PEPTIDE NUCLEIC ACID-ANTHRAQUINONE CONJUGATES - STRAND INVASION AND PHOTOINDUCED CLEAVAGE OF DUPLEX DNA

A bis-peptide nucleic acid (PNA)-anthraquinone imide (AQI) conjugate h as been synthesized and shown to form strand invasion complexes with a duplex DNA target, The two arms of the bis-PNA each consist of five c onsecutive thymine residues and are linked by a flexible, hydrophilic spacer, Probing with potassium permanganate reveals that the bis-PNA c omplexes to duplex DNA at A(5).T-5 sites with local displacement of th e T-5 DNA strand, The 5 bp sequence targeted by the PNA is the shortes t strand invasion complex reported to date, Irradiation of the strand invasion complex results in asymmetric cleavage of the displaced stran d, with more efficient cleavage at the 3'-end of the loop, This result indicates that the bis-PNA binds to the DNA such that the C-terminal T-5 sequence forms the strand invasion complex, leaving the N-terminal T-5 sequence to bind by tripler formation, thereby placing the AQI cl oser to the 3'-end of the displaced strand, consistent with the observ ed photocleavage pattern, The ability of the PNA to directly report it s binding site by photoinduced cleavage could have significant utility in mapping the secondary and tertiary structure of nucleic acids.