Atomic force microscopy of parallel DNA branched junction arrays

Background: The four arms of the Holliday junction are known to stack in pairs forming two helical domains whose orientations are antiparallel, but twisted positively by about 60 degrees, based on electrophoretic, FRET and AFM measurements. Recent gel retardation studies suggest that a bowtie junction (containing 5',5' and 3',3' linkages in its crossover strands) may adopt a parallel conformation. Results: An AFM study of two-dimensional arrays produced by parallelograms of bowtie junctions shows that the angle between helical domains is in the range of -68+/-2 degrees. We demonstrate by AFM that the domains are parallel by constructing V-shaped structures whose arms are separated by similar to 68 degrees and similar to 112 degrees. Conclusions: The arms of the bowtie junction are parallel rather than antiparallel. The parallel or antiparallel nature of the junction apparently is determined by the local structure of the junction, but the sign of the angle appears to be a consequence of interarm electrostatic interactions.