Renaturation of alkali-denatured T7 DNA molecules complexed with ethidium bromide

Free and ethidium bromide (EB) complexed alkali denatured T7 DNA molecules were renatured at 58 and 62 degrees C respectively for 1--3 h. The structures of the renaturation products of the free candidates were as usual showing native like, branched and unrenatured DNA whereas the structures of the ethidium bromide complexed one were somewhat different, showing non-renatured loop-like and entangled regions present inbetween the renatured segments. On the basis of the linear base sequence of T7 DNA, these non-renatured parts are indicative of the inhibition of renaturation by the complexed EB molecules. Mapping of the non-renatured regions showed that they were present at some specific sites, which inturn suggested that the EB-binding has some base sequence specificity.