Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

Abstract

In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

Mineral-Mediated Oligoribonucleotide Condensation: Broadening the Scope of Prebiotic Possibilities on the Early Earth

“…The mineralogy of complex natural samples, such as the black smoker chimney, was determined via X-ray powder diffraction ( Appendix A ). A portion of montmorillonite (Volclay SPV-200) was treated via the Banin process [ 21 , 22 ] and used as a positive control to validate the experimental methods, as RNA oligomers produced in treated montmorillonite experiments are well characterized by a number of independent studies [ 15 , 20 , 56 ]. Untreated montmorillonite was also included in the experiments reported here in order to assess the ability of naturally occurring clays to enhance polymerization.…”

“…In the case of oligonucleotides and RNA, montmorillonite is one of the most widely implemented and effective routes currently identified for enhancing polymerization abiotically [ 15 , 17 , 18 , 19 , 20 ]. However, in all reported cases, the montmorillonite is first chemically optimized via the “Banin process”—a multi-step chemical treatment in which the clay is suspended and stirred in a strongly acidic solution to remove interlayer cations before an anion exchange resin is used to replace the anion of the free acid with hydroxide, which reacts with free hydrogen in the acidic suspension to form water.…”

“…Montmorillonite-focused studies continued beyond this point and included montmorillonite-driven Fischer–Tropsch-type synthesis of lipids [ 46 ] and catalysis of bilayer vesicle formation from fatty acid micelles [ 47 ]. Montmorillonite also became a “go-to” mineral for future abiotic RNA polymerization studies, including synthesis of longer RNA oligomers [ 48 ], polymerization following “in situ” nucleotide activation in aqueous solutions [ 19 ], and nucleotide selectivity during abiotic polymerization [ 20 ]. The narrow focus on montmorillonite is informative of the mechanism and specific parameters through which the mineral interacts with and contributes to abiotic chemical synthesis pathways but also limits the scope of knowledge gained regarding prebiotic synthesis to those environments in which montmorillonite is available, whereas the remainder of Earth’s vast mineralogical inventory remains largely untapped experimentally.…”

Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA

“…It has been proposed that early life on Earth used RNA to carry out both the informational and catalytic functions now performed by DNA and protein enzymes. − Accordingly, chemists have long sought, and in some cases demonstrated, model prebiotic syntheses for the canonical RNA nucleotides − and mechanisms for their polymerization, both de novo − and with the aid of pre-existing polymers. − Despite these advances, there remain chemical and biological challenges to the historical validity of RNA spontaneously emerging as the first informational polymer of life. − Additionally, chemists have now prepared numerous non-natural nucleic acids, so-called XNAs, which demonstrate that RNA is not unique in its ability to act as both an informational and a functional polymer. − We have proposed that RNA was preceded by an ancestral polymer, or proto-RNA, that more readily self-assembled on the prebiotic Earth and that this polymer was converted by chemical and/or biological evolution into RNA. − …”

Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate

“…The origin of genetic polymers remains a poorly understood phenomenon, but not from lack of investigation . For more than 50 years, speculation that RNA was the first polymer of lifethe RNA world hypothesishas motivated researchers to seek a prebiotic synthesis of RNA. − In this “strong” interpretation of the RNA world hypothesis, purely abiotic processes are considered the original source of the canonical ribonucleotides, which subsequently polymerized to provide the first RNA polymers. − Several proposed prebiotic routes to canonical RNA nucleotides have been reported, − and there have been proposals to account for how chemically activated mononucleotides could have polymerized without the aid of enzymes or pre-existing RNA templates. − Nevertheless, there remain ample reasons to retain the more cautious stance that the origin of RNA polymers is not a solved problem and to consider the alternative possibility that the earliest genetic polymers were of different constitution; in particular, polymers with a greater proclivity for spontaneous formation. , …”