We propose to develop a fundamentally new approach to nucleic acid targeting of DNA duplexes. In the proposed recognition complexes, the targeting strand of DNA inserts itself between the two Watson-Crick faces of the duplex to result in a new type of DNA triplex. These triplexes are termed Janus Wedge triplexes after the Roman god Janus. The targeting Janus Wedge (Jw) residue in the Janus Wedge helix contains two hydrogen bonding faces such that after insertion into the DNA duplex, the Janus Wedge residue is hydrogen bonded to both Watson-Crick faces of the target base pair. The final three-stranded complex contains significantly more interstrand hydrogen bonds than does the target Watson-Crick DNA duplex. We will examine both pyrimidine-like and purine-like analogues for the Janus Wedge residues. Initial studies will focus on the nature of the Janus Wedge triplex - those formed without competing Watson-Crick interactions. Subsequently we will focus on strand invasion processes that will be necessary to permit the targeting of duplex DNA. In this respect, the peptide nucleic acid (PNA) oligomers, other oligomers with neutral backbones, selected tethered ligands, and the process of DNA breathing may all be valuable to the strand invasion process. The results of this study will provide a new approach for the targeting of double-stranded DNA, one that can be used for both purine-pyrimidine and pyrimidine-purine base pairs equally. It will generalize the process of sequence recognition to include essentially any DNA sequence.
