Purine‐Derived Nitroxides for Noncovalent Spin‐Labeling of Abasic Sites in Duplex Nucleic Acids

A series of purine‐based spin labels was prepared for noncovalent spin‐labeling of abasic sites of duplex nucleic acids through hydrogen bonding to an orphan base on the opposing strand and π‐stacking interactions with the flanking bases. Both 1,1,3,3‐tetramethylisoindolin‐2‐yloxyl and 2,2,6,6‐tetramethylpiperidine‐1‐oxyl (TEMPO) were conjugated to either the C2‐ or C6‐position of the purines, yielding nitroxide derivatives of guanine, adenine, or 2,6‐diaminopurine. The isoindoline‐derived spin labels showed extensive or full binding to abasic sites in RNA duplexes, whereas the TEMPO‐derived spin labels showed limited binding. An adenine‐derived spin label ( 5 ) bound fully at low temperature to abasic sites in both DNA and RNA duplexes when paired with thymine and uracil, respectively, complementing the previously described guanine‐derived spin label Ǵ , which binds efficiently opposite cytosine. Compound Ǵ was also shown to bind to abasic sites in DNA–RNA hybrids, either in the DNA‐ or the RNA‐strand. Ǵ showed only a minor flanking‐sequence effect upon binding to abasic sites in RNA. When the abasic site was placed close to the end of the RNA duplex, the affinity of the spin label Ǵ was reduced; full binding was observed at the fourth position from the duplex end. In summary, spin labels 5 and Ǵ showed full binding to abasic sites in both DNA and RNA duplexes and are promising spin labels for structural studies of nucleic acids by pulsed EPR methods.