Synthesis of Oligonucleotides Containing 2′-Deoxyisoguanosine and 2′-Deoxy-5-methylisocytidine Using Phosphoramidite Chemistry

The synthesis of oligonucleotides containing 2′‐deoxy‐5‐methylisocytidine and 2′‐deoxyisoguanosine using phosphoramidite chemistry in solid‐phase oligonucleotide synthesis is described. Supporting previous observations, the N,N‐diisobutylformamidine moiety was found to be a far superior protecting group than N‐benzoyl for 2′‐deoxy‐5‐methylisocytidine. 2′‐Deoxy‐N2‐[(diisobutylamino)methylidene]‐5′‐(4,4′‐dimethoxytityl)‐5‐methylisocytidine 3′‐(2‐cyanoethyl diisopropylphosphoramidite) (1c) incorporated multiple consecutive residues during a standard automated synthesis protocol with a coupling efficiency > 99% according to dimethoxytrityl release. Extending coupling times of the standard protocol to ≥ 600s using 2′‐deoxy‐N6‐[(diisobutylamino)methylidene]‐5′‐O‐(dimethoxytrityl)‐O2‐(diphenylcarbamoyl)isoguanosine, 3′‐(2‐cyanoethyl diisopropylphosphoramidite) (7e) led to successful incorporation of multiple consecutive 2′‐deoxyisoguanosine bases with a coupling efficiency > 97% according to dimethoxytrityl release.