STRUCTURE AND DYNAMICS OF CURVED DNA FRAGMENTS IN SOLUTION - EVIDENCEFOR SLOW MODES OF CONFIGURATIONAL TRANSITIONS

DNA fragments with unusually low electrophoretic mobility due to intri nsic curvature have been analyzed by comparison of electrooptical data with results of hydrodynamic simulations. Electrooptical data have be en collected for three fragments with 161, 196 and 399 base pairs deri ved from the DNA of Chironomus thummi thummi as repetitive elements by Alu I restriction. The dichroism decay time constants reflecting over all rotational diffusion, the bending time constants and the bending a mplitudes measured at low salt concentrations (2.4 mM Na+ and 100 muM Mg2+) are rather close to those observed for standard DNA fragments. A t high salt concentration (0.1 M Na+ and 10 mM Mg2+) the temperature d ependence of the overall rotational time constants indicates a slightl y increased degree of curvature at low temperature (2-degrees-C). The experimental data are complemented by hydrodynamic simulations based o n predictions of DNA trajectories given by Bolshoy et al. [Proc. Natl. Acad. Sci. USA 88 (1991) 2312]. These trajectories are converted into bead models, which are then subjected to thermal fluctuations using a Monte Carlo procedure. For standard values of the persistence length and the torsional flexibility, thermal fluctuations induce considerabl e variations of the equilibrium curvature. As a first attempt to find conditions where the predicted trajectories are consistent with our hy drodynamic data, we tested a model with a high internal mobility, whic h has been commonly applied for standard DNA fragments. However, the o verall rotational time constants predicted for this case are clearly s maller than the observed ones, even at high values of the persistence length. Then, we simulated time constants in the limit of low internal mobility by calculation of electrooptical transients for large number s of individual configurations. The average of these transients could be fitted by two exponentials at high accuracy, although the simulatio ns led to broad distributions of configurations. In this respect the s imulated curves are very similar to the experimental ones. For standar d values of the persistence length and of the torsional flexibility, t he large time constants tau2, reflecting overall rotational diffusion, are still smaller than the experimental ones. Tau2-values simulated a s a function of the persistence length p show a maximum, which appears at p almost-equal-to 1000 angstrom for the Alu-fragments. The tau2-va lues simulated at these maxima are consistent with the experimental on es within the limits of accuracy. Thus, provided that the curvature ha s been estimated correctly by the model based on gel mobilities and on circularization experiments curved DNA fragments show a relatively lo w rate of the internal dynamics and also appear to be less flexible th an standard DNA's with respect to the dynamic persistence. The differe nce in the dynamic persistence is negligible, however, if the apparent persistence length of standard DNA has a major contribution from intr insic curvature, corresponding to an average static persistence length of about 800 angstrom. In summary, our results indicate that the ''de viations from linearity'' of our curved fragments are not much differe nt from those of standard DNA's; however, our results are consistent w ith the view that curved DNA fragments are ''curved'' preferentially i n one direction with relatively slow modes of configurational transiti ons and with a relatively high rigidity, whereas standard DNA is subje ct to bending by thermal motion in all directions with (almost) equal probability.