Biomod/2012/TeamSendai/Design: Difference between revisions

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We decided to use the structure of the hexagonal tube.The reason is because We think there is a reference on the hexagonal structure of DNA origami（ショーンの論文を紹介）, and can take advantage of that knowledge.Next, We made a simulation in order to examine the size of the structure.Must not the size that it is the tube through anything.It must be large enough to be passed through the desired product, however.We also have the aim of this GATE stab in the cell membrane, it can not sting in the cell membrane of normal hexagonal tube.However, We can create a tube with a different structure by exchanging some staple.We have designed a simple tube first,and I have to be attached anywhere in the structure to replace the staple .We can later add functionality to an existing structure using this method.We thought that to have an affinity for lipid membrane with the DNA that can be modified cholesterol on the side of the tube by this method.In addition, we have also designed DNA-like beard at the entrance of the tube.We expect the effect of electrostatically repel force with DNA which are not intended.Our tube is small,so we designed the tube to connect to each other and be long in order to easily confirmed using AFM. By replacing the staple, this structure is also removably.
We decided to use the structure of the hexagonal tube.The reason is because We think there is a reference on the hexagonal structure of DNA origami（ショーンの論文を紹介）, and can take advantage of that knowledge.Next, We made a simulation in order to examine the size of the structure.Must not the size that it is the tube through anything.It must be large enough to be passed through the desired product, however.We also have the aim of this GATE stab in the cell membrane, it can not sting in the cell membrane of normal hexagonal tube.However, We can create a tube with a different structure by exchanging some staple.We have designed a simple tube first,and I have to be attached anywhere in the structure to replace the staple .We can later add functionality to an existing structure using this method.We thought that to have an affinity for lipid membrane with the DNA that can be modified cholesterol on the side of the tube by this method.In addition, we have also designed DNA-like beard at the entrance of the tube.We expect the effect of electrostatically repel force with DNA which are not intended.Our tube is small,so we designed the tube to connect to each other and be long in order to easily confirmed using AFM. By replacing the staple, this structure is also removably.
<img src=" http://openwetware.org/images/e/ec/Tsutsucadnano1.png
<img src=" http://openwetware.org/images/e/ec/Tsutsucadnano1.png
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<img src=" http://openwetware.org/images/a/a4/TsutsucaDNAno2.png
<img src=" http://openwetware.org/images/a/a4/TsutsucaDNAno2.png
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" align="right" width="700px" height="398px">


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Revision as of 05:35, 25 October 2012

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<!-- Menu --> <ul id="menu"> <li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Top</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea ">Project</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation">Simulation</a> </li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design">Design</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment ">Experiment</a> <ul> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Method">Method</a> <ul> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Porter">Porter</a> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Cylinder">Cylinder</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result# Vesicle">Vesicle</a> </li> </ul> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result">Result</a> <ul> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Porter">Porter</a> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Cylinder">Cylinder</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result# Vesicle">Vesicle</a> </li> </ul> </li> </ul> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Achievement">Achievement</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Diary">Diary</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Team ">Team</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/FAQ">FAQ</a> </li> </ul>

<!-- コンテンツ --> <div id="Content"> <h1>Three experiment parts</h1> <p> We divided our project into 3 parts, and did experiment. </p> <img src=" http://openwetware.org/images/f/f1/Format_cellgate_kakudai.jpg " align="right" width="927px" height="398px">


<h1>Gate</h1> <p>

</br> We decided to use the structure of the hexagonal tube.The reason is because We think there is a reference on the hexagonal structure of DNA origami（ショーンの論文を紹介）, and can take advantage of that knowledge.Next, We made a simulation in order to examine the size of the structure.Must not the size that it is the tube through anything.It must be large enough to be passed through the desired product, however.We also have the aim of this GATE stab in the cell membrane, it can not sting in the cell membrane of normal hexagonal tube.However, We can create a tube with a different structure by exchanging some staple.We have designed a simple tube first,and I have to be attached anywhere in the structure to replace the staple .We can later add functionality to an existing structure using this method.We thought that to have an affinity for lipid membrane with the DNA that can be modified cholesterol on the side of the tube by this method.In addition, we have also designed DNA-like beard at the entrance of the tube.We expect the effect of electrostatically repel force with DNA which are not intended.Our tube is small,so we designed the tube to connect to each other and be long in order to easily confirmed using AFM. By replacing the staple, this structure is also removably. <img src=" http://openwetware.org/images/e/ec/Tsutsucadnano1.png " align="right" width="700px" height="398px"> <img src=" http://openwetware.org/images/a/a4/TsutsucaDNAno2.png " align="right" width="700px" height="398px">

</p>

<h1>Porter</h1> <p> We named the single stranded DNA “Porter” which stand in line in the GATE and transport the target. Porter is designed to be more complementary sequence to the target molecule as going back from the entrance. These designs enable to move to the inner porter because of the stability of combination. This way makes it possible to move the target. We did a simulation to find the best length and space of the porter. The result of simulation, we have found that not more than a certain distance away from the gate is the target DNA was negatively charged by electrostatic force so that the gate can be in the DNA. The solution of this phenomenon, we have to make the first Porter have enough length to beyond the original length and bring the target into the tube.

So we design the Porter to take a loop structure when bound to the target molecule. It was believed that the Porter would be able to go beyond the distance to the complementary sequences in the various parts of Porter, inaccessible electrostatically by target molecule is bound in a stepwise manner, pull the material into the Gate. In actual experiment, we compare the トーホールド and rope structure to use following sequence(配列載せる). And, this is for electrophoresis, so it’s the sequence to extract only the part related to the binding of the target. Actual Gate’s sequence integrate about 10bp spacer sequence to reduce the Coulomb force which affected by the wall when moving. </p>

<h1>Membrane</h1> <p> We use liposomes as a model of cell membrane. We prepared a preliminary step to that cell gate insert into the liposome. We designed a smaller tube and attempted to insert into liposomes using it. Similar to the cell gate, we stretched single-stranded DNA of 10 bases that can be modified cholesterol from the side of this tube. We attached cholesterol to the single-stranded DNA, and expected that these enter into the hydrophobic portion of the liposome. Then, it is likely to that the tube stick to the liposome. However, it is considered that the tube would be in a state of lying on the liposome. So, when we designed the tube, we made one side too much for the extra M13 deliberately. We expect that the electrostatic symmetry of the tube is broken by this, and the tube penetrate the membrane standing vertically by repulsion.


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