A new family of sequence-specific DNA-cleaving agents directed by triple-helical structures: Benzopyridoindole-EDTA conjugates

Sequence-specific DNA recognition can be achieved by oligonucleotides that bind to the major groove of oligopyrimidine oligopurine sequences. These in termolecular structures could be used to modulate gene expression and to cr eate new tools for molecular biology. Here we report the synthesis and bioc hemical characterization of triple helix-specific DNA cleaving reagents. It is based on the previously reported tripler-specific ligands, benzo[g]pyri doindole (BePI) and benzo[g]pyridoindole (BgPI), covalently attached to eth ylenediaminotetraacetic acid (EDTA). In the presence of iron, a reducing ag ent and molecular oxygen, BgPI-EDTA.Fe-II but not BePI-EDTA.Fe-II induced a double-stranded cut in a plasmid DNA at the single site where a tripler-fo rming oligonucleotide binds. At single nucleotide resolution, it was found that upon tripler formation BePI-EDTA.Fe-II led to cleavage of the pyrimidi ne strand and protection of the purine strand. BgPI-EDTA.Fe-II cleaved both strands with similar efficiency. The difference in cleavage efficiency bet ween the two conjugates was rationalized by the location of the EDTA.Fe-II moiety with respect to the grooves of DNA (major groove: BePI-EDTA.Fe-II, m inor groove: BgPI-EDTA.Fe-II). This work paves the way to the development o f a new class of triple helix directed DNA cleaving reagents. Such molecule s will be of interest for sequence-specific DNA cleavage and for investigat ing triple-helical structures, such as H-DNA, which could play an important role in the control of gene expression in vivo.