Biomod/2012/TeamSendai/Design - Revision history

Kazuki Hirahara at 02:43, 28 October 2012

Kazuki Hirahara — Sun, 28 Oct 2012 02:43:08 GMT

←Older revision		Revision as of 02:43, 28 October 2012
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	{{:Biomod/2012/Tohoku/Team_Sendai/header}}		{{:Biomod/2012/Tohoku/Team_Sendai/header}}

Kazuki Hirahara at 23:53, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 23:53:23 GMT

←Older revision		Revision as of 23:53, 27 October 2012
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	'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer		'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer
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	※Porter3 use only electrophoresis.		※Porter3 use only electrophoresis.
	----		----

Kazuki Hirahara at 23:52, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 23:52:43 GMT

←Older revision		Revision as of 23:52, 27 October 2012
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	'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer		'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer
		+	※Porter3 use only electrophoresis.
	----		----
	[[Image: スクリーンショット 2012-10-28 8.38.23.png\|center\|400px]]		[[Image: スクリーンショット 2012-10-28 8.38.23.png\|center\|400px]]

Kazuki Hirahara at 23:50, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 23:50:08 GMT

←Older revision		Revision as of 23:50, 27 October 2012
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	[[Image: スライド15.jpg \|340px]]		[[Image: スライド15.jpg \|340px]]
	[[Image: スライド16.jpg \|340px]]		[[Image: スライド16.jpg \|340px]]
-	~~[[Image: Cadnanogazou.png\|680px]]~~	+	<youtube width="450" align="left">XMiheA1sWOA</youtube>
	{{-}}		{{-}}
-

	<h3>Potential Barrier</h3>		<h3>Potential Barrier</h3>

Kazuki Hirahara at 23:42, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 23:42:45 GMT

←Older revision		Revision as of 23:42, 27 October 2012
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	'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer		'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer
	----		----
-	[[Image: ~~Porter'sdesignaota~~.png\|center\|~~300px~~]]	+	[[Image: スクリーンショット 2012-10-28 8.38.23.png\|center\|400px]]
	We should note these described above are the sequences for electrophoresis experiments. Additional sequences to attach the GATE are included in the designed Porter sequences of the GATE.		We should note these described above are the sequences for electrophoresis experiments. Additional sequences to attach the GATE are included in the designed Porter sequences of the GATE.

Kazuki Hirahara at 22:11, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 22:11:06 GMT

←Older revision		Revision as of 22:11, 27 October 2012
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	<h1>Design</h1>		<h1>Design</h1>
-	<h1>~~Design of~~ Gate</h1>	+	<h2>Gate</h2>
-	<h2>Size / Structure</h2>	+	<h3>Size / Structure</h3>
	What structure is most suitable for the Gate? 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.<br>		What structure is most suitable for the Gate? 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.<br>
	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 242433nm. This size is suitable to transport the target.<br>		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 242433nm. This size is suitable to transport the target.<br>
	{{-}}		{{-}}

-	<h2>DNA origami</h2>	+	<h3>DNA origami</h3>
	We used caDNAno to design the hexagonal tube structure. This Gate tube is made from 6792bp M13mp18 and a lot of single stranded DNAs. And the Gate has double hexagonal structure because I think that is stronger than single hexagonal structure.		We used caDNAno to design the hexagonal tube structure. This Gate tube is made from 6792bp M13mp18 and a lot of single stranded DNAs. And the Gate has double hexagonal structure because I think that is stronger than single hexagonal structure.

