Project
Background
Nanotechnology is the realm of technological prowess dedicated to the manipulation of materials at the nanoscale, encompassing entities such as molecules and atoms. It boasts the capacity to construct arbitrary two-dimensional and three-dimensional structures, offering the promise of novel materials, innovative devices, and envisioning applications in the realm of nanorobotic therapies. At present, an ingenious technique known as 'structural DNA nanotechnology' has been devised for the purpose of fabricating nanoscale structures employing DNA as the primary material. This approach capitalizes on the autonomous formation of double-helical structures stemming from the complementarity of Watson-Crick base pairs, thereby enabling the semi-autonomous construction of intricate structures.

DNA origami, another innovative technique, involves the folding of DNA to craft arbitrary two- and three-dimensional structures. As an applied technology within structural DNA nanotechnology, it employs a singular elongated DNA strand, known as the 'staple strand,' to define the shape of the intended nanoscale construct. To stabilize this structure, an abundance of shorter clamping DNA strands, referred to as 'scaffold strands,' is used. By meticulously regulating temperature, including both heating and cooling processes, the extended DNA strand is precisely molded into a configuration mirroring the original design.

In the dynamic field of nanotechnology, novel structural proposals surface on a daily basis, encompassing a plethora of deformable structures. However, structures with varying vertex numbers have not yet been introduced. The introduction of fresh structural designs is anticipated to serve as a catalyst for the advancement of diverse nanotechnologies. Hence, we have presented structures like those in this project.

Problem & Solution
One of the most famous nanostructures using DNA is the DNA BOX. The DNA BOX changes its structure when it receives a signal. DNA BOX is expected to be applied to drug delivery. However, in the medical field, nanodevices with more complex functions are required, and their application has not progressed. We propose a DNA nanostructure with a varying number of vertices as a solution to this problem. Our structure, which applies the theory of duality, has a complex function in which the number of vertices changes depending on the signal. This structure, "Vertex-Switcher," will accelerate the application of DNA nanotechnology to the real world.
Our goals and achievements
The basic goal of our project is to construct a vertex-switcher that can change the structure of six vertex form, eight vertex form, and intermediate form. To achieve this goal, we set the following three milestones.

① Design of vertex-switcher
☑ design of transformative mechanism
First, the basic structure of the vertex-switcher, the intermediate form, was designed using the wire frame DNA origami as the basic framework. In addition, we designed a mechanism using strand displacement reactions to achieve structural transformation.

② Evaluation of structural stability of vertex-switcher in sillico
☑ intermediate from
☑ 6 vertex form
☑ 8 vertex form
To confirm the stability of the designed structures, we conducted MD simulations of three forms of structures, 6 vertex form, 8 vertex form, and intermediate form, using oxDNA.

③ Construction and Confirming of vertex-switcher
☑ intermediate form
☑ intermediate from → 6 vertex form
☑ intermediate from → 8 vertex form
6 vertex form → intermediate from → 8 vertex form
8 vertex form → intermediate from → 6 vertex form
To confirm the structural transformation in the in vitro experiment, we conducted electrophoresis and TEM observation.

In summary, we were able to achieve most of the milestones we set using in silico and in vitro experiments. However, we were not able to confirm the complete structural transformation, although we obtained results suggesting a multi-step structural transformation from a 6-vertex form to an intermediate from to an 8-vertex form in some parts of the structure.