Atomic force microscopy of parallel DNA branched junction arrays

Area of Science:

• Molecular Biology
• Structural Biology
• Biophysics

Background:

• Holliday junctions typically have antiparallel helical domains twisted positively.
• Previous studies suggested bowtie junctions might adopt a parallel conformation.

Purpose of the Study:

• To investigate the structural conformation of bowtie junctions.
• To determine the orientation of helical domains in bowtie junctions.

Main Methods:

• Atomic Force Microscopy (AFM) was used to study 2D arrays of bowtie junctions.
• V-shaped structures were constructed to analyze domain separation angles.

Main Results:

• AFM revealed an angle of -68+/-2 degrees between helical domains in bowtie junctions.
• The study confirmed parallel domain orientation in bowtie junctions.

Conclusions:

• Bowtie junction arms are parallel, not antiparallel.
• Local junction structure dictates parallel/antiparallel orientation, while electrostatic interactions influence the angle's sign.