Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis

Abstract

The molecules of life were created by a continuous physicochemical process on an early Earth. In this hadean environment, chemical transformations were driven by fluctuations of the naturally given physical parameters established for example by wet-dry cycles. These conditions might have allowed for the formation of (self)-replicating RNA as the fundamental biopolymer during chemical evolution. The question of how a complex multistep chemical synthesis of RNA building blocks was possible in such an environment remains unanswered. Here we report that geothermal fields could provide the right setup for establishing wet-dry cycles that allow for the synthesis of RNA nucleosides by continuous synthesis. Our model provides both the canonical and many ubiquitous non-canonical purine nucleosides in parallel by simple changes of physical parameters such as temperature, pH and concentration. The data show that modified nucleosides were potentially formed as competitor molecules. They could in this sense be considered as molecular fossils.

Fig. 1

RNA nucleoside formation pathway. A geothermal environment provides the right set up for the depicted transformations by establishing wet–dry cycles. The prebiotic starting materials are produced from a prebiotic atmosphere and washed into an aqueous environment (e.g. by rain). Major atmospheric components are written in larger letters, whereas minor components are written in smaller letters. Transformations are taking place in different environments, illustrated by various rivers (in light blue). Each environment provides the right setup for different chemistries, leading to several different chemical transformations. This geochemical setup leads to a set of canonical and non-canonical RNA building blocks by continuous synthesis (6a, m¹G: R¹ = O, R² = Me, R³ = NH₂; 6b, ms²A: R¹ = NH, R² = H, R³ = SMe; 6c, A: R¹ = NH, R² = H, R³ = H; 6d, m²G: R¹ = O, R² = H, R³ = NHMe; 6e, m²₂G: R¹ = O, R² = H, R³ = N(Me)₂; 6f, G: R¹ = O, R² = H, R³ = NH₂; 6g, DA: R¹ = NH, R² = H, R³ = NH₂; 6h, m²A: R¹ = NH, R² = H, R³ = Me)

Fig. 2

Chemical complexity created by physical fluctuations. a Relative changes of temperature (in blue) and pH (in red) are shown for each synthetic step for the continuous synthesis of purine RNA building blocks from small organic and inorganic molecules. Several wet–dry cycles establish fluctuations of the depicted physical parameters that enable the physical enrichment of intermediates. Gray backgrounds denote compounds that are enriched by crystallization from an aqueous solution. b Formation of an organic salt consisting of amidine derivatives 2a-d and (hydroxyimino)malononitrile 3. The salt is selectively crystalized by concentrating a dilute mixture of organic and inorganic compounds by slow evaporation. The crystal structures of the four crystalized organic salts are depicted (Supplementary Tables 1–4)

Fig. 3

Reaction scheme and physical enrichment of intermediates. a Dry-state reactions of salts containing 2a-d and 3 provide nitroso-pyrimidines 4a-d, which can be further diversified by hydrolysis (red arrows) or aminolysis (blue arrows) to give a set of nitroso-pyrimidines (nitrosoPys) 4a-i. In the presence of elementary Fe and Ni and dilute formic acid, formation of the formamidopyrimidines (FaPys) 5a-h as direct purine base precursors takes place. In square brackets: non-isolated reaction intermediates. b Second physical enrichment of the nitroso-pyrimidines isolated in high purity and yield. c Third physical enrichment of the formed FaPys 5a-h as nucleoside precursors from nitroso-pyrimidines

Fig. 4

Formation of RNA nucleosides from nucleobase precursors. a Reaction mechanism for the formation of canonical and non-canonical RNA nucleosides 6a-h from formamidopyrimidines (FaPys) 5a-h and ribose. The reaction provides the four expected isomers α/β ribopyranosides (α/β−p) and α/β–ribofuranosides (α/β−f). b LC-MS analysis of the reaction products from 5a-h and ribose. Compounds identified by MS detection are labeled (β−p or α/β−f). The UV- and MS-chromatograms show all four expected isomers for each compound (labeled with the retention time or asterisk (*) in the UV-chromatogram). The structural assignment was assisted by co-injection (Co-inj.) studies. The MS traces show in red the co-injection signal obtained with the naturally occurring isomer (β−f)