Saturation-recovery EPR with nitroxyl radical-Dy(III) spin pairs: distances and orientations

We describe a method for measuring the distance between a radical and a Dy(III) ion using saturation-recovery electron paramagnetic resonance (EPR) and demonstrate its application using four chemically modified DNA duplexes. The four DNA duplexes contain a terminal nitroxide spin-label and a midsequence, EDTA-bound Dy(III) ion but differ in the nitroxyl radical (NO)-Dy(III) distance. Distances can be determined with high precision because of their sixth-root dependence on the experimentally determined dipolar rate constant. Furthermore, the orientation of the NO-Dy(III) interspin vector in the Dy(III) g-tensor reference frame can be determined for two of the DNA duplexes. The shortest mean NO-Dy(III) distance, 18.3 ± 0.3 Å, and the longest, 50.3 ± 2.4 Å, are near the lower and upper distance limits of what can be measured with the NO-EDTA(Dy(III)) pair at X-band. These methods are applicable to structural studies of nucleic acids, proteins, and their complexes.