It's
already possible to make nanoparticles and in some cases, fashion them into
microscopic tools. But self-replicating nanomaterials in my book, borders on
the realm of sci-fi and as far as I knew, wasn't possible.
Researchers
at Sungkyunkwan University and Tohoku University, however, have demonstrated
that it is possible, using Nature's own self-replicating molecule, DNA
(Deoxy-Ribonucleic Acid) to create self-replicating geometric designs for basic
machines as reported in the article “Self-replicating
nanostructures made from DNA”, published May 28 2015 by Heather Zeiger, Physorg.
The
researchers involved are again a long list of researchers representing a
collaboration between
Sungkyunkwan
University and Tohoku University in Japan:
1.
Dr. Junghoon Kim
2.
Dr. Junwye Lee
3.
Dr. Shogo Hamada
4.
Dr. Satoshi Murata
5.
Dr. Sung Ha Park
This
is the same Tohoku University in Japan that did a study on mice and deterrmined
that a liquid diet as reported in my blog article
entitled “Tohoku
University in Japan Studies Powdered Food Diet in Mice – Great for Active
Teenagers and Millennials, not so for Baby Boomers”.
I'm
not surprised that they used DNA to build self-replicating molecules, as its complex
macromolecular structure lends it readily to storing information on a molecular
level. DNA is the building block of Chromosomes, which is made up of a pairs of
chromatid molecules.
Each
Chromosome is composed of DNA molecules that are structured in organized
combinations of nucleotide bases called Adenine (A), Guanine (G), Cytosine (C)
or Thiamine (T) in helix shaped ladder-like structure.
Each
nucleotide base is only attracted to another nucleotide base via weak
electrostatic forces called Hydrogen bonds, created when Hydrogen is covalently
bonded to an atomic nucleus that has a stronger positive attraction for the
negative electrons in the covalent bond. As such, because of the shape of each
nucleotide base, Adenine (A) can only bond with Thiamine (T) and Guanine (G)
can only bond with Cytosine (C).
Groups
of three (3) of these nucleotide bases representing a single amino acid is
called a Codon.
These
Codon representing an Amino Acid when combined represent a protein molecule of
various length. It is these complete sets of Codons representing a protein
molecule that are called Genes.
Groups
of these Genes make up the Chromatids in a Chromosome. Groups of these Chromosomes
are what compose a Genome, the complete set of instructions to produce all the
proteins needed to make a living organism.
Given
this knowledge, it's a great place to start on the road towards making
self-replicating nano-machines, even it if does involving using nature's
materials instead of fabricating our own.
So
how did the researchers at Sungkyunkwan University and Tohoku University
achieve this incredible feat?
Sungkyunkwan University and Tohoku University
create self-replicating Nanostructures
The
researchers designed two (2) sets of DNA T-motifs using DNA. The DNA T-motifs, labeled
r1 and r2, had functional domain referred to as Alpha or Beta
domains.
Alpha
and Beta domains represent the different shapes of the Hydrogen bonding between
nucleotide bases Adenine (A) and Thiamine (T) that involves only two (2) Hydrogen
bonds and the Hydrogen bonding between Guanine (G) and Cytosine (C) that
involves only three (3) Hydrogen bonds.
These
different Hydrogen bonds are the Alpha and Beta domains that the researcher are
referring to, as nucleotide bases Adenine (A), which can only bond with
Thiamine (T) and Guanine (G) which can only bond with Cytosine (C).
Just
in case there was a need for a longer DNA molecule, the researchers also
created an extension motif.
The
researchers, realizing that the inherent Hydrogen bonds meant that only certain
nucleotide bases would bond with certain nucleotide bases, created twelve (12)
units of the r1 DNA T-motifs and another twelve (12) units of the r2
DNA T-motifs by cutting off certain lengths of a particular DNA molecule from a
particular plant or animal.
No
doubt they use enzymes to do this and took care to cut the DNA molecules in
such a manner that all of them were sufficiently long enough so that they'd be
able to coil upon themselves into a closed loops or circles.
They
also made sure that these strands of DNA had a reactive section at the end with
nucleotide base that could react EXCLUSIVELY with the appropriate nucleotide
bases at its opposite end i.e. it could react to form a closed loop or circle.
Thus
the r1 DNA T-motifs could only react with other r1 DNA
T-motifs with the same nucleotide bases at the opposite end or with itself. The
r2 DNA T-motifs could only react with other r2 DNA
T-motifs and the extension motif with the same nucleotide bases at the opposite
end.
How to get DNA to dance in the Windmills
of your Petri Dish - Invader single strands of DNA do the Tango
Then
the researchers did something else which thought was pretty clever.
The
designed some of the r1 DNA T-motifs so that one half of the double
helix of the DNA molecule was slightly longer, resulting in strand of
nucleotide bases possibly three (3) nucleotide base units or a Codon longer
than the end of the DNA molecule.
The
result was r1 DNA T-motifs and r2 DNA T-motifs that had
an extra single strand protrusion when a circle was formed, which the
researchers called a toehold. This toehold extended from the end of a close
loop or circle and was able to react with other nucleotide bases that matched
according to the shape of their Alpha or Beta domains i.e. Hydrogen bonds.
When
this occurred, the researchers referred to closed loop or circle as being
fertilized i.e. being able to self-replicate and produce more copies of itself.
This is exactly what happened, as when the researchers introduced complimentary
invader single strands of DNA, it reacts to the toehold and eventually beaks
off from the original ring.
As
these pieces break off, the electrostatic forces of attraction between
nucleotide bases Adenine (A), which can only bond with Thiamine (T) and Guanine
(G) which can only bond with Cytosine (C), cause them to intertwine into
another r1 DNA T-motifs or r2 DNA T-motifs.
This
process resulted in the r1 DNA T-motifs or r2 DNA
T-motifs self-assembling into another close loop or ring, thanks to the
presences of an opposite end that can only react EXCLUSIVELY with the appropriate
nucleotide bases at its opposite end.
DNA-based
Nanoparticle self-replicating machines – Research points to the development of
Organic Computers
Interestingly,
the self-assembly pathway occurs in one of two (2) ways:
1.
Exponentially
2.
Fibonacci Sequence
Apparently
the invader single strands of DNA were tailored so as to match the r1 DNA
T-motifs and r2 DNA T-motifs and the self-assembly pathway was dependent on the
type of invader single strands of DNA introduced in solution.
To
verify that this was actually taking place as per design, the researchers used
AFM and absorbance studies to determine the average concentration of Rings at
each phase.
Then
when they added the invader single strands of DNA, they studied the individual
phases using gel electrophoresis and extraction of the results from each phase.
In so doing, they confirmed that the rings had replicated as a result of
toehold-mediated strand displacement instead of residual r1 DNA
T-motifs and r2 DNA T-motifs self-assembling.
Dr.
Junghoon Kim self-replicating DNA motifs were proven to self-replicate without
the need for cellular structure involving enzymes, mRNA or tRNA. This study
demonstrates the feasibility of making self-assembling nanostructures from DNA
only.
It
also points out a mechanism by which DNA can be used to create nano-structures
based data encryption sequences to build an organic computer that can do
complex mathematical operations e.g. cracking complex data encryption in
minutes, that would take silicon based computers years to calculate.
This
may be the first tentative steps to not only creating nanoparticle
self-replicating machines but also organic computers designed to solve complex
mathematical problems that their silicon and even quantum based counterparts
cannot solve in real-time.
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