Improved targeting of the flanks of a DNA stem using α- oligodeoxynucleotides.-The enhanced effect of an intercalator

Article abstract of DOI:10.1080/07328319808004323

2'-Deoxy-5'-O-(4,4'-dimethoxytrityl)-5-methyl-N⁴-(1-pyrenylmethyl)-α- cytidine (5) was prepared by reaction of 1-pyrenylmethylamine with an appropriate protected 4-(1,2,4-triazolyl)-α-thymidine derivative 3 which was synthesized from 5-O-DMT protected α-thymidine 1. Aminolysis of 3 afforded 3'-O-acetyl-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)-5-methyl-α-cytidine (8). Benzoylation of 8 and removal of acetyl afforded N⁴-benzoyl-2-deoxy-5-O- (4,4'-dimethoxytrityl)-5-methyl-α-cytidine (10). The amidites of compounds 5 and 10 were prepared and used in α-oligonucleotide synthesis. DNA three-way junction (TWJ) is stabilized when an α-ODN is used for targeting the dangling flanks of the stem in a DNA hairpin. Further stabilization of the TWJ is observed when 5 is inserted into the α-ODN at the junction region.