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Oxidative DNA Cleavage with Clip‐Phenanthroline Triplex‐Forming Oligonucleotide Hybrids

A systematic study of several new types of hybrids of Cu‐chelated clamped phenanthroline artificial metallonuclease (AMN) with triplex‐forming oligonucleotides (TFO) for sequence‐specific cleavage of double‐stranded DNA (dsDNA) is reported. The synthesis of these AMN–TFO hybrids is based on application of the alkyne–azide cycloaddition click reaction as the key step. The AMN was attached through different linkers at either the 5′‐ or 3′‐ends or in the middle of the TFO stretch. The diverse hybrids efficiently formed triplexes with the target purine‐rich sequence and their copper complexes were studied for their ability to cleave dsDNA in the presence of ascorbate as a reductant. In all cases, the influence of the nature and length of the AMN–TFO, time, conditions and amounts of ascorbate were studied, and optimum conjugates and a procedure that gave reasonably efficient (up to 34 %) cleavage of the target sequence, while rendering an off‐target dsDNA intact, were found. The footprint of cleavage on PAGE was identified only in one case, with low conversion; this means that cleavage does not proceed with single nucleotide precision. On the other hand, these AMN–TFO hybrids are useful for the selective degradation of target dsDNA sequences. Future improvements to this design may provide higher resolution and selectivity.