Effect of N3 modifications on the affinity of spin label ç for abasic sites in duplex DNA.

Noncovalent site-directed spin labeling (NC-SDSL) of abasic sites in duplex DNAs with the spin label ç, a cytosine analogue, is a promising approach for spin-labeling nucleic acids for EPR spectroscopy. In an attempt to increase the affinity of ç for abasic sites, several N3 derivatives were prepared, and their binding affinities were determined by EPR spectroscopy. Most of the N3 substituents had a detrimental effect on binding. The triazole-linked polyethylene-glycol derivative (12 a) showed a 15-fold decrease in affinity, whereas the binding affinities of ethyl azido (8 b) and hydroxyl (8 c) derivatives were five- to sixfold lower. The spin-labeled nucleoside Ç showed only a twofold decrease, thus binding better than 8 c, even though it contains the larger 2'-deoxyribose substituent at N3 instead of a 2-hydroxyethyl group. N3 derivatives that contained the basic ethyl amino (9) or ethyl guanidino (10) substituents had both higher binding affinity and solubility, attributed to their cationic charge at neutral pH. Compounds 9 and 10 are promising candidates for NC-SDSL of nucleic acids, for distance measurements by pulsed EPR spectroscopy.