Flexibility of duplex DNA on the submicrosecond timescale

Using a site-specific, Electron Paramagnetic Resonance(EPR)-active spin pro be that is move rigidly locked to the DNA than any previously reported, the internal dynamics of duplex DNAs in solution were studied. EPR spectra of linear duplex DNAs containing 14-100 base pairs were acquired and simulated by the stochastic Liouville equation for anisotropic rotational diffusion using the diffusion tensor for a right circular cylinder. Internal motions have previously been assumed to be on a rapid enough time scale that they c aused an averaging of the spin interactions. This assumption, however, was found to be inconsistent with the experimental data. The weakly bending rod model is modified to take into account the finite relaxation times of the internal modes and applied to analyze the EPR spectra. With this modificati on, the dependence of the oscillation amplitude of the probe on position al ong the DNA was in good agreement with the predictions of the weakly bendin g rod theory. From the length and position dependence of the internal flexi bility of the DNA, a submicrosecond dynamic bending persistence length of a round 1500 to 1700 Angstrom was found, Schellman and Harvey (Biophys. Chem. 55:95-114, 1995) have estimated that, out of the total persistence length of duplex DNA, believed to be about 500 Angstrom, approximately 1500 Angstr om is accounted for by static bends and 750 Angstrom by fluctuating bends. A measured dynamic persistence length of around 1500, leads to the suggesti on that there ave additional conformations of the DNA that relax on a longe r time scale than that accessible by linear CW-EPR. These measurements ave the first direct determination of the dynamic flexibility of duplex DNA in 0.1 M salt.