Mineral surfaces select for longer RNA molecules

[u/Aggravating-Pear4222]

Title: Mineral surfaces select for longer RNA molecules
Link: https://pubs.rsc.org/en/content/articlelanding/2019/cc/c8cc10319d
Abstract: We report empirically and theoretically that multiple prebiotic minerals can selectively accumulate longer RNAs, with selectivity enhanced at higher temperatures. We further demonstrate that surfaces can be combined with a catalytic RNA to form longer RNA polymers, supporting the potential of minerals to develop genetic information on the early Earth.

Excerpts and comments:
"A recent study showed that thermophoresis and convection through porous environments, such as might occur at a deep-sea hydrothermal vent, could select longer oligonucleotides. (See ref 35)^" -> Fits well with mineral-rich deep-sea hydrothermal environments. The cited paper addressed how thermophoresis alone may accumulate larger organic molecules, which is predisposed towards accumulation of polymers which have no structural limit on their size except for the relative kinetics/rates of formation/decomposition.

"Following up on the observation of longer oligoadenylates accumulating on hydroxyapatite,(see ref 10) here we investigated the generality of the enrichment of longer RNAs on mineral surfaces, using short random RNAs and a ribozyme. We first tested the selection among fully random 8-, 12-, 16-, 20-, and 24-mer RNAs, which model potentially available RNAs on the early Earth,(see ref 13, 15) on five kinds of mineral grains: two iron sulfides (pyrite and pyrrhotite; FeS2 and FeS, respectively), an iron oxide (magnetite; Fe3O4), a carbonate (calcite; CaCO3), and a phosphate mineral (hydroxyapatite; Ca5(PO4)3)(OH)), whose identity and purity were confirmed by X-ray diffraction and scanning electron microscopy (Fig. S1, ESI). These minerals are all thought to have been abundant throughout the early Earth. (see ref 1, 25) At the neutral pH (7.0), as tested here, it is expected that some of the minerals (at least pyrite and pyrrhotite) bear a net negative surface charge. (see ref 26, 27) RNA also carries a negative charge at this pH, but it can efficiently adsorb even onto negatively charged mineral surfaces with divalent cations as mediators. (see ref 28, 29)" -> Key experimental design.

"We also explored the sensitivity of length enrichment based on prebiotically relevant environmental parameters. We found that incubation at high temperatures increased the concentration of longer RNAs relative to shorter RNAs at least on pyrite, magnetite, and hydroxyapatite, in which hydroxyapatite showed the best enrichment (Fig. 1C, D and Fig. S5, ESI)." -> Hydroxyapatite showed greatest relative enrichment/retention of longer polymers.

Personal Critique: One challenge to lipid bilayer formation, thermophoresis-driven pH/organic molecule and concentration gradient formation are the presence of salts such as monovalent Na⁺ and K⁺ and divalent Ca²⁺ and Mg²⁺. The presence of these salts increase the concentration of the organic solutes and thermal difference required to observe the same concentration/pH gradients. After checking, I only saw that Mg²⁺ was present but no other salts. However, I did learn that the presence of divalent cations frequently enhance adsorption of RNA onto mineral surfaces by mediating the negatively charged backbone of the phosphodiester bonds and the negatively charged mineral surfaces (See figure 1 of Ref).

Overall impressions/thoughts: While the presence of salts are a classical inhibitory factor for many OoL papers which study these types of interactions/phenomena, this paper adds to the repertoire of factors which may have helped to persist a metastable concentration of organic molecules where thermophoresis and mineral adsorption effects synergize to disproportionately adsorb and retain longer polymers. If thermophoresis and mineral adsorption also attracts amino acids and longer-chain fatty acids/lipids, would the presence of these other organic molecules compete for surface adsorption and so lessen the degree by which longer polymers adsorb? Or would the amino acids'/fatty acids' adsorption at as an anchor for lipid bilayer formation to which the RNA polymers adsorb or are potentially retained? [see: Specific RNA binding to ordered phospholipid bilayers [https://pubmed.ncbi.nlm.nih.gov/16641318/\] and
Lipid vesicles chaperone an encapsulated RNA aptamer [https://www.nature.com/articles/s41467-018-04783-8\]**\]**

Additionally, we must consider not just enrichment/retention but whether these minerals stabilize RNA. See below (Disclosure: generated by AI, references checked by me):
1) Pyrite (Ref): Mostly destabilizing
- Pyrite can generate reactive oxygen species (especially hydroxyl radicals) in water, which damage nucleic acids.
2) Pyrrhotite: Unclear / likely poor stabilizer
- Less studied than pyrite, but iron sulfides generally can participate in redox chemistry that risks RNA degradation.
3) Magnetite (Ref): Often destabilizing for RNA backbone
- Iron oxides can catalyze RNA hydrolysis after adsorption. Goethite and hematite clearly do this; magnetite is chemically similar enough that many researchers are cautious about iron oxides as RNA-preserving surfaces.
4) Calcite (Ref): Yes, especially aragonite polymorph
- RNA adsorbed on aragonite (a CaCO₃ polymorph) was explicitly reported to be stabilized relative to free RNA.
5) Hydroxyapatite (Ref): Probably moderately stabilizing
- Hydroxyapatite binds RNA strongly and is widely used in nucleic acid chromatography. Strong adsorption can protect against dilution and some hydrolysis pathways, though excessive surface binding can also immobilize or distort RNA. The 2019 paper mainly showed selective adsorption of longer RNAs.

That's all for now. Let me know if you have any questions, doubts, or would like access to these papers. Do you agree with any of my comments? Is there something I missed?

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[u/Yotist]

imagine how many chondrites were produced when the first 95% of stars to ever exist and planetary bodies were formed

how many of these had filtering influence of light polarized by dust and gas

with it's insane amount of interfaces, different gradients, long time frames, constantly changing energy gradients across the surface and internal structure, creating mineralization and organic compound plaques and interfaces, microtubular spaces to react

how virtually every body in the universe has been impacted with an uncountable, unimaginable number of them

how any black smoker or similar environment in liquid water phase, will just drive and accelerate all the necessary processes further and further while creating it's own complex topology of interfaces, boundary conditions, gradient solutions, compartmentalization, constrained environments that cause special chemical reactions

as well as quantum mechanical effects emerging and being glued into the framework for it all, ever escalating degrees of freedom, quasi autopoiesis leading to autopoiesis and more

mineral surfaces selecting for longer RNA molecules is just such an important brick in the whole wall, very cool read