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<td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/Protocols|<font face="Comic Sans MS,cursive,Arial" color="black">Experiment</font>]] </td>
<td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/Protocols|<font face="Comic Sans MS,cursive,Arial" color="black">Experiment</font>]] </td>
<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Experiment|<font face="Comic Sans MS,cursive,Arial" color="white">New design</font>]] </td>
<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Experiment|<font face="Comic Sans MS,cursive,Arial" color="white">Further experiment</font>]] </td>
<td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/New sources|<font face="Comic Sans MS,cursive,Arial" color="black">New sources</font>]] </td>
<td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/New sources|<font face="Comic Sans MS,cursive,Arial" color="black">Future plan</font>]] </td>
<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Sources|<font face="Comic Sans MS,cursive,Arial" color="white">protocol</font>]] </td>
<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Sources|<font face="Comic Sans MS,cursive,Arial" color="white">protocol</font>]] </td>
<td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/sponser|<font face="Comic Sans MS,cursive,Arial" color="black">Sponser</font>]] </td>
<td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/sponser|<font face="Comic Sans MS,cursive,Arial" color="black">Sponser</font>]] </td>
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=New design=
We thought the structure couldn’t be formed either due to electrostatic repulsion or due to bouding power between origamis. Figure 13 depicts schematic diagram of these problems. Regarding electrostatic repulsion, the paper has been reported that modified some dumbbell hairpins on edge of rectangular origami controlled a three-dimensional warp by electrostatic repulsion <sup><cite>1</cite></sup>. In our case, we anticipated that electrostatic repulsion occurred between many dumbbell hairpins and rectangular origami. So there is some possibility of occurring large warps on our origami. As for bouding power between each origamis, our design origami had joining surface at top and bottom. But it had no joining surface at helix direction. Therefore binding interactions between origamis were weakly. And they couldn’t connect each other. So we tried to demonstrate the possibility to do two experiments.
<br><br>


[[Image:Rfig4.png|left|400px]]
[[Image:Figure13ofkansai.png|center|1000px]]


Figure 13 depicts the outline of old design. In old design, the method of formation is connecting 3 kinds of rectangular, the interaction of connecting each origami is only a formation of double helix by joints staple. And furthermore, the area between each origami is acted on a power of electrostatic interaction; it is possible to impede the formation of structure. We considered that only this power couldn’t be stable a structure. It was reported that origamis are connected by using stacking interaction with a base of DNA<sup><cite>1</cite></sup>. They made a plan that the design of DNA origami is zigzag joining surface such as jigsaw peace. It has the surface that each origami contacts with the helix direction. Hence, we contrived the innovative design that stacking interaction influences a connection. Figure 15 depicts the outline of new design. Origami A and origami C are a point-symmetrical structure. To save the money, we designed that staple DNA of origami A, B and C are almost same. As a point at issue of old design, the joints staples of connected each origami are common, the desired structure wasn’t formed. At new design, the sequence of joints staple between origami A and origami B and between origami B and origami C are different. So, these can guard against wayward formation of DNA origami.
'''''Ex 1'''''<br>
 
To solve electrostatic repulsion, we make DNA origami modified no dumbbell hairpin. We form dimer out of its origami. By means of agarose gel electrophoresis, we compare mobility of bandsof DNA origami modified dumbbell hairpins with mobility of band of it modified no dumbbell hairpin. We study how influence of electrostatic repulsion between dumbbell hairpins and origami. We study whether electrostatic repulsion between dumbbell hairpins and origami influences forming dimer or trimer. To solve problem of binding power, we found new design on existing DNA origami design.
<br><br>
 
'''''Ex 2'''''<br>
 
To solve problem of binding power, we found new design on existing DNA origami design. It can work π-π stacking interaction between each origami. Fig 14 depicts outline of the design of DNA origami after modification. Part of blunt end stick to another blunt end. Some staples overhang another origami. We consider that bouding power increases. Using agarose gel electrophoresis, we compare mobility of the DNA origami with former DNA origami as well. We study how π Stacking interaction influences dimer and trimer formation that are modified dumbbell hairpin.
 
[[Image:Figure14ofkansai.png|center|600px]]
 
<br><br>
By these experiments, we investigate the reason that expected structure wasn’t formed as the design.
If we confirm stabilization of the structure by π Stacking, we show Future plan to next page…
<br>
<br>
=Original Adobe Illustrator files of design changes=
<br>
[[Image:Design changes origami.zip]]
<br><br>
 
=References=
<div style="text-align:justify;">
<biblio>
#1  Hao Yan ''et al.'', ''Langmuir'', '''2012''', 28 (4), 1959–1965
</biblio>

Latest revision as of 01:40, 25 October 2014








Top Team Project Design Sources

Experiment Further experiment Future plan protocol Sponser


We thought the structure couldn’t be formed either due to electrostatic repulsion or due to bouding power between origamis. Figure 13 depicts schematic diagram of these problems. Regarding electrostatic repulsion, the paper has been reported that modified some dumbbell hairpins on edge of rectangular origami controlled a three-dimensional warp by electrostatic repulsion [1]. In our case, we anticipated that electrostatic repulsion occurred between many dumbbell hairpins and rectangular origami. So there is some possibility of occurring large warps on our origami. As for bouding power between each origamis, our design origami had joining surface at top and bottom. But it had no joining surface at helix direction. Therefore binding interactions between origamis were weakly. And they couldn’t connect each other. So we tried to demonstrate the possibility to do two experiments.

Ex 1

To solve electrostatic repulsion, we make DNA origami modified no dumbbell hairpin. We form dimer out of its origami. By means of agarose gel electrophoresis, we compare mobility of bandsof DNA origami modified dumbbell hairpins with mobility of band of it modified no dumbbell hairpin. We study how influence of electrostatic repulsion between dumbbell hairpins and origami. We study whether electrostatic repulsion between dumbbell hairpins and origami influences forming dimer or trimer. To solve problem of binding power, we found new design on existing DNA origami design.

Ex 2

To solve problem of binding power, we found new design on existing DNA origami design. It can work π-π stacking interaction between each origami. Fig 14 depicts outline of the design of DNA origami after modification. Part of blunt end stick to another blunt end. Some staples overhang another origami. We consider that bouding power increases. Using agarose gel electrophoresis, we compare mobility of the DNA origami with former DNA origami as well. We study how π Stacking interaction influences dimer and trimer formation that are modified dumbbell hairpin.



By these experiments, we investigate the reason that expected structure wasn’t formed as the design. If we confirm stabilization of the structure by π Stacking, we show Future plan to next page…

Original Adobe Illustrator files of design changes


File:Design changes origami.zip

References

  1. Hao Yan et al., Langmuir, 2012, 28 (4), 1959–1965

    [1]
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