Biomod/2013/Komaba/Design

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Cylinder

The cylinder is put in the center of the motor as an axis supporting the rotation. DNA strands of staples and a scafold are formed into a cylindrical shape using DNA Origami technology. It was designed with cadnano software, which "simplifies and enhances the process of designing three-dimensional DNA origami nanostructures".(Figure 1)

In order to bind footing DNAs on its surface spirally, 10mer long DNA strands which we call footings of footings come up from the cylinder's surface. After the cylinder with the footing of footings are formed, one of the three legs of DNA spiders is connected to a specific strand at the start point on the cylinder's surface. Then the footings get connected to the footing of footings. The footing tracks, each of which consists of three lanes of the footings, enable DNA Spiders to orbit the cylinder. In detail, there are two tracks of DNA footings and two spiders can walk on each track. In addition, in order to make it easy to observe the direction of spiders' walk, a small sub-cylinder is attached at the end of the footing tracks.

The diameter of the cylinder is 25.4 nm and height is 43.5 nm. This is calculated considering that the cylinder can be observed with an Atomic Force Microscope and that the interval between the two tracks are wide enough for spiders not to jump to next footing track.

(Figure 2)

[Figure 1:cadnanoのデータ][Figure 2:シリンダーの絵]

DNA Spider

Our DNA screw rotates by using DNA spiders produced by Lund, et al.. DNA Spider consists of a core and three legs. These legs move on the footing by cutting strands with DNAzyme. Since legs orbit the cylinder, they rotate the DNA Ring.

In this paragraph, how to create DNA spiders is described. This method is the same as the way Lund, et al. did. First, Streptavidin(STV) and capture leg [5’ - GCC GAG AAC CTG ACG CAA GT/iSp18//iSp18//3Bio/ - 3] are connected in a solution. To create one-to-one product (“STV-(C)1” ), ion exchange is used. Second, deoxyribozyme legs [5’ - /5BioTEG//iSp18//iSp18//TCT CTT CTC CGA GCC GGT CGA AAT AGT GAA AA – 3’ ] are attached to the STV-(C) i.e. NICK3.4A+1. Third, Cy3 MONO NHS ester dissolved in DMSO is added in the solution containing NICK3.4A+1.

By increasing the number of DNA spiders and DNA tracks, it would be possible to stabilize the rotating speed of the ring.

Rotary Ring

It is the DNA ring that actually rotates. It has a shape　of　a cylinder short in the axial direction and is also composed with DNA Origami technology. Two 10mer long strands come up from the inner side of the ring and are connected to the DNA spiders. The diameter of the ring is 50.9 nm, and so it can hold the cylinder and spiders inside of the ring. The thickness of ring is 10.9 nm in consideration of Atomic Force Microscope visibility.

DNA Screw (Combination of above parts)

The DNA screw is realized by assembling the above four parts: the cylinder, footings, DNA Spiders, and the rotary ring.