Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template.

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′-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2′-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2′-endo and C3′-endo 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 wea...