Automated Synthesis of Duplex-Forming Recognition-Encoded Oligomers

Abstract

The functional properties of biological polymers are encoded by the sequence of monomer building blocks. Synthetic polymers made from sequences of different monomer building blocks would allow exploration of chemical space for new structures with functional properties in non- aqueous media. Previously in the Hunter group, recognition-encoded melamine oligomers (REMOs) composed of alternating piperazine and triazine units, equipped with phenol and phosphine oxide hydrogen-bonding groups, have been shown to form sequence- and length- selective duplexes and are a promising candidate for such a system. An automated solid-phase synthesis (SPS) route was optimised to yield high-purity REMOs with precise sequence control. Loaded Wang resin was reacted alternatingly with piperazine and dichlorotriazine monomers, appended with phenol donor (D) or phosphine-oxide acceptor (A) recognition units, under microwave conditions. Major side products were identified using liquid chromatography-mass spectrometry (LCMS) and the undesired reactions were supressed by the choice of resin, solvent and coupling conditions. A 42-mer REMO was synthesised and purified by high-performance liquid chromatography, displaying the scope of the SPS approach. The tetramer sequence DADA, appended with terminal azide and alkyne groups, was synthesised via SPS. Duplex formation in dichloromethane was investigated by using the copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction to trap the species present. LCMS was used to identify the macrocyclic self-complementary duplex as a major product. This trapping approach, as well as 31P NMR denaturation and Förster resonance energy transfer, were used to investigate duplex formation by complementary homo-oligomers A6•D6 and A12•D12. CuAAC trapping was also used to demonstrate sequence selective duplex formation in mixed sequence libraries of 6-mers prepared by SPS. In the Hunter group, an oligotriazole trimer equipped with benzoic acid and phenol recognition units was previously replicated via covalent template-directed synthesis, but folding of the backbone led to significant side-reactions. Here, attempts were made towards a new, more rigid oligotriazole replicator. The backbone was assembled via CuAAC reactions between dialkyne bearing phenol or benzoic acid monomers and an aryl diazide linker. Attempts to replicate a benzoic acid trimer via covalent template-directed synthesis yielded none of the desired trimer copy, and base-pair formation by esterification of carboxylic acid units on the template proved more challenging on this backbone, which limited the ultimate utility of this approach.