MINOR-GROOVE DNA ALKYLATION DIRECTED BY MAJOR GROOVE TRIPLEX FORMING OLIGODEOXYRIBONUCLEOTIDES

We describe sequence-specific alkylation in the minor groove of double -stranded DNA by a hybridization-triggered reactive group conjugated t o a tripler forming oligodeoxyribonucleotide (TFO) that binds in the m ajor groove, The 24 nt TFOs (G/A motif) were designed to form triplexe s with a homopurine tract within a 65 bp target duplex, They were conj ugated to an N5-methylcyclopropapyrroloindole (MCPI) residue, a struct ural analog of cyclopropapyrroloindole (CPI), the reactive subunit of the potent antibiotic CC-1065. These moieties react in the DNA minor g roove, alkylating adenines at their N3 position, In order to optimize alkylation efficiency, linkers between the TFO and the MCPI were varie d both in length and composition, Quantitative alkylation of target DN A was achieved when the dihydropyrroloindole (DPI) subunit of CC-1065 was incorporated between an octa(propylene phosphate) linker and MCPI, The required long Tinker traversed one strand of the target duplex fr om the major groove-bound TFO to deliver the reactive group to the min or groove, Alkylation was directed by relative positioning of the TFOs , Sites in the minor groove within 4-8 nt from the end of the TFO bear ing the reactive group were selectively alkylated.