Skip to main content

Prebiotic Synthesis of Pyrimidine Nucleosides: New Insights into RNA Evolution

Periodic Reporting for period 1 - PRENUCRNA (Prebiotic Synthesis of Pyrimidine Nucleosides: New Insights into RNA Evolution)

Reporting period: 2017-06-01 to 2019-05-31

Understanding how life evolved on Earth is widely regarded as one of the most formidable challenges in modern science. The exploration of the mechanisms regarding the origin of life not only expands our understanding of natural sciences, but also provides new clues regarding the search for life forms and Earth-like conditions on planets other than our own. Ribonucleic acid (RNA) is widely regarded by the scientific community as the key molecule that gave rise to the origin of life due to its ability to function both as genetic storage and as a catalyst. In order to support this “RNA World” hypothesis, scientists over the years have attempted to reproduce the conditions present on the early-earth to afford nucleosides in a prebiotic manner. The most challenging part is the synthesis of RNA building blocks called purine nucleosides (A, G) and pyrimidine nucleosides (C, U). Although two research groups demonstrated the prebiotic synthesis of each group of nucleosides respectively, their conditions differed significantly hence giving rise to the question of how the canonical nucleosides emerged from the prebiotic world together in equal abundances. In order to gain a deeper understanding of the early evolution of RNA, a uniform synthetic pathway affording canonical purine and pyrimidine nucleosides is a crucial subject of research. Moreover, investigation of the potential occurrence of a more primitive prebiotic molecule that might have evolved into RNA is also of great necessity to expand the view point of prebiotic evolution of RNA and hence the first life form. To this end, this project aims to study the prebiotic emergence of pyrimidine and pyrimidine-like nucleosides by developing a novel chemical route which works under plausible prebiotic conditions. The chemical pathway for the canonical pyrimidine nucleosides is designed in the way that it complements the purine synthesis pathway reported by Carell et al. Furthermore, prebiotic synthesis of novel pseudo-cyclic pyrimidines nucleosides bearing non-heterocyclic nucleobase surrogates will also be investigated in order to examine their potential validity as candidates for primitive RNA. This project will provide new insight into the evolution of RNA as well as a deeper understanding of the origin of life event on the early earth.
In order to accomplish simultaneous prebiotic syntheses of all four canonical nucleosides, a new chemical pathway for pyrimidine nucleosides was designed in such a way that it complements that of purine nucleoside reported by the Carell group. More specifically, a nucleophilic pyrimidine precursor is synthesized from a prebiotic molecule called cyanoacetylene. The pyrimidine precursor is subsequently reacted with ribose to establish the N-glycosidic bond. Finally, this ribose-nucleobase precursor conjugate is treated with base under reductive conditions to furnish pyrimidine nucleosides. When this pathway was experimentally investigated, indeed the formation of pyrimidine nucleosides were observed in high yield, thus establishing the simultaneous formation of all canonical nucleosides under plausible prebiotic conditions. In addition to the above mentioned prebiotic synthesis of canonical nucleosides, the potential emergence of non-standard nucleosides which functioned in prebiotic world as a component of early RNA species or proto-RNA was also investigated. In particular, it was speculated that prebiotically available urea derivatives mimic canonical nucleobases by forming intramolecular hydrogen bonds. When these urea derivatives were reacted with ribose under plausible prebiotic conditions, formation of the corresponding nucleoside or pseudo-cyclic pyrimidine nucleosides was observed. These pseudo-cyclic pyrimidine nucleosides were then incorporated into RNA strands using modern synthetic methods to investigate their functions. Remarkably, it was revealed that these non-standard nucleosides form a relatively stable base pair with guanosine in the complementary strands. Taken all together, these results indicate the potential emergence and function of non-standard pseudo-cyclic pyrimidine nucleosides as a component of proto-RNA. In summary, through the PRENUCRNA project we discovered a unified prebiotic pathway for all four canonical nucleosides as well as potential evidence for the emergence and function of non-standard nucleosides on early earth.
How the first life appeared on the early earth is one of the most formidable yet interesting scientific questions, and attracts the attention of wide range of people from both scientific as well as non-scientific communities. Formation of RNA on the early earth is believed to have played important role to begin the primitive life forms, and therefore the elucidation of the plausible chemical route to the prebiotic synthesis of RNA has been a long-standing goal in the field. Although it seems plausible prebiotic pathways have been demonstrated for both canonical pyrimidine and purine nucleosides from different research groups, there is critical contradiction among the reported pathways; the chemical conditions utilized for the reported purine and pyrimidine nucleoside synthesis differ significantly. This inconsistency must be addressed as it gives rise to the question of how the canonical nucleosides emerged from the prebiotic world together in equal abundancies, hence the validity of “RNA World” theory. With the results obtained from this project, it is now clear that all canonical nucleosides can be formed simultaneously under the same conditions. The results drastically strengthen the “RNA World” hypothesis by solving its Achilles’ heel and will facilitate the origin of life research by providing new insight for the scientists throughout the field. In addition, it was discovered that non-standard nucleosides bearing urea moieties as nucleobase surrogates are capable of forming stable base pairs, thus providing new insight into the possible existence of proto-RNA or more preliminary RNA that functioned in the origin of life event. Such results obtained in this study should be of great interest not only to scientists who work in the filed but also to the people who are not in scientific communities. Ultimately, these results could attract the curiosity and eager minds of a general audience to the wonders of origin-of-life sciences, not only as a career pathway but also as a way of inspiring the new generation of scientists interested in the origin of life, creation of life and space exploration.
The formation of nucleosides from small molecule building blocks under prebiotic conditions