An artist's rendering of a game of tic-tac-toe played with DNA tiles.
Credit: Caltech
The
researchers used a technique for shaping structures out of strands of DNA, a
process known as DNA origami. Unlike previous
techniques, a structure once created could not be altered. However, the researchers
could reshape an already-constructed DNA structure using this new technique. To
demonstrate the powerful new technique, they used it to play game of
tic-tac-toe using a DNA board.
Putting the Pieces
Together
That swapping mechanism combines two previously developed DNA
nanotechnologies.
Both technologies make use of DNA's ability to be programmed
through the arrangement of its molecules. Each strand of DNA consists of a
backbone and four types of molecules known as bases. These bases adenine, guanine,
cytosine, and thymine, abbreviated as A, T, C, and G can be arranged in any
order, with the order representing information that can be used by cells, or in
this case by engineered nanomachines.
The second property of DNA that makes it useful for building
nanostructures is that the A, T, C, and G bases have a natural tendency to pair
up with their counterparts. The A base pairs with T, and C pairs with G. By
extension, any sequence of bases will want to pair up with a complementary
sequence. For example, ATTAGCA will want to pair up with TAATCGT.
However, a sequence can also pair up with a partially
matching sequence. If ATTAGCA and TAATACC were put together, their ATTA and
TAAT portions would pair up, and the nonmatching portions would dangle off the
ends. The more closely two strands complement each other, the more attracted
they are to each other, and the more strongly they bond.
The other technology, self-assembling tiles, is more
straightforward to explain. Essentially, the tiles, though all square in shape,
are designed to behave like the pieces of a jigsaw puzzle. Each tile has its
own place in the assembled picture, and it only fits in that spot.
The result is tiles that can find their designated spot
in a structure and then kick out the tile that already occupies that
position. They invented the mechanism of tile displacement, which follows
the abstract principle of strand displacement but occurs at a larger scale
between DNA origami structures. This is the first mechanism that can be used to
program dynamic behaviors in systems of multiple interacting DNA origami
structures.
Let's Play
To get the tic-tac-toe game started, they mixed up a solution
of blank board tiles in a test tube. Once the board assembled itself, the
players took turns adding either X tiles or O tiles to the solution. Because of
the programmable nature of the DNA they are made from, the tiles were designed
to slide into specific spots on the board, replacing the blank tiles that had
been there. An X tile could be designed to only slide into the lower left-hand
corner of the board.
The goal is to use the technology to develop nanomachines
that can be modified or repaired after they have already been built.
With this tile displacement process we discovered, it becomes
possible to replace and upgrade multiple parts of engineered nanoscale machines
to make them more efficient and sophisticated.
Ref: Philip Petersen, Grigory Tikhomirov, Lulu
Qian. Information-based autonomous reconfiguration in systems of
interacting DNA nanostructures. Nature Communications, 2018; 9
(1) DOI: 10.1038/s41467-018-07805-7
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