A palindromic triplex architecture for DNA-templated synthesis designed for the core of a synthetic ribosome

Abstract

We demonstrate a triplex-based architecture for DNA-templated synthesis. This study is motivated by progress towards the development of a synthetic ribosome – autonomous, genetically programmable, molecular machinery for synthesis. Such schemes for the creation and evolution of chemically diverse DNA-tagged chemical libraries rely on hybridization reactions of oligonucleotide adapters to control sequential, DNA-templated reactions of covalently attached building blocks. To enable parallel one-pot library synthesis it is desirable that any building block can be incorporated at any position in a product oligomer: this is incompatible with geometries commonly used for DNA-templated synthesis which require alternate reactants to be attached to 3′ and 5′ termini of their adapters. Our triplex-based architecture overcomes this problem by templating reactions between building blocks attached to adapters with identical structures. It is intended to form the core of programmable molecular machinery for multistep synthesis. Here, we use single-step coupling reactions to characterize the triplex reaction template.