New study hints at spontaneous appearance of primordial DNA

April 7, 2015 by Noel Clark, University of Colorado at Boulder
New study hints at spontaneous appearance of primordial DNA
The image shows a droplet of condensed nano-DNA and within it smaller drops of its liquid crystal phase which show up in polarized light on the left. The liquid crystal droplets act as “micro-reactors" where short DNA can join together into long polymer chains without the aid of biological mechanisms. Credit: Noel Clark, University of Colorado

The self-organization properties of DNA-like molecular fragments four billion years ago may have guided their own growth into repeating chemical chains long enough to act as a basis for primitive life, says a new study by the University of Colorado Boulder and the University of Milan.

While studies of ancient mineral formations contain evidence for the evolution of bacteria from 3.5 to 3.8 billion years ago—just half a billion years after the stabilization of Earth's crust—what might have preceded the formation of such unicellular organisms is still a mystery. The new findings suggest a novel scenario for the non-biological origins of nucleic acids, which are the building blocks of living organisms, said CU-Boulder physics Professor Noel Clark, a study co-author.

A paper on the subject led by Tommaso Bellini of the University of Milan was published in a recent issue of Nature Communications. Other CU-Boulder co-authors of the study include Professor David Walba, Research Associate Yougwooo Yi and Research Assistant Gregory P. Smith. The study was funded by the Grant PRIN Program of the Italian Ministries of Education, Universities and Research and by the U.S. National Science Foundation.

The discovery in the 1980's of the ability of RNA to chemically alter its own structure by CU-Boulder Nobel laureate and Distinguished Professor Tom Cech and his research team led to the development of the concept of an "RNA world" in which primordial life was a pool of RNA chains capable of synthesizing other chains from simpler molecules available in the environment. While there now is consensus among origin-of-life researchers that RNA chains are too specialized to have been created as a product of random chemical reactions, the new findings suggest a viable alternative, said Clark.

The new research demonstrates that the spontaneous self-assembly of DNA fragments just a few nanometers in length into ordered liquid crystal phases has the ability to drive the formation of chemical bonds that connect together short DNA chains to form long ones, without the aid of biological mechanisms. Liquid crystals are a form of matter that has properties between those of conventional liquids and those of a solid crystal—a liquid crystal may flow like a liquid, for example, but its molecules may be oriented more like a crystal.

"Our observations are suggestive of what may have happened on the early Earth when the first DNA-like appeared," said Clark.

For several years the research group has been exploring the hypothesis that the way in which DNA emerged in the early Earth lies in its structural properties and its ability to self-organize. In the pre-RNA world, the spontaneous self-assembly of fragments of (DNA and RNA) may have acted as a template for their chemical joining into polymers, which are substances composed of a large number of repeating units.

"The new findings show that in the presence of appropriate chemical conditions, the spontaneous self assembly of small DNA fragments into stacks of short duplexes greatly favors their binding into longer polymers, thereby providing a pre-RNA route to the RNA world," said Clark.

Explore further: Jumping hurdles in the RNA world

More information: "Abiotic ligation of DNA oligomers templated by their liquid crystal ordering." Nature Communications 6, Article number: 6424 DOI: 10.1038/ncomms7424

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3.5 / 5 (11) Apr 07, 2015
"While there now is consensus among origin-of-life researchers that RNA chains are too specialized to have been created as a product of random chemical reactions,".

Except that any such consensus* was blown out of the water by the recent find of exactly that. " We show that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of ​hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry."

The paper even synthesize a plausible geological scenario for its "many pots" synthesis of RNA.

[ http://www.nature...M-201504 ]

And of course, DNA is even harder to find "as a product of random chemical reactions"...

