Transient Electric Birefringence of Linear and Circular DNA: A Comparison of Kinetic Theory Predictions

The use of monodisperse DNA and restriction enzyme modification allows the preparation of model samples of polymer rings and linear chains with a precision that is not possible by conventional synthetic routes. These samples allow direct comparisons of the predictions of polymer kinetic theories. Transient electric birefringence allows rapid imposition or forces (similar to 100 mu s) and monitoring of conformational changes (similar to 0.7 mu s). We determined the relaxation spectra of once-cut linear Phi X-174 (5386 bp), twice-cut linear Phi X-174 (2693 bp), and relaxed ring (5386 bp) (Phi X-174 with transient electric birefringence. This allows comparison of the relaxation dynamics of a linear chain and a polymer loop with exactly the same contour length. The relaxed loop and the twice-cut DNA had the longest relaxation times of 1039 and 1076 mu s, respectively. The loop was measured both in the native supercoiled state and in the relaxed state. We found the birefringence decayed in agreement with bead- spring (Rouse/Zimm) models for polymer dynamics determined by both a model-independent average relaxation time and deconvolution of the decay into a sum of exponentials. Deconvolution was performed by CONTIN and by the Pade-Laplace method. For both the relaxed ring and the linear fragments, we found the longer time constants tau(1) and tau(2) were discrete and had a spacing that was in agreement with the Rouse model without hydrodynamic interaction (tau(1)/tau(2) = 0.25), which would be expected for a chain with 20 statistical segments. The excitation of higher relaxation modes could be observed as the electric field pulse length increased.