Effect of backbone flexibility on covalent template-directed synthesis of linear oligomers

Covalent template-directed synthesis can be used to replicate synthetic oligomers, but success depends critically on the conformational properties of the backbone. Here we investigate how the choice of monomer building block affects the flexibility of the backbone and in turn the efficiency of the replication process for a series of different triazole oligomers. Two competing reaction pathways were identified for monomers attached to a template, resulting in the formation of either macrocyclic or linear products. For flexible backbones, macrocycles and linear oligomers are formed at similar rates, but a more rigid backbone gave exclusively the linear product. The experimental results are consistent with ring strain calculations using molecular mechanics: products with low ring strain (20-30 kJ mol^-1) formed rapidly, and products with high ring strain (>100 kJ mol^-1) were not observed. Template-directed replication of linear oligomers requires monomers that rigid enough to prevent the formation of undesired macrocycles, but not so rigid that the linear templating pathway leading to the duplex is inhibited. Molecular mechanics calculations of ring strain provide a straightforward tool for assessing the flexibility of potential backbones and the viability different monomer designs before embarking on synthesis.