Prompt site-selective DNA hydrolysis by Ce(iv)–EDTA using oligonucleotide multiphosphonate conjugates

Abstract

Oligodeoxyribonucleotide multiphosphonate conjugates have been prepared by on-support oximation of aminooxy-functionalized oligonucleotides with 2-(4-formylphenoxy)ethyl esters of nitrilotris(methylenephosphonic acid) (NTP) and ethylenediaminetetrakis(methylenephosphonic acid) (EDTP). These conjugates, along with the corresponding oligonucleotides bearing hydroxy or monophosphate termini, were hybridized with a longer substrate DNA leaving a narrow single-stranded gap site in the substrate between the two additive oligonucleotides. Gap sites flanked by two of the multiphosphonate groups, in particular EDTP, were hydrolyzed by the Ce(IV)–EDTA complex significantly faster than the corresponding gap sites flanked by only hydroxy or monophosphate termini. Using the new oligonucleotide conjugates, efficient site-selective hydrolysis of the substrate DNA can be achieved at Ce(IV) concentrations where other single-stranded regions remain intact. At high Ce(IV) concentrations, the cleavage rate becomes independent on [Ce(IV)] and little improvement by the new multiphosphonate conjugates over oligonucleotides with monophosphate termini is observed, suggesting that the origin of the rate acceleration is the higher affinity of the NTP or EDTP ligands to Ce(IV) compared to hydroxy or monophosphate ligands.