Analysis of double-helix motions with spin-labeled probes: binding geometry and the limit of torsional elasticity

The e.p.r.⁵ spectra of a family of spin-labeled probes non-covalently bound to DNA have been measured as functions of helix orientation, packing density and temperature. The spectra are interpreted in terms of the geometrical relations between the helix axis and the orbital containing the unpaired electron and in terms of the motions of the helix. Torsional and flexural motions can be distinguished.Spectra from well-ordered helices have been obtained using fully hydrated DNA fibers that are in thermodynamic equilibrium with unbound probe in dilute salt solution. The binding equilibria are similar to the equilibria in dilute DNA solution. The spatial relations between the spin label and the helix, inferred from the spectra, correspond closely to the structure expected on the basis of intercalation perpendicular to the helix axis and a sterically hindered amide bond between the spin label and the intercalating moiety of the probe. Viscometric measurements with one probe also indicate intercalation.Linear e.p.r. spectra of solutions, randomly condensed DNA, and fibers show substantial torsional motion but no detectable flexure on the linear e.p.r. time scale (> 300 ns). The correlation time of a propidium-based probe is much longer than that of aminoacridine intercalators. The probes with short correlation times are considered to be too weakly coupled to the adjacent base-pairs to be reliable indicators of DNA dynamics. For the propidium probe the correlation time, 30 nanoseconds, and its temperature dependence are compared with the properties expected according to four models: tight rotational coupling along the entire length of the helix; swivels at fixed intervals; a two-state exchange; and elastic rotational coupling between adjacent nucleotide pairs. In terms of the fourth model, the results suggest that each nucleotide pair undergoes random oscillation with an r.m.s. amplitude of not more than 4 ° to 5 ° at room temperature. That value agrees with estimates made in other ways.