The helix, of DNA fame, may have arisen with startling ease

The helix, of DNA fame, may have arisen with startling ease
Artwork for the study shows the chemical structure of the helix that self-assembled in the lab, producing surprisingly bountiful results. Credit: Georgia Tech / Nick Hud

Trying to explain how DNA and RNA evolved to form such neat spirals has been a notorious enigma in science. But a new study suggests the rotation may have occurred with ease billions of years ago when RNA's chemical ancestors casually spun into spiraled strands.

In the lab, researchers at the Georgia Institute of Technology were surprised to see them do it under conditions thought to be common on Earth just before first life evolved: in plain water, with no catalysts, and at room temperature.

The neat spiraling also elegantly integrated another compound which today forms the backbone of RNA and DNA. The resulting structure had features that strongly resembled RNA.

Pivotal twists

The study has come a step closer to answering a chicken-egg question about the evolutionary path that led to RNA (from which DNA later evolved): Did the spiral come first, and did this structure influence which molecular components made it later into RNA because they fit well into the spiral?

"The spiraling could have had a reinforcing effect. It could have facilitated the molecules getting connected together that have the same chirality (curve) to connect into a common backbone that is compatible with the helical twist," said the study's principal investigator Nicholas Hud, a Regents Professor in Georgia Tech's School of Chemistry and Biochemistry.

The researchers published the new study in the journal Angewandte Chemie in December 2018. The research was funded by the National Science Foundation and the NASA Astrobiology Program under the Center for Chemical Evolution. The center is headquartered at Georgia Tech, and Hud is its principal investigator.

The study's resulting polymers were not RNA but could be have been an important intermediate step in the early evolution of RNA. For , the researchers used base molecules referred to as "proto-nucleobases," highly suspected to be precursors of nucleobases, main components that transport genetic code in today's RNA.

Nucleobase paradox

The study had to work around a paradox in :

Making RNA or DNA using their actual nucleobases in the lab without the aid of the enzymes of living cells that usually do this job is more than a herculean task. Thus, although RNA and DNA are ubiquitous on Earth now, their evolution on pre-life Earth would appear to have been an anomaly requiring erratic convergences of extreme conditions.

By contrast, the Georgia Tech researchers' model of chemical evolution holds that precursor nucleobases self-assembled easily to into ancestral prototypes—that were polymer-like and referred to as assemblies—which later evolved into RNA.

"We would call these 'proto-nucleobases' or 'ancestral nucleobases,'" Hud said. "For our overall model of chemical evolution, we're saying that these proto-nucleobases, which self-assemble into these long strands, could have been part of a very early stage before modern nucleobases were incorporated."

One main suspected proto-nucleobase in this experiment—and in previous experiments on the possible the evolution of RNA—was triaminopyrimidine (TAP). Cyanuric acid (CA) was another. The researchers highly suspect TAP and CA were parts of a proto-RNA.

The that hold together assemblies of the two suspected proto-nucleobases were surprisingly strong but non-covalent, which is akin to connecting two magnets. In RNA the main bonds holding together modern nucleobases are covalent bonds, akin to welding, and enzymes make those bonds in cells today.

Helical biases

A helix can spiral two ways, left-handed or right-handed. In chemistry, a molecule can also be handed, or chiral, making for "L" or "D" forms of the molecule.

The helix, of DNA fame, may have arisen with startling ease
A proto-nucleobase next to a nucleobase. Hard to tell the difference. Credit: Georgia Tech / Fitrah Hamid

Incidentally, the building blocks of today's RNA and DNA are all the D form, which make a right-handed helix. Why they evolved like this is still a mystery.

Batches of TAP and CA the researchers started out with produced roughly equal amounts of right and left-handed helices, but something stood out: Whole regions of a batch were biased in one direction and were separate from other regions that spiraled mostly the other way.

"The propensity for the molecules to choose one helical direction was so strong that large regions of the batches were made up predominantly of assemblies that were unidirectionally twisted," Hud said.

This was surprising because the individual molecules of TAP and CA had no chirality of their own, neither L nor D. Still, the twists had a preferred direction.

'world record'

The researchers added two more experiments to test how strongly their RNA-like assemblies preferred making one-handed helices.

First, they introduced a smidgeon of compounds similar to TAP and CA, but which had L or D chirality, to nudge the spiraling direction. The whole batch conformed to the chirality of the respective additive, resulting in assemblies twisting in a unified direction as helices do in RNA and DNA today.

"It was the new world record for the smallest amount of a chiral dopant (additive) that would flip a whole solution," said Suneesh Karunakaran, the study's first author and a graduate researcher in Hud's lab. "This demonstrated how easy it would be in nature to get abundant amounts of unified helices."

Second, they put the sugar compound ribose-5-phosphate together with TAP to more closely emulate the current building blocks of RNA. The ribose fell into place, and the resulting assembly spiraled in a direction dictated by the ribose chirality.

"This molecule easily formed an RNA-like assembly that was surprisingly stable, even though the pieces were only held together by non-covalent bonds," Karunakaran said.

