Conformational transitions of nitroxide labeled and unlabeled nucleic acids were analyzed by esr and uv spectroscopy to evaluate potential perturbation effects caused by chemical modifications of nucleic acids with spin labels. The melting temperature ( T m) determined by uv or esr melting profiles of 2 → 1 or 3 → 1 transitions is similar for labeled and unlabeled polyadenylic acid [(A) n ] and polyuridylic acid [(U) n ] complexes provided spin-labeled (A) n with a nitroxide to nucleotide ratio of 0.002 is used. Complexes formed with spin-labeled (A) n of greater spin-labeling extent display a noticeable perturbation of their thermal melting profiles. The studies reconfirm the existence of a low temperature esr transition at about 20 °C with calf thymus and T4 DNA duplexes spin-labeled with a nitroxide to nucleotide ratio of about 0.006. The uv melting profiles of the spin-labeled duplexes reveal no low-temperature discontinuity, but the T m values reflecting the 2 → 1 transitions were reduced by several degrees versus those of the unlabeled duplexes. Thus, these studies suggest that with homopolymers, chemically modified to a low extent with nitroxides, the monitoring of local conformational transitions of duplexes or triplexes reflect the overall 2 → 1 or 3 → 1 transitions. In the case of the heteropolymers the possibility that the chemical modification is responsible for the low-temperature phenomenon cannot be ruled out.