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The effect of phosphorylation events on the sequence-independent binding proteins of p53 is examined using two DNA substrates, one resembling Holliday junctions and the other containing extra base bulges. Gel retardation assays showed that diphosphorylation of serine 392 in the C-terminal domain of p53 greatly reduce Holliday junction and lesion recognition.

Type II DNA topoisomerases actively reduce the fractions of knotted and catenated circular DNA below thermodynamic equilibrium values. To explain this surprising finding, we designed a model in which topoisomerases introduce a sharp bend in DNA. Because the enzymes have a specific orientation relative to the bend, they act like Maxwell's demon, providing unidirectional strand passage. Quantitative analysis of the model by computer simulations proved that it can explain much of the experimental data. The required sharp DNA bend was demonstrated by a greatly increased cyclization of short DNA fragments from topoisomerase binding and by direct visualization with electron microscopy.