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-	<h2>Potential Barrier</h2>	+	<h3>Potential Barrier</h3>
	[[Image: Potential_energy.png\|340px]]		[[Image: Potential_energy.png\|340px]]
	Our Gate is made of DNA, so it has negative electric charge. Single stranded DNA has negative electric charge, too. Here is a graph at potential energy around the tube. 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.		Our Gate is made of DNA, so it has negative electric charge. Single stranded DNA has negative electric charge, too. Here is a graph at potential energy around the tube. 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.
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-	<h1>~~Design of~~ Porter</h1>	+	<h2>Porter</h2>
-	<h2>Principle</h2>	+	<h3>Principle</h3>
	[[Image:スライドGif.gif\|left\|400px]]		[[Image:スライドGif.gif\|left\|400px]]
	In the concept of Cell Gate, there are two problems. for making CELL-GATE.		In the concept of Cell Gate, there are two problems. for making CELL-GATE.
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	{{-}}		{{-}}

-	<h2>Simulation</h2>	+	<h3>Simulation</h3>
	Coarse grained simulation in which one nucleotide is assumed as one bead indicates that long Porter can bind to the target, but toehold structure of the same affinity cannot catch the target.<br>		Coarse grained simulation in which one nucleotide is assumed as one bead indicates that long Porter can bind to the target, but toehold structure of the same affinity cannot catch the target.<br>
	<table border="0" align="left" vertical-align: middle;>		<table border="0" align="left" vertical-align: middle;>
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-	<h1>~~Design of~~ Membrane: How to implement the GATE</h1>	+	<h2>Membrane: How to implement the GATE</h2>
-	<h2>Cell model</h2>	+	<h3>Cell model</h3>
	To insert the Gate in cell membranes is essential for the CELL GATE. We used artificial lipid membrane, liposomes, as model cell membranes, to test implementation of our CELL GATE into membrane. As a preliminary step to insertion of the GATE into the liposome, we designed a smaller Gate named Mini-gate. We attempted to insert the Gate and Mini-gate into liposomes and we confirmed they inserted into liposomes by fluorescence microscopy or by SPR analysis.		To insert the Gate in cell membranes is essential for the CELL GATE. We used artificial lipid membrane, liposomes, as model cell membranes, to test implementation of our CELL GATE into membrane. As a preliminary step to insertion of the GATE into the liposome, we designed a smaller Gate named Mini-gate. We attempted to insert the Gate and Mini-gate into liposomes and we confirmed they inserted into liposomes by fluorescence microscopy or by SPR analysis.
-	<h2>Cholesterol-leg</h2>	+	<h3>Cholesterol-leg</h3>
	To implement the Gate in membranes, we attached single-stranded DNA of 10 bases at the middle point of the GATE outside surface. A hydrophobic molecule, Cholesterol, was conjugated into the complementary DNA of the attached DNA. We expected that the GATE with cholesterol legs can be implemented into the hydrophobic portion of the liposome.<br>		To implement the Gate in membranes, we attached single-stranded DNA of 10 bases at the middle point of the GATE outside surface. A hydrophobic molecule, Cholesterol, was conjugated into the complementary DNA of the attached DNA. We expected that the GATE with cholesterol legs can be implemented into the hydrophobic portion of the liposome.<br>
	There is a possibility that the GATE with cholesterol legs lie on the membrane surface, and is not inserted. Thus, installing a module for insertion was required. For the aim, we designed that the Mini-gate remains a large amount of single stranded region of M13. We expected that this single stranded region of M13 breaks electrostatic symmetry of the Mini-Gate, and enables to stand vertically to penetrate the membrane by repulsion.		There is a possibility that the GATE with cholesterol legs lie on the membrane surface, and is not inserted. Thus, installing a module for insertion was required. For the aim, we designed that the Mini-gate remains a large amount of single stranded region of M13. We expected that this single stranded region of M13 breaks electrostatic symmetry of the Mini-Gate, and enables to stand vertically to penetrate the membrane by repulsion.

