Project

　Our project is to make a DNA net that can wrap intended materials. DNA net are made by using DNA tiles. Our net is made from a three-point-star structure and a joint that connect the edges of the three-point-star. The stiff three-point-star maintains the honeycomb structure while the joint changes the flexibility of the whole structure. An external signal changes the hardness of the joint that makes the tile a flexible curbed surface from a hard plane. By an entropic effect, the edges fasten up like a zipper after the edges of the curbed surface collide at stochastic events, which achieve DNA tile wrapping.

Idea

Annealing products made out of simple y-motifs are too soft, resulting in a sphere-like structure [1]. On the other hand, using a 3-point-star structure, a stiff y-shape structure, enables us to make a big DNA tile sheet stably [2]. If we can move from each of these two conditions to the other, we may be able to make the DNA tile sheet change into a sphere-like structure. This transition will enable us to wrap materials up.
For stiffness transition, we should change the hardness of the joints that connect the three-point-star. Double stranded DNAs are stiff (persistence length: 50 nm), while single stranded DNAs are very soft (persistence length: 1-3 nm). Thus, we thought that making the DNA tile sheet with double stranded DNAs and then changing the joints to single stranded DNAs by using external signals will realize the wrapping transition.

Project Goal

The goal is to give flexibility to a micro-sized stiff DNA sheet flexible after forming, and changing it into a sphere to wrap materials up.
In order to achieve this, we set the sub goals as shown below.

Design

We will be making a tile structure that is going to transform on the way. In order to realize this, the following 2 factors are needed:
(A) The formation of the tile sheet
(B) A unit to change the flexibility of the tile sheet
We designed two units as follows.

Parts

Structure: Three-point-star(TPS)

A modified structure of original three-point- star in reference [2]

It has an edge made of two double stranded DNA and is bundled in the center, making it strong enough to form a net.

For details

Joint: Flexibility controller

A DNA that will be adjoining the 3-point-stars together. At first it is a stiff double stranded structure, but becomes a flexible single stranded structure after addition of a complementary strand of one of the strands that peel the strand off.

For details

How the bonding looks like

The tile is made by combining the 3-point-star and the joint alternately.
By adding Capture DNA, the joints become a flexible single strand so the whole DNA tile becomes flexible.

Mechanism

The formation of flexible DNA tile sheets

After annealing the mixture of DNA strands for the parts of TPS and joints, DNA tiles assembles as the left figure, and form micro- to mm-sized sheets (DNA tile sheets). In this stage, the DNA sheets is stiff. The DNA sheets can become flexible after the additon of Capture DNA, which realizes DNA tile wrapping.

The mechanism of making the structure flexible

The bond between the 3-point-star and the joint is not completely complementary. Thus, by putting a perfect complementary strand of the same length as a strand of the joint DNA, the strand peels off making the joint a single strand. Therefore, it will lose its stiffness and becomes flexible.

The mechanism of wrapping

After making the joint flexible, the sheet of DNA tiles will become a curbed surface due to structural fluctuation (driven by Brownian motion). This change into a curbed surface increases the probability of collision of the edges of the tile. Since the edges of the DNA tiles are able to bond, bonding one point as a course of stochastic events facilitate nearest edges’ bonding like a zipper by a entropy-driven manner.

Wrapping movie

Reference

[1] Matsuura, K., Yamashita, T., Igami, Y., & Kimizuka, N. (2003). ‘Nucleo-nanocages’: designed ternary oligodeoxyribonucleotides spontaneously form nanosized DNA cages. Chemical Communications, (3), 376-377.

[2] He, Y., Chen, Y., Liu, H., Ribbe, A. E., & Mao, C. (2005). Self-assembly of hexagonal DNA two-dimensional (2D) arrays. Journal of the American Chemical Society, 127(35), 12202-12203.