An electron spin resonance study of DNA dynamics using the slowly relaxing local structure model

A systematic analysis is presented of the ESR spectra from DNA oligomers of a range of sizes, including a polymer, spin-labeled with nitroxide moieties attached by different tethers. The complexity of the DNA dynamics is dealt with by the use of the general slowly relaxing local structure (SRLS) model, wherein the nitroxide moiety is reorienting in a restricted local environment, which itself is relaxing on a longer time scale. The slower motion describes the global tumbling of the DNA lattice, and the faster motion, the internal dynamics. in the present analysis, the correlation times for the axially symmetric global tumbling were those obtained from hydrodynamic theory, while the correlation times for the internal dynamics and the order parameter, which directly measures its restricted range of motion, were determined by nonlinear least-squares fits to the spectra. The principal result is the observation and characterization of two types of spectra from these labeled DNA systems. These two spectra represent components that differ fi om each other with respect to their local environments, one a highly restricted site yielding a large order parameter (0.61) and slower internal motions and the other a much less restricted site (with order parameter of 0.18) and faster internal motions. Whereas the one-atom tethered DUTA exhibits both sites (in roughly 9:1 ratio with the more restricted site more prevalent), the two-atom tethered DUMTA and five-atom tethered DUAT exhibit just the more restricted site, but the five-atom tethered DUAP exhibits only the less restricted site. (DUAP differs from DUAT and the others in having a less flexible tether.) Tt is suggested that the spin labels trapped in the highly restricted/slow motional site have a stronger interaction with the base than those in the ether site. In general, the longer the tether, the faster are the correlation times for internal dynamics. For all tethers, it is found that the correlation time for internal motion perpendicular to the internal symmetry axis systematically becomes slower as the size of the oligomer increases. It is suggested that this may be a manifestation of collective modes of motion of the DNA. It is pointed out that the simpler models used in previous ESR studies are simplified cases of the more realistic SRLS model.