRP for 1 hour in 37C constant temperature bath and HRP to TMB. As a whole solution, 0.2µM TMB, 2µMHRP, excess trypsin and 50mM acetate (TMB buffer), 50mM trisHCl (HRP buffer) are contained.
* (No.4) We added the solution in which we reacted trypsin, HRP and Shell for 1 hour in 37C constant temperature bath and HRP to TMB. 0.2µM TMB, 2µMHRP, 2nM DNA Shell, excess trypsin and 50mM acetate (TMB buffer), 50mM trisHCl (HRP buffer) are contained.
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Revision as of 13:06, 15 October 2013

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</style> </head> <body> <div id="indexing"> <div id="sitemap"> <p id="sitemapTitle">SITEMAP | BIOMOD 2013 NANO CREATORS | Aarhus University</p> <div id="footer-contents"> <div class="footer-section"> <p class="footer-section-title">INTRODUCTION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus">Home, abstract, animation and video</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Introduction">Introduction</a></li </ul> </div> <div class="footer-section"> <p class="footer-section-title">RESULTS AND DISCUSSION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/System_In_Action">System in action</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">MATERIALS AND METHODS</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/System_In_Action">System in action</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Methods">Methods</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">SUPPLEMENTARY</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Team_And_Acknowledgments">Team and acknowledgments</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Optimizations">Optimizations</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Data">Supplementary data</a></li> 

                                               <li><a

href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Informations">Supplementary informations</a> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/References">References</a></li> </ul> </div> </div> <div> <p id="copyright">Copyright (C) 2013 | BIOMOD Team Nano Creators @ Aarhus University | Programming by: <a href="mailto:pvskaarup@gmail.com?Subject=BIOMOD 2013:">Peter Vium Skaarup</a>.</p> </div> </div>

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