Biomod/2014/Kansai/Experiment: Difference between revisions
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We | 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. | ||
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'''''Ex 1'''''<br> | '''''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 | 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. | ||
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'''''Ex 2'''''<br> | '''''Ex 2'''''<br> | ||
To solve problem of | 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]] | [[Image:Figure14ofkansai.png|center|600px]] | ||
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By these experiments, we investigate the reason that expected structure wasn’t formed as the design. | By these experiments, we investigate the reason that expected structure wasn’t formed as the design. | ||
If we confirm stabilization of the structure by | If we confirm stabilization of the structure by π Stacking, we show Future plan to next page… | ||
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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
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Hao Yan et al., Langmuir, 2012, 28 (4), 1959–1965
