Structure and dynamics of a DNA-based model system for the study of electron spin-spin interactions

We report on the structure and dynamics of a model system for measuring long-range distances in biological macromolecules by saturation-recovery EPR. Four DNA duplexes that incorporate a paramagnetic dysprosium ion (Dy(III)) and a nitroxide spin-label were examined by electron paramagnetic resonance (EPR), circular dichroism (CD), and ultra-violet absorbance (UV) spectroscopy. Dy(III) is chelated by the modified base deoxythymidine-EDTA, (dT-EDTA). Electron spin-spin interactions between the Dy(III) ion and the nitroxide radical are observed at distances as great as ∼5.3 nm. A slight change in the conformation of those nucleotides lying between the EDTA(Dy(III)) complex and the nitroxide spin-label results in a “stiffening” of the DNA helix on the EPR time scale. Changes in conformation and helix dynamics are due to the binding of the EDTA(Dy(III)) complex to the phosphodiester backbone of the complementary strand. Molecular mechanics calculations indicate that binding occurs in the 5′ direction on the complementary strand, at a position 3 or 4 phosphates distant from the dT-EDTA(Dy(III)) * dA base pair.