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 unpair ed sequences, each inserted in the center of the duplex, has been inve stigated by measuring the polarization anisotropy decay of intercalate d 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 em ploying Brownian dynamics simulations, it is shown that the FPA result s from the fragment with the double insertion can be interpreted by as suming a softening of the elastic constant at the bulge. Estimates of the torsion and the bending rigidities at the bulge site are also give n.