title: Atomic force microscopy of parallel DNA branched junction arrays.
abstract: 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 approximately 68 degrees and approximately 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.
authors.affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.
authors.forename: R
authors.initials: R
authors.lastname: Sha
authors.forename: F
authors.initials: F
authors.lastname: Liu
authors.forename: D P
authors.initials: DP
authors.lastname: Millar
authors.forename: N C
authors.initials: NC
authors.lastname: Seeman
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D006860:Hydrogen Bonding; D018625:Microscopy, Atomic Force / Q000379:methods; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012984:Software
chemical_list: D004247:DNA