Toward encoding reactivity using double-stranded DNA. Sequence-dependent native chemical ligation of DNA binding polyamides

The coupling reaction between distamycin-related polyamides equipped with cysteine and thioester groups can be accelerated in the presence of double-stranded (ds) oligonucleotides with selected sequences. While the coupling reaction of reactive partners containing three pyrrole units is accelerated by dsDNAs containing ATTTTA or ATGTTA sites, the heterodimeric coupling between a tripyrrole and a polyamide equipped with two pyrroles and one imidazole, is accelerated by the latter DNA, but not by the other containing the A/T rich tract. These differences can be exploited for selecting preferred coupling pairs from a mixture of reactive monomers; therefore the reaction outcome depends on the instructions provided by the dsDNA sequence.