Illustration of how linear DNA can be generated by cleavage-ligation or branch migration of Holliday junctions in the context of a circular chromosome.

A. cis and trans configurations of DNA ends on a linear fragment are joined by an odd number of Holliday junctions. Cleavage-ligation of the junctions liberates the linear DNA. B. cis and trans configurations of DNA ends on a linear fragment are joined by an odd number of Holliday junctions. Branch migration will not liberate linear DNA. Instead it will convert an alpha-shaped molecule to a sigma-shaped molecule. C. cis and trans configurations of DNA ends on a linear fragment are joined by an even number of Holliday junctions. Cleavage-ligation of the junctions will liberate linear DNA. D. cis and trans configurations of DNA ends on a linear fragment are joined by an even number of Holliday junctions. Branch migration of the junctions will liberate linear DNA.