Biomod/2015/Kansai/Protocols

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Experiment

　All staples (cho 1~180, choMD 1~20 and choEND 1~20) and the M13mp18 were mixed together and

annealed from 90˚C to 25˚C at rate of -1.0˚C/min using a PCR thermal cycler.

　At first, we investigated that weather DNA origami structure has cylindrical shape.

We observed it by AFM. Figure 1 is the AFM image. It shows that almost structures have cylindrical shape.

We also performed height analysis. As a result, The height was about 5nm.

Plane DNA origami structure is about 2nm, so we judged that cylindrical shape was constructed.

Fig. 1A AFM image 1

Fig. 1B Height analysis

In the next place, we observed Open motif (OM) and Closed motif (CM).

We prepared two type staples to close the part of mouth of chochin.

One is choLOCK that is closed perfectly opening/closing part, the other is choOM that is closed imperfectly opening/closing part. (sticky end)

Fig. 1B Height analysis

Fig. 1B Height analysis

First, we investigated the opening/closing of the part of mouth by changing staples.

We prepared four staple DNA mixes they are closed opening/closing part.

1　choLOCK2,11,18,19

2　choLOCK2,5,7,11,14,16,18,19

3　choLOCK5,7,14,16

4　all locations

We mixed cho1~180, choEND1~20, MD1,20 and M13 and annealed.

Then, we add above four mixes and pumped.

We electrophoresed with agarose gel these four samples and one is not added staple DNA to

opening/closing part (only cho1~180, choEND1~20, M13), then we observed these five bands.

Fig. 1B Height analysis

Fig. 1B Height analysis