Atomic force microscopy of parallel DNA branched junction arrays

Background: The four arms of the Holliday junction are known to stack in pa irs forming two helical domains whose orientations are antiparallel, but tw isted positively by about 60 degrees, based on electrophoretic, FRET and AF M measurements. Recent gel retardation studies suggest that a bowtie juncti on (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 parall el 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 antip arallel. The parallel or antiparallel nature of the junction apparently is determined by the local structure of the junction, but the sign of the angl e appears to be a consequence of interarm electrostatic interactions.