Novel topologically knotted DNA from bacteriophage P4 capsids: Studies with DNA topoisomerases

DNA molecules isolated from bacteriophage P4 are mostly linear with cohesive ends capable of forming cicular and concatemeric structures. In contrast, almost all DNA molecules isolated from P4 tailless capsids(heads) are monomeric DNA circles with their cohesive ends hydrogen-bonded. Different from simple DNA circles, such P4 head DNA circles contain topological knots. Gel electrophoretic and electronmicroscopic analyses of P4 head DNA indicate that the topological knots are highly complex and heterogeneous. Resolution of such complex knots has been studied with various DNA topoisomerases. The conversion of highly knotted P4 DNA to its simple circular form is demonstrated by type II DNA topoisomerases which catalyze the topological passing of two crossing double-stranded DNA segments{Liu, L. F., Liu, C. C. & Alberts, B. M. (1980) Cell, 19, 697-707}. The knotted P4 head DNA can be used in a sensitive assay for the detection of a type II DNA topoisomerase even in the presence of excess type I DNA topoisomerases.