DETECTION OF INTERNAL AND OVERALL DYNAMICS OF A 2-ATOM-TETHERED SPIN-LABELED DNA

DNA motions consist of several components which couple, making their i nvestigation difficult. This study describes an approach for obtaining dynamical information by EPR when spin-labeled nucleic acids are exam ined. The analysis is accomplished by implementing two motional models . The first model (i.e., dynamic cylinder model) views the spin-labele d helix as a diffusing cylinder containing internal dynamics which are characterized by an order parameter. The second model (i.e., base dis k model) provides correlation times describing the diffusion of the sp in-labeled base. In each model, the nitroxide motion consists of both global and internal contributions. Dynamic cylinder and base disk simu lations of four duplexes containing nitroxides attached to thymidine b y a two-atom tether (DUMTA)-(dT)(7)DUMTA-(dT)(7) .(dA>(15), [(dT)7DUMT A(dT)(7)](2) .(dA)(30), [(dT)(7)DUMTA(dT)(7)](3) .(dA)(45), and [(dT)( 7)DUMTk(dT)(7)](m) .-(dA)(n)-demonstrate the useful application of thi s approach. From dynamic cylinder simulations, the order parameter for internal motions is found to be independent of the helix length (S = 0.32 +/- 0.01). Previous base disk simulations of a DNA 26mer and poly mer labeled with a five-atom-tethered nitroxide seemed to indicate tha t tau(perpendicular to) was only sensitive to internal dynamics. Resul ts from base disk simulations of DUMTA-labeled DNA indicate that the p erpendicular component of the base disk correlation time (tau(perpendi cular to) 1.4-6.2 ns) is sensitive to global dynamics. Thus, tau(perpe ndicular to) is a quantitative indicator of both internal and global d ynamics, Comparison of the two models reveals that tau(perpendicular t o) proportional to S-2 tau(rb), where tau(rb) represents the rigid-bod y diffusion of the DNA helix. This relationship between S and tau(perp endicular to) provides a framework for studying conformational changes and size-dependent phenomena in spin-labeled nucleic acids. Applicati on of the dynamic cylinder model to a B-Z transition generates distinc t values of S for each of the conformations, indicating that Z-DNA is more rigid than B-DNA.