Biomod/2014/Kansai/Results: Difference between revisions
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<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai|<font face="Comic Sans MS,cursive,Arial" color="white">Top</font>]] </td> | <td width="180" bgcolor="#000000">[[Biomod/2014/Kansai|<font face="Comic Sans MS,cursive,Arial" color="white">Top</font>]] </td> | ||
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<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Project|<font face="Comic Sans MS,cursive,Arial" color="white">Project</font>]] </td> | <td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Project|<font face="Comic Sans MS,cursive,Arial" color="white">Project</font>]] </td> | ||
<td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/Results|<font face="Comic Sans MS,cursive,Arial" color="black">Design</font>]] </td> | <td width="180" bgcolor="#FFFFFF">[[Biomod/2014/Kansai/Results|<font face="Comic Sans MS,cursive,Arial" color="black">Design</font>]] </td> | ||
<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Etc.|<font face="Comic Sans MS,cursive,Arial" color="white">Sources</font>]] </td> | |||
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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="#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">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="#FFFFFF">[[Biomod/2014/Kansai/sponser|<font face="Comic Sans MS,cursive,Arial" color="black">Sponser</font>]] </td> | |||
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< | =Design= | ||
We designed one kind of DNA nano QR code.
A black part on QR code is expressed by dumbbell hairpin.
The nano QR code is a secret until we create it at nano size. | |||
[[Image:Rfig1.png|left|500px]]<br><br><br><br><br><br><br><br><br><br><br><br> | |||
We had difficulty to coupling dumbbell hairpins on the direction orthogonal to the origami. | |||
To solve it, we designed that interval of dumbbell hairpins is 2 pitch (6.8 nm) on row direction and 2 helices (6 nm) on column direction. | |||
The below figure is the sequence of it . Its height is 2.5 nm and its width is 4.5 nm.<br><br> | |||
[[Image:Rfig2.png|left|500px]]<br><br><br><br><br><br><br><br><br> | |||
Thereby, a new problem has occurred. Our making QR code is version 1 and consists of 21 cells × 21 cells. | |||
10.5 bases × 40 pitches = 420 bases. 21 cells correspond to 420 base pairs. In addition, we need margins at both side. | |||
So including the margin, it needs 512 bases per a line. Because M13 scaffold is 7249 bases, we can only make fourteen lines from one M13 scaffold. | |||
That means 7 cells. But column direction need 21 cells, it is not enough. So, we resolved to use 3 sheets of DNA origami.<br><br> | |||
[[Image:Rfig3.png|left|500px]] | |||
<br><br><br><br><br><br><br><br> | |||
We planed how to combine between origami. | |||
This is a design of joint points between part A and part B.
<sup><cite>1</cite></sup> Sequences indicated red lines connect them.
They also exist between part B and part C.
So, the structure is constructed to connect three kinds of part. <br><br> | |||
[[Image:Rfig4.png|left|400px]]<br><br><br><br><br><br><br><br><br><br><br> | |||
To construct DNA nano QR code uses 3 types of DNA origami. | |||
Normally, they have required 600 pieces of DNA staple (200 pieces per one DNA origami). | |||
We devised the sequences of Staple DNA, they were shared among 3 types of DNA origami. | |||
Thus we required only 359 pieces of DNA staple. | |||
=Original Adobe Illustrator files of DNA origami designs= | |||
<br> | |||
[[Image:New design QR codekigot.zip]] | |||
<br> | |||
<br> | <br> | ||
= | =References= | ||
<div text-align: | <div style="text-align:justify;"> | ||
<biblio> | |||
#1 #1 A. Kuzuya and M. Komiyama ''et al.'', ''ChemBioChem'', '''2009''', ''10'', 1811-1815. | |||
</biblio> |
Latest revision as of 00:52, 24 October 2014
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/d/dd/TOP.png/1000px-TOP.png)
Top | Team | Project | Design | Sources |
Experiment | Further experiment | Future plan | protocol | Sponser |
Design
We designed one kind of DNA nano QR code. A black part on QR code is expressed by dumbbell hairpin. The nano QR code is a secret until we create it at nano size.
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/9/9b/Rfig1.png/500px-Rfig1.png)
We had difficulty to coupling dumbbell hairpins on the direction orthogonal to the origami.
To solve it, we designed that interval of dumbbell hairpins is 2 pitch (6.8 nm) on row direction and 2 helices (6 nm) on column direction.
The below figure is the sequence of it . Its height is 2.5 nm and its width is 4.5 nm.
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/a/ac/Rfig2.png/500px-Rfig2.png)
Thereby, a new problem has occurred. Our making QR code is version 1 and consists of 21 cells × 21 cells.
10.5 bases × 40 pitches = 420 bases. 21 cells correspond to 420 base pairs. In addition, we need margins at both side.
So including the margin, it needs 512 bases per a line. Because M13 scaffold is 7249 bases, we can only make fourteen lines from one M13 scaffold.
That means 7 cells. But column direction need 21 cells, it is not enough. So, we resolved to use 3 sheets of DNA origami.
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/2/29/Rfig3.png/500px-Rfig3.png)
We planed how to combine between origami.
This is a design of joint points between part A and part B.
[1] Sequences indicated red lines connect them.
They also exist between part B and part C.
So, the structure is constructed to connect three kinds of part.
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/0/0e/Rfig4.png/400px-Rfig4.png)
To construct DNA nano QR code uses 3 types of DNA origami. Normally, they have required 600 pieces of DNA staple (200 pieces per one DNA origami). We devised the sequences of Staple DNA, they were shared among 3 types of DNA origami. Thus we required only 359 pieces of DNA staple.
Original Adobe Illustrator files of DNA origami designs
File:New design QR codekigot.zip
References
-
#1 A. Kuzuya and M. Komiyama et al., ChemBioChem, 2009, 10, 1811-1815.