Sequence‐Specific Recognition and Modification of Double‐Helical DNA by Oligonucleotides

Abstract Nucleic acids can be selectively recognized by a large number of natural and synthetic ligands. Oligonucleotides provide the highest specificity of recognition. They can bind to a complementary single‐stranded sequence by forming Watson–Crick hydrogen bonds. They can also recognize the major groove of double‐helical DNA at specific sequences by forming Hoogsteen or reverse Hoogsteen hydrogen bonds with purine bases of the Watson‐Crick base pairs, resulting in a triple helix. Triple‐helix formation through oligonucleotide binding to DNA is a sequence–specific interaction involving primarily homopurine·homopyrimidine sequences in the double‐helical target. Extending the range of recognition sequences remains a challenge to chemists. Both thermodynamic and kinetic parameters for triplex formation have been determined. These parameters indicate, for example, that triple‐helix formation is a much slower process than duplex formation. Nuclease‐resistant oligonucleotides synthesized with the anomers of nucleosides (instead of the natural β‐anomers) also form triple helices with double–stranded DNA. Triple‐helix‐forming oligonucleotides can be modified, for example, by attaching DNA intercalating agents to enhance their binding affinity. They may also be modified with reagents that induce irreversible reactions in their target sequence upon chemical or photochemical activation. Thus, artificial nucleases can be developed with very high sequence specificity on megabase‐size DNA. Furthermore, triple‐helix‐forming oligonucleotides can be used to selectively control gene expression. When bound to the regulatory region(s) of specific genes they may prevent activation (or repression) of transcription. When binding occurs near or downstream from the transcription initiation site, elongation of the transcript may be inhibited. Therefore, the potential exists for developing new gene‐blocking agents with therapeutic applications in the treatment of gene disorders.