Synthesis and Incorporation of k2U into RNA

Milda Nainyte,Thomas Carell

doi:10.1002/hlca.202000016

Abstract

AbstractLysidine (k2C) is one of the most modified pyrimidine RNA bases. It is a cytidine nucleoside, in which the 2‐oxo functionality of the heterocycle is replaced by the ϵ‐amino group of the amino acid lysine. As such, lysidine is an amino acid‐containing RNA nucleoside that combines directly genotype (C‐base) with phenotype (lysine amino acid). This makes the compound particularly important in the context of theories about the origin of life and here especially for theories that target the origin of translation. Here, we report the total synthesis of the U‐derivative of lysidine (k2U), which should have the same base pairing characteristics as k2C if it exists in the isoC‐like tautomeric form. To investigate this question, we developed a phosphoramidite building block for k2U, which allows its incorporation into RNA strands. Within RNA, k2U can base pair with the counter base U and isoG, confirming that k2U prefers an isoC‐like tautomeric structure that is also known to dominate for k2C. The successful synthesis of a k2U phosphoramidite and its use for RNA synthesis now paves the way for the preparation of a k2C phosphoramidite and RNA strands containing k2C.

Highlights

RNA contains a vast variety of modified nucleosides.[1]
From a prebiotic point of view in which genotypephenotype discussions address the question of whether life started with nucleic acids or peptides, the most interesting modified nucleosides are those which are modified with amino acids.[3]
To investigate how k2U is affecting the structure and properties of RNA, we started the synthesis of k2U as its phosphoramidite building block (k2U-PA) and investigated procedures that allow its incorporation into RNA

Summary

Introduction

RNA contains a vast variety of modified nucleosides.[1] Many of the modified bases are just methylated versions of the canonical nucleosides A, C, G and U, but other are highly modified This is achieved with the help of dedicated biosynthesis machineries.[2] From a prebiotic point of view in which genotypephenotype discussions address the question of whether life started with nucleic acids or peptides, the most interesting modified nucleosides are those which are modified with amino acids.[3] These molecules are chemical structures between genotype and phenotype. RNA potentially with peptide-like properties, we were interested to study the lysine modified uridine base This compound is a close derivative of lysidine, which we name k2U. A major difference could be that while k2C is protonated, k2U is likely not. k2C protonation is supposed to occur at N(6) and it does not change the base pairing properties.[10,24]

Results and Discussion

Conclusions

General Methods