Biomod/2012/TeamSendai/Design

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<h2>Principle</h2>
<h2>Principle</h2>
[[Image: Perportergifkoyama.gif|right|340px]]
[[Image: Perportergifkoyama.gif|right|340px]]
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When we consider making Cell Gate, there are two problems. One is how to pull the target oligonucleotide into Gate, and the other is how to pass the target. To solve these problems, we propose a nano structure of ssDNA and named it “Porter”. Porter stands in line in Gate, pulls the target, and transports it.
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There are essentially two problems for making CELL-GATE.  
 +
<ul>How to pull the target DNA into GATE ?</ul>
 +
<ul>How to pass the target through GATE ?</ul>
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The Gate simulation shows that things by itself don’t come in Gate. So Porter has to pull and carry the target inside Gate.
+
To solve these problems, we propose a nano-system made of ssDNA and named it Porter. Porter stands in line in GATE, pulls the target DNA, and transports it.
-
+
-
We designed Porter having some loop structures when it hybridizes with the target. Porter has some complementary sequences to the target here and there. So after the target attaches to Porter at the end of Porter, Porter shrinks and pulls the target. Finally the target comes in Gate, otherwise unable to go through.
+
-
The inner Porter has more complementary sequences to the target and has higher bonding energy from the entrance of Gate. This design enables the target to move to the inner Porter because of the combination stability. In experiment, we apply the sequences below.
+
This idea is supported by GATE simulation, which shows that target DNA can not enter GATE by itself. So, the work of PORTER is to pull and bring the target DNA inside GATE.
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<DNA sequences>(実際の配列をお願いします) These are the sequences for electrophoresis, and only a part of the actual Porter sequence. These are the extracted region binding to the target. When planted in the gate, Porter has more spacer sequences of 10base at the root in addition to the sequences above, to reduce the Coulomb's force produced by the wall of Gate.
+
We designed PORTER having some loop structures when it hybridizes with the target. Porter has some complementary sequences to the target here and there. So after the target attaches to Porter, Porter shrinks, or in other words it pulls the target DNA. Finally the target enter GATE.
 +
 
 +
The inner Porter has more complementary sequences to the target and has higher bonding energy than from the one at the entrance of Gate. This design enables the target to move to the inner Porter because of the combination stability. In experiment, we apply the sequences below.
 +
 
 +
<DNA sequences>(実際の配列をお願いします) These are the sequences for electrophoresis, and correspond to only a part of the actual Porter sequence. These are sequences that are complementary to the target. When planted in the gate, Porter has spacer sequences of 10 nucleotides length at its foot in addition to the sequences above; this is to reduce the Coulomb force produced by the wall of GATE.
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Revision as of 07:06, 27 October 2012

Team Sendai Top


Contents

Cell-gate

Our project "Cell-gate" is left. Our project is divided into major three parts, Gate, Porter, and Membrane. Gate is Cell-gate itself.  Porter is function to transport the target inside and outside cell membrane.  Membrane is liposome which is model of cell membrane. We divided our project into above three group and did experiment. On this page, we descript how we determined our robot design.

Design

Design of Gate

Size / Structure

The Gate has to connect inside and outside of the cell. So we decided to apply a hexagonal tube nanostructure made of DNA origami.

We refer "A logic-gated nanorobot for targeted transport of molecular payloads" (SM Douglas, I Bachelet, GM Church - Science Signalling, 2012) for the hexagonal tube structure of DNA origami.

Next, we made a simulation in order to examine the size of the structure. The size of the tube must be small enough not to pass freely through anything. However, it must be large enough to pass through the desired product. The gate which made of DNA origami has negative electric charge. So if the gate is too small, target can't enter the Gate. According to simulation, our Gate size determined 24*24*33nm. This size is suitable to transport the target.

DNA origami

We used caDNAno to design the hexagonal tube structure.



Potential Barrier

Our Gate is made of DNA, so it has negative electric charge. Single stranded DNA has negative electric charge, too. Here is a graph about potential energy of the tube.(藤原さんに頂いた下のグラフ載せる。) GATE size means the length of the Gate. If the potential energy is high, it is difficult for single stranded DNAs to enter the Gate. If the radius of the Gate is 1.5 times larger than now design, potential energy decreases and to enter the Gate is easier. So our Gate is well designed.


Design of Porter

Principle

There are essentially two problems for making CELL-GATE.

    How to pull the target DNA into GATE ?
    How to pass the target through GATE ?

To solve these problems, we propose a nano-system made of ssDNA and named it Porter. Porter stands in line in GATE, pulls the target DNA, and transports it.

This idea is supported by GATE simulation, which shows that target DNA can not enter GATE by itself. So, the work of PORTER is to pull and bring the target DNA inside GATE.

We designed PORTER having some loop structures when it hybridizes with the target. Porter has some complementary sequences to the target here and there. So after the target attaches to Porter, Porter shrinks, or in other words it pulls the target DNA. Finally the target enter GATE.

The inner Porter has more complementary sequences to the target and has higher bonding energy than from the one at the entrance of Gate. This design enables the target to move to the inner Porter because of the combination stability. In experiment, we apply the sequences below.

<DNA sequences>(実際の配列をお願いします) These are the sequences for electrophoresis, and correspond to only a part of the actual Porter sequence. These are sequences that are complementary to the target. When planted in the gate, Porter has spacer sequences of 10 nucleotides length at its foot in addition to the sequences above; this is to reduce the Coulomb force produced by the wall of GATE.


Simulation

We compared the ability to catch the target of Porter with that of toehold structure.

How to implement

Cell model

Cholesterol

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.


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