3.5 / 5 (11) Apr 07, 2015

* I doubt such a consensus existed. There was a recent strategy to go for pre-RNA systems, since spontaneous RNA synthesis was not immediately seen. But: "To some biochemists, Hud's attempts to find an evolutionary precursor to ribonucleic acid may have seemed a fool's errand. The dominant theory to explain the origins of life — known as the RNA world hypothesis — regards ribonucleic acid as the first biological molecule." [ https://www.quant...-to-rna/ }
1.4 / 5 (11) Apr 07, 2015
The finding that linked the light-induced de novo creation of amino acids to the RNA-mediated amino acid substitutions that differentiate all cell types in all genera via the physiology of their reproduction appears to link what is known about physics and chemistry to the molecular mechanisms of ecological adaptation in the context of a model of everything that replaces claims about any "theory of everything."

"Mysterious desert fairy circles share pattern with skin cells" http://www.scienc...4848.htm

However, all patterns may arise coincidentally and also be explained in the context of ridiculous theories by theoretical physicists and evolutionary biologists.
2 / 5 (8) Apr 07, 2015
You've got to be kidding me with this "spontaneous" appearance of primordial DNA. But then, I suppose if the universe can "spontaneously" appear, why not DNA? As long as we are careful not to use G word, anything and everything can get accepted as "science".

More seriously, this is not even a testable hypothesis so why are we even posting on this thread? That just lends unnecessary credibility to crackpot "theories".
1 / 5 (9) Apr 07, 2015
I'm posting here to show TL_OM is biolgoically uninformed

The testable hypothesis was that the de novo creation of light-induced amino acids linked the epigenetic landscape to the physical landscape of DNA in the organized genomes of all genera via amino acid substitutions that differentiate the cell types.

See Origin-of-life puzzle cracked http://www.scienc...98.short and Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins http://www.pnas.o...abstract

Others have linked the anti-entropic epigenetic effect of the sun's biological energy from nutrient-dependent microRNAs to cell type differentiation that is perturbed by the viral microRNAs linked from viruses to physiopathology instead of the nutrient-dependent physiology of reproduction that enables the fixation of amino acid substitutions that stabilize organized genomes.
5 / 5 (3) Apr 07, 2015
More testing. Always more testing.
1 / 5 (7) Apr 08, 2015
More testing. Always more testing.

I wonder how much longer the de novo creation of amino acids and the link from amino acid substitutions to cell type differentiation in all genera will be ignored, as if ridiculous theories were more important than experimental evidence of biologically-based cause and effect.

Evolution over the weekend: http://www.the-sc...ewiring/

For comparison, see: "We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms." http://www.nature...306.html
4.3 / 5 (6) Apr 09, 2015
@brad: " this is not even a testable hypothesis". The image above disagrees. They do see spontaneously ordered DNA strings, so the hypothesis passed a basic test.

That is not the problem, see my previous comment.

@JVK: Stop putting words in my mouth. At least read my comments, before attempting a description.

And this is probably all I have to say in response to you in any and all questions, since it appears, at least to me, that you show no interest in the science this site posts.
1 / 5 (4) Apr 09, 2015
And this is probably all I have to say in response to you in any and all questions...

Thanks. What other options do biologically uninformed science idiots have when they are confronted with facts?

See also: http://www.scienc...1422.htm

"We now have even better evidence that this same chemistry exists elsewhere in the Universe, in regions that could form solar systems not unlike our own."

That suggests what is known about physics and the conserved molecular mechanisms of nutrient-dependent physiology of reproduction is the same, which links the light-induced de novo creation of amino acids to the amino acid substitutions that differentiate all cell types in all genera on this planet.
1 / 5 (4) Apr 09, 2015
Conclusion from the abstract:
"This implies that complex organics accompany simpler volatiles in protoplanetary disks, and that the rich organic chemistry of our solar nebula was not unique."

In the misrepresentation of biologically-based cause and effect linked to amino acids, the implication becomes "better evidence"

"We now have even better evidence that this same chemistry exists elsewhere in the Universe, in regions that could form solar systems not unlike our own."

"Cyanides, and most especially methyl cyanide, are important because they contain carbon-nitrogen bonds, which are essential for the formation of amino acids, the foundation of proteins and the building blocks of life."

UV light was linked to the de novo creation of amino acids on Earth, not to their spontaneous formation in deep space. Why can't theorists understand the difference between earthly experimental evidence and deep space implications.

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