Biophysical and biological properties of splice-switching oligonucleotides and click conjugates containing LNA-phosphothiotriester linkages

Antisense oligonucleotides hold great promise in the treatment of disease, but their efficacy is limited by modest bioavailability and toxicity. Charge-neutral phosphorus-based backbones can potentially improve biological properties, but oligonucleotides with such modifications are challenging to synthesize. Here, we report the straightforward synthesis of a range of oligonucleotides containing multiple LNA alkyl phosphothiotriester nucleotides and evaluate their biophysical and biological properties. Several functional groups were incorporated into the triester linkages, including 2-butyl, 2-hexyl, 3-octyl, 4-trifluoromethyl cyclohex-1-yl, hexadecyl, and 4-pentyn-2-yl. The alkyne triesters were functionalized with carbohydrates, amino acids, heptaethylene glycol, spermine, and thiazole orange through CuAAC click chemistry. Analysis of over 60 oligonucleotides showed that almost all displayed excellent duplex stability with both complementary DNA and RNA and good splice-switching activity in an in vitro reporter assay. Amino acid conjugates showed significantly higher activity than carbohydrate conjugates via gymnosis.