Evolution revolution

The study's results under such simple conditions represent a leap forward in for how the helical twist of biomolecules could have already been in place long before life emerged.

The research also expands a growing body of evidence supporting an unconventional hypothesis by the Center for Chemical Evolution, which dispenses with the need for a narrative that rare cataclysms and unlikely ingredients were necessary to produce life's early building blocks.

Instead, most biomolecules likely arose in several gradual steps, on quiet, rain-swept dirt flats or lakeshore rocks lapped by waves. Precursor molecules with the right reactivity enabled those steps readily and produced abundant materials for further evolutionary steps.

Basement engineer

In the lab, helix self-assemblage was so productive that it outstripped a detection device's capacity to examine the output. Regions a square millimeter or more in size were packed with unidirectionally spiraled polymer-like assemblies.

"To look at them I had to make adjustments to the equipment," said Karunakaran. "I punched holes in a foil and put it in front of the beam of our spectropolarimeter."

That worked but needed improvement, so Hud took to his basement at home to build an automated scanner that could handle the experiment's bountiful results. It revealed large regions of helices with the same handedness.

Explore further

Missing links brewed in primordial puddles?

More information: Suneesh C. Karunakaran et al, Spontaneous Symmetry Breaking in the Formation of Supramolecular Polymers: Implications for the Origin of Biological Homochirality, Angewandte Chemie International Edition (2018). DOI: 10.1002/anie.201812808
Citation: The helix, of DNA fame, may have arisen with startling ease (2019, January 24) retrieved 18 July 2019 from
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Jan 25, 2019
when RNA's chemical ancestors casually spun into spiraled strands.

Of course first you have to get an RNA molecule from randomly available chemicals...that's the trick. The whole enchilada.
Researchers are chasing their own tails trying to get life to pop up spontaneously from a pond of scum. Doing all kinds of hard work and experiments in the lab to get life to arise from dead materials. Just so they can claim - "see, there's nothing to it - no intelligence required!"

So the helix forms spontaneously but what about the information content? Does that spontaneous helix spell out how to make an intelligent, signalling and blocking cell wall or form an artery or vein that allows neutraphil extravasation or provide the recipe for blood clotting?

How DOES one get an abstract entity like INFORMATION from purely materialistic processes? How indeed?

Jan 25, 2019
This is cretinist bait.

The cause is the chirality of the ribose.

Jan 25, 2019
I am mildly enthusiastic about the predilection of biochemists trying to explore production pathways that are in tension with the biological and geological record. Moreover the superstitious imagery of Hud is an attempt at humor failing me.

We don't know that there were precursors to RNA. Instead we know that there are pathways to nucleotides and even nucleotide strand formation that do not require enzymes or "convergences" or other "extreme conditions", these things have been demonstrated to occur with ease in alkaline hydrothermal vents. We also know that our genetic machinery still retain several chiral filters indicating that early evolution happened in a partially non-chiral mix.

The interesting thing is that they demonstrated that chiral strand formation in such partial mixes, as Da Schneib notes mediated by the backbone sugars, are one more system of chirality breaking to add to earlier known ones. This helps explain early replication.

Jan 25, 2019
information content

An organized superstition talking point which never had relevance for research into evolutionary processes; note: no reference!

Moreover precisely the evolution of life from geological formations was solved already 2016 [ https://www.natur...l2016116 ].

So why are we still seeing this tedious twaddle trolling when it is *also* outdated!?

Jan 25, 2019
Abstract (pay wall excuse) does suggests it "ate" geological formations. Does it prove where it started(?).

Jan 26, 2019
Abstract (pay wall excuse) does suggests it "ate" geological formations. Does it prove where it started(?).

You mean my reference?

Well, interestingly it was both produced by and initially consumed the biochemicals that the vent geology it split from, the ocean fed by such chemicals and in a larger sense the atmosphere (amino acids producer at the time) produced. Later it could evolve independence. The results show, by this dependent interaction and the time it would take to evolve independence, but also by the consistent methyl group decoration of metabolic and genetic key machinery in a methane producing environment, that the lineage was long tied to the alkaline hydrothermal vent environment.

The authors saw no reason to expect that the lineage both somehow started in a less conducive environment and somehow made it there later.

Jan 27, 2019
Thank you for the informative reply. IIRC a article reported modelling heat driven differentiation in small proto-planetary "mudballs". I have lost the link :( . Looking at the most recent image of 2014 MU69, I find it easy to imagine each of the two lobes are themselves composed of a cluster of bodies. I have seen it often suggested "our" protoplanetary nebula was only one of many developing essentially simultaneously. If so, the number of such "mudballs" formed and slung about within, even between, protoplanetary systems could have been staggering. At what point might we see rigorous comparison between model hypotheses such as "Life arose independently on our planet" vs "Life (or advanced but not quite living materials) arose in steaming mudballs haphazardly fresh frozen for delivery, inoculating (our) planetary surface? It would be good to someday obtain a surface sample of 2014 MU69, to say nothing of Pluto!

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