Zinc‐Binding Oligonucleotide Backbone Modifications for Targeting a DNA‐Processing Metalloenzyme

A series of chemically‐modified oligonucleotides for targeting the DNA repair nuclease SNM1A have been designed and synthesised. Each oligonucleotide contains a modified internucleotide linkage designed to both mimic the native phosphodiester backbone and chelate to the catalytic zinc ion(s) in the SNM1A active site. Dinucleoside phosphoramidites containing urea, squaramide, sulfanylacetamide, and sulfinylacetamide linkages were prepared and employed successfully in solid‐phase oligonucleotide synthesis. All the modified oligonucleotides were found to interact with SNM1A in a gel electrophoresis‐based assay, demonstrating the first examples of inhibition of DNA damage repair enzymes for many of these groups in oligonucleotides. One strand containing a sulfinylacetamide‐linkage was found to have the strongest interaction with SNM1A and was further tested in a real‐time fluorescence assay. This allowed an IC50 value of 231 nM to be determined, significantly lower than previously reported substrate‐mimics targeting this enzyme. It is expected that these modified oligonucleotides will serve as a scaffold for the future development of fluorescent or biotin‐labelled probes for the in vivo study of DNA repair processes. DNA oligonucleotides bearing a modified internucleotide linkage that enables chelation of zinc ions were synthesized. Modifications included urea, squaramide, sulfanylacetamide and sulfinylacetamide moieties. The interaction of the oligonucleotides with the zinc‐dependent DNA repair enzyme SNM1A was studied. The oligonucleotides were capable of strong binding to SNM1A, and the most potent compound inhibited SNM1A activity with an IC50 of 231 nM.