Figure 2.

Geometry of a DNA braid. (A) Straight, left-handed braid formed by two DNA molecules (blue and red); P is the braid pitch; R is the braid diameter (distance between the centerlines of the molecules); and α is the tilt angle of the molecules. (B) Lateral cross-section of the braid, after tilting the molecular axes parallel to the braid centerline. Solid circles depict phosphate strands; the angles Φ₁ and Φ₂ represent azimuthal orientation of the center of the minor groove of each molecule with respect to the line connecting the two centerlines (see the Supporting Material). (C) Crossover geometry in a left-handed braid. Phosphate strands on the back side of the red molecule are aligned parallel to the strands and grooves on the front side of the blue molecule, making this crossover more energetically favorable than parallel alignment (compare to Fig. 1). (D) Crossover geometry in a right-handed braid. Phosphate strands on the back side of the blue molecule are aligned perpendicular to the opposing strands and grooves on the front side of the red molecule, making this crossover less favorable than parallel alignment.