Activated Ribonucleotides Undergo a Sugar Pucker Switch upon Binding to a Single-Stranded RNA Template

Abstract

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5′-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3′-<i>endo</i> sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2′-<i>endo</i> conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2′-<i>endo</i> and C3′-<i>endo</i> conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5′-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2′-<i>endo</i> in the free state to C3′-<i>endo</i> upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2′-deoxyribonucleotides maintain a C2′-<i>endo</i> sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions