Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.

Wen Zhang,Chun Pong Tam,John C Chaput,Victor S Lelyveld,Seohyun Chris Kim,Jack W Szostak,Saikat Bala

doi:10.1093/nar/gkaa1215

Abstract

The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3′-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.

Highlights

Studies of the path from the prebiotic world to the RNA World have long contended with the chemical complexity of RNA
We find that activated threose nucleic acid (TNA) monomers alone are not effective substrates for multistep nonenzymatic primer extension reactions, and even single activated threo-nucleotides in an otherwise all-RNA context are incorporated with poor efficiency
Our results suggest that the reactive intermediate in primer extension, an imidazolium-bridged dinucleotide composed of 3 -3 linked threo-nucleotides, is both generated very slowly and once formed, binds to the template with suboptimal geometry for primer 3 -OH attack

Summary

Introduction

Eschenmoser proposed a comprehensive synthetic approach, suggesting that the origin of RNA might be elucidated by a systematic exploration of the properties of its chemical analogues and structural relatives [1,2]. Such a constructive approach addresses several seemingly intractable questions in abiogenesis. It was quickly recognized that, in order to have been a true ancestor of RNA, any such a polymer would require the ability to transmit its information to RNA [3].

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Conclusion