A Covalent Dinucleotide Intermediate in Nonenzymatic RNA Polymerization

Abstract

The origin of life on Earth encompasses the prebiotic synthesis of chemical compounds to the formation of the first cells and eventually, the last universal common ancestor. The exact nature of the earliest life forms capable of replication on Earth is a source of much speculation, but RNA has long been presumed to play a key role in the origin of life for its dual capacity of storing genetic information and performing catalytic functions. However, a life form predominantly based upon RNA replication and evolution has yet to be proven experimentally. A major obstacle toward demonstrating this hypothesis is the difficulty of copying RNA without the aid of protein enzymes. To address this limitation, my dissertation work has focused on understanding the chemical mechanism of nonenzymatic RNA polymerization in order to identify new strategies that will help enable RNA self-replication. My interrogation of the mechanism led to the identification of a covalent dinucleotide intermediate that is characterized by an imidazolium moiety linking the phosphate groups of two nucleotides. This imidazolium-bridged intermediate accounts for the majority of the rate of nonenzymatic RNA polymerization, and is pre-organized to specifically undergo template-directed phosphodiester bond formation. The improved understanding of the reaction mechanism explains many enigmatic features of nonenzymatic RNA polymerization and suggests a variety of new strategies to improve the yield and rate of this reaction.