Theme 3
Oligonucleotide (ON) therapeutics are synthesised primarily through solid phasephosphoramidite chemistry, where the activation of phosphoramidites is a key step controlling coupling efficiency and overall yield. Understanding the reaction kinetics and mechanism of phosphoramidite activation is therefore critical for improving synthesis efficiency and scalability in therapeutic ON production.
DFT calculations are being used to systematically evaluate the activation reactions for substrates and activators relevant to oligonucleotide synthesis, to support experimental work in Theme 1.
The calculations consider:
(i) different sugar modifications, including fluorinated and non-fluorinated sugars;
(ii) substrates incorporating each of the five nucleobases (C, G, A, T, U);
(iii) both R and S configurations of the phosphorus centre in phosphoramidites; and
(iv) three commonly used activators in ON synthesis; 4,5 dicyanoimidazole (DCI), 5-ethylthio-1H-tetraxole (ETT) and benzylthiotetrazole (BTT). Initial calculations focused on the 2′-fluoro-C-phosphoramidite (FCP) substrate and examined both R and S configurations in the presence of DCI, using B3LYP/6-31G(d,p) with an SMD implicit model of acetonitrile solvent.