My Thoughts on Technology and Jamaica: Sungkyunkwan University and Tohoku University create Self-Replicating Nanostructures - How DNA dances with Wolves Petri Dish points to Organic Computers

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Friday, July 3, 2015

Sungkyunkwan University and Tohoku University create Self-Replicating Nanostructures - How DNA dances with Wolves Petri Dish points to Organic Computers

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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