Kazuki Hirahara at 21:45, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 21:45:13 GMT

←Older revision		Revision as of 21:45, 27 October 2012
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-	<h1>How to implement the GATE ~~into Membrane~~</h1>	+	<h1>Design of Membrane: How to implement the GATE</h1>
	<h2>Cell model</h2>		<h2>Cell model</h2>
	To insert the Gate in cell membranes is essential for the CELL GATE. We used artificial lipid membrane, liposomes, as model cell membranes, to test implementation of our CELL GATE into membrane. As a preliminary step to insertion of the GATE into the liposome, we designed a smaller Gate named Mini-gate. We attempted to insert the Gate and Mini-gate into liposomes and we confirmed they inserted into liposomes by fluorescence microscopy or by SPR analysis.		To insert the Gate in cell membranes is essential for the CELL GATE. We used artificial lipid membrane, liposomes, as model cell membranes, to test implementation of our CELL GATE into membrane. As a preliminary step to insertion of the GATE into the liposome, we designed a smaller Gate named Mini-gate. We attempted to insert the Gate and Mini-gate into liposomes and we confirmed they inserted into liposomes by fluorescence microscopy or by SPR analysis.

Kazuki Hirahara at 21:43, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 21:43:29 GMT

←Older revision		Revision as of 21:43, 27 October 2012
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-	<h1>How to implement</h1>	+	<h1>How to implement the GATE into Membrane</h1>
	<h2>Cell model</h2>		<h2>Cell model</h2>
	To insert the Gate in cell membranes is essential for the CELL GATE. We used artificial lipid membrane, liposomes, as model cell membranes, to test implementation of our CELL GATE into membrane. As a preliminary step to insertion of the GATE into the liposome, we designed a smaller Gate named Mini-gate. We attempted to insert the Gate and Mini-gate into liposomes and we confirmed they inserted into liposomes by fluorescence microscopy or by SPR analysis.		To insert the Gate in cell membranes is essential for the CELL GATE. We used artificial lipid membrane, liposomes, as model cell membranes, to test implementation of our CELL GATE into membrane. As a preliminary step to insertion of the GATE into the liposome, we designed a smaller Gate named Mini-gate. We attempted to insert the Gate and Mini-gate into liposomes and we confirmed they inserted into liposomes by fluorescence microscopy or by SPR analysis.

Naito Ushio at 20:19, 27 October 2012

Naito Ushio — Sat, 27 Oct 2012 20:19:32 GMT

←Older revision		Revision as of 20:19, 27 October 2012
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	<h1>Design of Porter</h1>		<h1>Design of Porter</h1>
	<h2>Principle</h2>		<h2>Principle</h2>
-	[[Image: ~~Perportergifkoyama~~.gif\|~~right~~\|~~340px~~]]	+	[[Image:スライドGif.gif\|left\|400px]]
	In the concept of Cell Gate, there are two problems. for making CELL-GATE.		In the concept of Cell Gate, there are two problems. for making CELL-GATE.
	<ul>How to pull the target DNA into GATE ?</ul>		<ul>How to pull the target DNA into GATE ?</ul>

Kazuki Hirahara at 20:13, 27 October 2012

Kazuki Hirahara — Sat, 27 Oct 2012 20:13:11 GMT

←Older revision		Revision as of 20:13, 27 October 2012
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	{{:Biomod/2012/Tohoku/Team_Sendai/header}}		{{:Biomod/2012/Tohoku/Team_Sendai/header}}
-	~~__NOTOC__~~	+

	<div id="Container">		<div id="Container">
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	<div id="Content">		<div id="Content">

-		+	<h1>Design</h1>
	<h1>Design of Gate</h1>		<h1>Design of Gate</h1>
	<h2>Size / Structure</h2>		<h2>Size / Structure</h2>
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	'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer		'''Blue''':Target '''Red''':This part is complementary with target '''Green''':Spacer
	----		----
-	[[Image: Porter'sdesignaota.png\|~~left~~\|300px]]	+	[[Image: Porter'sdesignaota.png\|center\|300px]]
	We should note these described above are the sequences for electrophoresis experiments. Additional sequences to attach the GATE are included in the designed Porter sequences of the GATE.		We should note these described above are the sequences for electrophoresis experiments. Additional sequences to attach the GATE are included in the designed Porter sequences of the GATE.