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

5 years ago

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

Nilesh R. Kamble, Snorri Th. Sigurdsson

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. Binding without bonding: Isoindoline-derived purine spin-labels bind efficiently to abasic sites of duplex DNA and RNA when they can form hydrogen bonds to the orphan base on the opposing strand; the adenine-derived spin label 5 pairs with uracil (or thymine) and the guanine-derivative Ǵ pairs with cytosine. The latter also binds to abasic sites in DNA–RNA hybrid duplexes and shows a minimal flanking-sequence effect upon binding to abasic sites in RNA.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/chem.201705410