Sequence-Specific Recognition and Cleavage of Duplex DNA by Derivatized Oligonucleotides

Abstract

A homopyrimidine 11-mer oligodeoxynucleotide selectively recognizes a 11-bp homopurine. homopyrimidine sequence in duplex DNA of simian virus 40 (SV40). Binding occurs in the major groove via Hoogsten base pairing of thymine and protonated cytosine to Watson-Crick A.T and G.C base pairs, respectively. The 11-mer oligonucleotide was covalently linked to 5-amino-1,10-phenanthroline via different linkers. Efficient cleavage of SV40 circular DNA was observed in the presence of Cu2+ and a reducing agent when a pentamethylene carboxamide linker was used to tether phenanthroline to a 5’-thiophosphate group of the 11-mer oligonucleotide. The distribution of the cleavage sites on the two strands was asymmetric. They were shifted towards the 3’-side indicating that cleavage occurred from the minor groove. Recognition of the major groove by the oligonucleotide and intercalation of phenanthroline at the triplex-duplex junction account for the observed sequence-specific cleavage reaction from within the minor groove. An ellipticine derivative was covalently attached to the 3’-end of the 11-mer oligonucleotide. Upon irradiation at wavelengths longer than 300 nm the DNA target was cleaved at the positions expected if the oligonucleotide binds in a parallel orientation to the homopurine sequence. In addition it was shown that triple helix formation by the unsubstituted 11-mer oligonucleotide targeted a photo-induced cleavage by free ellipticine derivatives at the triplex-duplex junctions. Molecular modeling and energy minimization studies revealed that the distortion at the triplex-duplex junctions could account for these results.KeywordsTriple HelixMinor GrooveMajor GrooveIntercalate AgentOligonucleotide BindingThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.