Motions of short DNA duplexes: an analysis of DNA dynamics using an EPR-active probe

Abstract

The dynamics of a series of four DNA duplexes of length 12, 24, 48, and 96 base pairs have been studied using an electron paramagnetic resonance (EPR) active nitroxide spin-label covalently attached to a thymidine located near the center of each duplex. The linear EPR spectra were simulated by solving the stochastic Liouville equation for anisotropic rotational diffusion. The diffusion tensor for global rotation of the duplex was predicted from hydrodynamic theory for a right circular cylinder. All internal motions, assumed to be rapid, are modeled by reduced electron Zeeman and hyperfine tensor anisotropies. Best fit simulations to the data were then obtained by adjusting the total amplitude of all internal dynamics. The local, length-independent and the collective, length-dependent contributions to the internal dynamics were separated by determining the total amplitude of internal motion as a function of duplex length. The major axis of the spin tensors was determined to be tilted 20 degrees from the helix axis. As a result, the spin-label is most sensitive to flexural motions of the DNA duplex. It is found that the global tumbling of duplex is accurately modeled by hydrodynamic theory. The length-independent motion is characterized by a root-mean-squared amplitude of oscillation of 10 degrees in two dimensions at 20 degrees C and has a strong temperature dependence, indicating that the local structure of the DNA changes with temperature. The length dependence of the internal dynamics leads to an estimate of the dynamic flexural persistence length of 2500 +/- 340 A. There was no statistically significant difference between models assuming a harmonic or a square-well local bending potential.