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Replication of Sequence Information in Recognition-Encoded Synthetic Polymers https://doi.org/10.17863/CAM.116047 Smith, Joseph Hunter, Christopher Replication of molecular information in Nature is achieved by enzyme-catalysed polymerisation of monomers on nucleic acid templates and can be used in directed evolution processes to yield functional polymers. If directed evolution could be applied to synthetic oligomers, then new classes of functional polymers might be discovered. To reach this goal, new methods for replication of information-encoded synthetic oligomers must be realised. Previously, the templated synthesis of oligomers equipped with benzoic acid and phenol recognition units, that form ester base pairs, was developed using a copper-catalysed azide-alkyne cycloaddition (CuAAC) polymerisation reaction. However, the irreversible polymerisation reaction resulted in some scrambled sequence copies as a result of mis-couplings. Here, a new templating scheme was investigated using dynamic imine oligomerisation chemistry as an alternative to the CuAAC reaction, which should provide a pathway for error correction. The effective molarity for the intramolecular reactions that lead to templating using this system was determined to be 3 mM, meaning that oligomerisation reactions had to be carried out at low concentrations. Difficulty in performing dynamic imine chemistry at these low concentrations precluded the further development of this approach for the templated synthesis of oligomers. The Hunter group has developed Recognition Encoded Melamine Oligomers (REMO) that form duplexes with H-bond donor and acceptor recognition units. The templated ligation of two REMO 3-mers, each containing three H-bonding recognition units, using SNAr chemistry was investigated. A 7-mer template was shown to ligate two bound 3-mers with an effective molarity of 5 mM. However, an off-template competing process where complementary 3-mers associate and react was found to be significantly more favourable than the on-template ligation with an effective molarity of 20 mM, limiting the potential for this system to be used for the templating of mixed-sequence oligomers. Ghadiri has previously used thioester exchange to generate dynamic copies of DNA templates using a base-filling approach, where recognition units are reversibly attached to a blank copy strand, and the template specifies the sequence by formation of a H-bonded duplex. The limitation of this approach is that the product cannot be isolated and used in iterative rounds of replication. In this thesis, a base filling scheme has been applied to the REMO architecture employing imine exchange chemistry, so that the copy strands can be kinetically trapped, isolated and reused. Template REMO strands equipped with either 4-nitrophenol (D) or phosphine oxide (A) H-bond recognition units as side-chains were attached to a blank oligo-aldehyde strand using ester chemistry. Exposure of this construct to amines equipped with complementary recognition units led to dynamic imine formation on the blank strand. The imines were trapped by reduction, and the sequences of recognition units incorporated into the copy strands were determined using LCMS. When DDD was used as the template, an 85% yield of the complementary AAA oligomer was obtained, and when AAD was used as the template, a 71% yield of the complementary DDA oligomer was obtained. This result represents one of the first examples of high-fidelity templating of mixed-sequence synthetic polymers. University of Cambridge 2024-09-17 Thesis Doctoral Doctor of Philosophy (PhD) eng EPSRC https://www.repository.cam.ac.uk/handle/1810/380418 embargo 2026-02-20 https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6b33757f-a21f-4e53-b974-02bc6de1d567/download f7fd8c6b3e21bc5619c9e88e5cf6258e https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/7115c50e-09b9-4e30-8ade-d45eeca7efce/download 87eda9de84448d1f82354d60eee3eb5f http://purl.org/NET/rdflicense/allrightsreserved Molecular replication Supramolecular chemistry Organic chemistry