Enhanced flexibility of a bulged DNA fragment from fluorescence anisotropy and Brownian dynamics

A fragment of DNA built from 50 base pairs and two five-adenine unpaired sequences, each inserted in the center of the duplex, has been investigated by measuring the polarization anisotropy decay of intercalated ethidium fluorescence (FPA). When the data from this bulged fragment are compared to those from a straight fully paired duplex or to those from a fragment bent by a five-adenine insertion in one strand, then systematic differences are found in the fluorescence parameters. By employing Brownian dynamics simulations, it is shown that the FPA results from the fragment with the double insertion can be interpreted by assuming a softening of the elastic constant at the bulge. Estimates of the torsion and the bending rigidities at the bulge site are also given