High affinity, chemically modified triplex-forming oligonucleotides (TFOs) and methods for use thereof are disclosed. TFOs are defined as triplex-forming oligonucleotides which bind as third strands to duplex
DNA in a sequence specific manner. Triplex-forming oligonucleotides may be comprised of any possible combination of nucleotides and modified nucleotides. Modified nucleotides may contain chemical modifications of the heterocyclic base,
sugar moiety or
phosphate moiety. A high affinity
oligonucleotide (Kd≦2×10−8) which forms a triple strand with a specific
DNA segment of a
target gene DNA is generated. It is preferable that the Kd for the high affinity
oligonucleotide is below 2×10−10. The
nucleotide binds or hybridizes to a target sequence within a
target gene or target region of a
chromosome, forming a triplex region. The binding of the
oligonucleotide to the target region stimulates mutations within or adjacent to the target region using
cellular DNA synthesis, recombination, and repair mechanisms. The
mutation generated activates, inactivates, or alters the activity and function of the
target gene.