Biomod/2014/Kansai/Results: Difference between revisions
No edit summary |
|||
| (82 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
[[Image:TOP.png|left|1000px]]<br><br><br><br><br><br><br> | |||
<Font Size="4"> | <Font Size="4"> | ||
<table border="1" cellpadding="4" width=" | <table border="1" cellpadding="4" width="1000" > | ||
<tr align="center"> | <tr align="center"> | ||
<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> | ||
| Line 8: | Line 8: | ||
<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> | |||
<td width="180" bgcolor="#000000">[[Biomod/2014/Kansai/Etc.|<font face="Comic Sans MS,cursive,Arial" color="white"> | |||
</tr> | </tr> | ||
</table> | </table> | ||
= | <Font Size="4"> | ||
< | <table border="1" cellpadding="4" width="1000" > | ||
<tr align="center"> | |||
<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> | |||
< | </tr> | ||
</table> | |||
< | =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 | |||
[[Image: | |||
= | =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
| 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.
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.
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.
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.
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.
