Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations

Using small angle neutron scattering we have measured the static form facto r of two different superhelical DNAs, p1868 (1868 bp) and pUC18 (2686 bp), in dilute aqueous solution at salt concentrations between 0 and 1.5 M Na+ i n 10 mM Tris at 0% and 100% D2O. For both DNA molecules, the theoretical st atic form factor was also calculated from an ensemble of Monte Carlo config urations generated by a previously described model. Simulated and measured form factors of both DNAs showed the same behavior between 10 and 100 mM sa lt concentration: An undulation in the scattering curve at a momentum trans fer q = 0.5 nm(-1) present at lower concentration disappears above 100 mM. The position of the undulation corresponds to a distance of similar to 10-2 0 nm. This indicated a change in the DNA superhelix diameter, as the undula tion is not present in the scattering curve of the relaxed DNA. From the me asured scattering curves of superhelical DNA we estimated the superhelix di ameter as a function of Na+ concentration by a quantitative comparison with the scattering curve of relaxed DNA. The ratio of the scattering curves of superhelical and relaxed DNA is very similar to the form factor of a pair of point scatterers. We concluded that the distance of this pair correspond s to the interstrand separation in the superhelix. The computed superhelix diameter of 16.0 +/- 0.9 nm at 10 mM decreased to 9.0 +/- 0.7 nm at 100 mM salt concentration. Measured and simulated scattering curves agreed almost quantitatively, therefore we also calculated the superhelix diameter from t he simulated conformations. It decreased from 18.0 +/- 1.5 nm at 10 mM to 9 .4 +/- 1.5 nm at 100 mM salt concentration. This value did not significantl y change to lower values at higher Na+ concentration, in agreement with res ults obtained by electron microscopy, scanning force microscopy imaging in aqueous solution, and recent MC simulations, but in contrast to the observa tion of a lateral collapse of the DNA superhelix as indicated by cryo-elect ron microscopy studies.