Scientists use 'sticky' DNA to build organized structures of gel blocks
Researchers show that molecular interactions between pieces of DNA can
drive the self-assembly of structures visible to the naked eye

Date:
January 31, 2022
Source:
Okinawa Institute of Science and Technology (OIST) Graduate
University
Summary:
Researchers have used microscopic strands of DNA to guide the
assembly of gel blocks that are visible to the naked eye.



FULL STORY ========================================================================== Researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) have used microscopic strands of DNA to guide the
assembly of gel blocks that are visible to the naked eye.


==========================================================================
The hydrogel blocks, which measure up to 2mm in length and contain DNA
on their surface, self-assembled in around 10-15 minutes when mixed in
a solution, the scientists reported today in the Journal of the American Chemical Society.

"These hydrogel blocks are, we believe, the largest objects so far
that have been programmed by DNA to form organized structures," said
Dr. Vyankat Sontakke, first author of the study and a postdoctoral
researcher in the OIST Nucleic Acid Chemistry and Engineering Unit.

The process of self-assembly -- in which an organized structure
spontaneously forms when two or more individual components interact
-- is common in nature, with cells and DNA able to self-assemble into
amazingly complex microscopic structures. But using interactions that
occur on the molecular scale to direct the assembly of macroscopic objects (meaning visible to the naked eye) is a relatively new field of research, particularly with DNA.

"We chose DNA because it is so programmable, which it owes to its
exquisite ability to recognize sequences," said senior author, Professor
Yohei Yokobayashi, who leads the Nucleic Acid Chemistry and Engineering
Unit.

A double-stranded molecule of DNA is formed by two single strands of DNA
that twist around each other to form a double helix shape. The strands are
kept together by bonding between bases, which fit together like a jigsaw
(A with T, and C with G). This specific base pairing ability means that scientists can design strands of DNA that match other strands precisely
and will bond together.



==========================================================================
In one of the experiments, the researchers attached molecules of
single- stranded DNA to the surface of red and green-colored blocks of hydrogel. The strands of DNA on the red blocks matched the strands of
DNA on the green blocks.

When the hydrogel blocks were shaken in a solution, the matching strands
of DNA paired together, acting like a "glue" that stuck the red and green blocks together. After ten minutes, the separated blocks self-assembled
into a simple branching structure of alternating colors.

Importantly, the DNA strands did not interact with the identical strands
of DNA on other blocks, so hydrogel blocks of the same color did not
stick together.

The scientists further tested the ability for the DNA to recognize only specific sequences, by designing four pairs of matching strands. They
attached the single stands from the first matching pair to the surface
of the red hydrogel cubes. The same process was done for the green,
blue and yellow hydrogel cubes.

When shaken together, despite the presence of many different DNA
sequences, the strands only bonded with their matching strand, resulting
in the previously mixed up hydrogel blocks self-sorting into groups of
the same color.



========================================================================== "This shows that the process of self-assembly is very specific and
easily programmable. By simply changing the sequence of DNA, we can
guide the blocks to interact with each other in different ways," said
Prof. Yokobayashi.

As well as self-assembly, the researchers also studied whether they
could use DNA to program the disassembly of a structure. They created two matching single strands of DNA, and then made a third shorter strand that matched part of the first strand. They attached the first strand, and the matching shorter strand to hydrogel cubes, which self-assembled when mixed
in solution. The longer strand of DNA that matched the first strand was
then added to the solution and over the process of an hour, the longer
strand displaced the shorter strand, causing the cubes to disassemble.

"This is really exciting because it means that by using DNA as the "glue"
to stick the hydrogel blocks together, the process is fully reversible,"
said Dr.

Sontakke. "This means that the individual components can also be re-used." While the structures formed so far are simple, the researchers hope to
add more complexity by increasing the number of different cubes that are incorporated into the structure and by targeting different DNA strands
to specific cube faces. They also plan to further increase the size of
the hydrogel blocks.

"This is still basic research, but in the future, these techniques
could be used for tissue engineering and regenerative medicine," said
Prof. Yokobayashi.

"It might be possible to place different types of cells inside hydrogel
cubes, which can then assemble into the complex 3-D structures needed
to grow new tissues and organs.

"But," he added. "Regardless of potential applications, it's incredible
to be able to witness chemistry as microscopic as interacting
DNA strands with our own eyes. It's a really fun piece of science." ========================================================================== Story Source: Materials provided by Okinawa_Institute_of_Science_and_Technology_(OIST)
Graduate_University. Original written by Dani Ellenby. Note: Content
may be edited for style and length.


========================================================================== Related Multimedia:
* DNA_sticks_hydrogel_blocks_together_according_to_color ========================================================================== Journal Reference:
1. Vyankat A. Sontakke, Yohei Yokobayashi. Programmable Macroscopic
Self-
Assembly of DNA-Decorated Hydrogels. Journal of the American
Chemical Society, 2022; DOI: 10.1021/jacs.1c10308 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/01/220131132809.htm

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