Results and Discussion
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Revision as of 21:35, 26 October 2013
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- The firstly synthesized anodizing alumina nanoporous substrate was observed by AFM and SEM, as shown in (fig.4-1 and fig.4-2), respectively. In the AFM image, pores with the inner diameter of 100 nm are aligned in a honeycomb structure. The height image shows that the pore has a conical shape, but not the straight pore which may better fit to the shaft of the weathercock. However, we actually observe the straight pores in the SEM image as expected. The cross-sectional SEM image shows that the holes are 400 nm in depth. Thus the conical shape observed in AFM is an artifact. However, the problem is that the diameter of the pore is still too large to fit the DNA shaft. Because anodizing alumina with the pores of down to 20 nm can be generally fabricated, we changed the synthetic condition and the synthesis is now on the way to go.
- We then designed the DNA weathercock by using a three-dimensional DNA-origami technique. We show the first design of the DNA weathercock in.(fig.4-3) The concept of the first design is (1) arrow shaped blade which is optimal for sensing the flow and (2) the rigid shaft to firmly held in the pore. We prepared staple DNAs as shown in (table1).
- We observed the synthesized DNA weathercock by AFM as shown in Fig.4-4. The cross sectional image is shown in Fig.4-5. We compare the observed shape with the designed one. The objects of the shapes similar to the designed DNA-origami were observed. The Fig.4-6 is a cross-sectional view of for the green line in the Fig.4-7. Thus the size of the observed objects (30 nm x 17 nm x 21 nm) is also similar to the size of the designed one (28 nm x 17 nm x 20 nm), indicating the successful formation. However,the size of the weathercock may be too small for the optical confocal laser microscope to detect the rotational motion of the fluorescence head. Because the number of the staple is limited, we can not design a large enough weathercock if we adopt the 3-dimensinal DNA-origami technique. Also, we don't like this design because this is very different from the image of the weathercock !
- So we redesigned the beautiful weathercock made of a simple 2-dimensional DNA-origami as shown Fig.4-8. However, unfortunately, this was still too small. So, we finally designed the DNA weathercock with the elongated body part of 56 nm (fig.4-9), so that the movement could be detected by the microscope. This finally designed DNA weathercock consists of the M13 scaffold DNA bound by the 97 short staple DNAs as shown in Table 2. We are now synthesizing this weathercock by annealing the mixture of all the materials.