Recognition of mixed-sequence duplex DNA by alternate-strand triple-helix formation

Oligodeoxyribonucleotide-directed triple-helix formation offers a chemical approach for the sequence-specific binding of double-helical DNA that is 10^6 times more specific than restriction enzymes. Because triple-helix formation by pyrimidine oligonucleotides is limited to purine tracts, it is desirable to find a general solution whereby oligonucleotides could be used to bind all four base pairs of intact duplex DNA (37 °C, pH 7.0). Approaches toward such a goal include the following: the search for other natural triplet specificities, such as G-TA triplets; the design of nonnatural bases for completion of the triplet code; the incorporation of abasic residues for nonreading of certain base pairs; and the design of oligonucleotides capable of binding alternate strands of duplex DNA by triple-helix formation. We report that a pyrimidine oligodeoxyribonucleotide-EDTA-Fe containing a 3'-3' phosphodiester and a 1,2-dideoxy-~ribose linker binds and cleaves a mixed-sequence double-helical DNA target site by alternate-strand triple-helix formation.