Biomod/2014/Kansai/Project

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Team

Project

Design

Experiment and Result

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Background

Fig.1 smile mark and a star mark ^[1]

　Deoxyribonucleic acid (DNA) is greatly useful materials for a building block in constructing extremely small structure. DNA nanotechnology has DNA tile at first generation and DNA origami at second generation. DNA origami is constructed by combining complementary chains between a long circlic DNA strand (Scaffold DNA) and more 200 kinds of short strands (Staple DNA) . Furthermore, Various structures could form by changing the sequences of staple DNAs in the self-organization. 　It has been reported various nanostructures made of DNA origami. For instance, these are two-dimensional structure, such as a smile mark and a star mark.^[1] And three-dimensional structure like DNA origami box.^{[2] [3]} In the other, DNA pliers are known that is moving DNA origami.^[4]

Our vision and the goal

　

Fig2. QR code

Originally, DNA maintains the genetic code that is difficult to observe visually. The number of base that is scaffold DNA (M13mp18) is 7249. This indicates that it is possible to have information of 4⁷²⁴⁹ (= 10⁴³⁶⁴) kinds. It is enormous. But the information is difficult to observe visually. So we use the scaffold DNA as visually information even though it might be smaller (2^21×21) compared with the former information content. In the past, paper has been reported to represent a character by origami of a sheet ^[5]. We thought that trying to have more information visually. So, we focused on QR code that is one kind of two-dimensional code (Fig. 2). QR code is possible to accommodate the large amount of data in a small space, and to accommodate not only umbers but also the language data such as English. QR code is will read in a camera apps which goes by the name of “QR reader”. It can convert black and white pattern into information such as figures and characters. Even if the QR code has wrong information, the QR reader can read the information. That has correction ability. In order to express it in nano size, we utilize height difference of DNA origami structure. We will give the height difference by inserting dumbbell hairpins

in the DNA origami^[1] (Fig. 3) .

Fig. 3 structure of a dumbbell hairpin

AFM can read nano-structure height by black and white contrast. For example, High

part is reflected white and low part is reflected black when the structure was observed by AFM. So, we certain the origami structure can represent QR code by reading it in an AFM. We design DNA origami modified dumbbell hairpins such as the QR code. And we have AFM read its construction. We analyze it. Finaly, if camera App can read the figure of nano QR code made of the origami, our project will be complete!

References

1. P. W. K. Rothemund, Nature, 2006, 440, 297-302.

2. A. Kuzuya and M.Komiyama, Chem. Commum., 2009, 4182-4184.

3. J. Kjems et al., Nature, 2009, 459, 73-76.

4. A. Kuzuya et al., Nature Commum., 2011, 2, 449.

5. H. Sugiyama et al., Chem. Eur. J., 2010, 16, 5362–5368.