1. Atomic force microscopy of parallel DNA branched junction arrays
Ruojie Sha, Furong Liu, David P Millar, Nadrian C Seeman 
Chemistry & Biology 
Volume 7, Issue 9, Pages (September 2000)
DOI: /S (00)

2. Figure 1
Conventional and bowtie branched junctions. (a) Conformational sign conventions. On the left, a view of a Holliday junction is shown down the axis connecting the double helical domains; yet perpendicular to both; the red vertical domain lies above the plane of the page, closer to the reader, and the green horizontal domain lies below it, further from the reader. In line with previous treatments [10], the rear domain rotates; its 5′ end is imagined to be coupled to the green arrow pointing right on the horizontal axis. When the 5′ end is above the horizontal, the structure is qualitatively ‘parallel’, and when it is below the horizontal, it is qualitatively ‘antiparallel’. The signs of the angles are illustrated in the four quadrants; thus, if the arrow were pointing in the upper right quadrant, the conformation would be positive-parallel, in the upper left, negative-parallel, the lower left, positive-antiparallel, and the lower right, negative-antiparallel. Two particular structures are indicated on this drawing by purple arrows: +63° antiparallel corresponds to the conformation of the conventional Holliday junction [12], and −68° parallel corresponds to the conformation of the bowtie junction, as determined here. At the right of the larger diagram, two smaller diagrams are shown, illustrating the nearly ideal antiparallel and parallel structures. They are placed directly above the parallel and antiparallel schematics in (c); for clarity, they have been rotated 15° into the positive quadrants from purely antiparallel or parallel. (b) Schematic drawings. The upper drawing shows the well-characterized immobile branched junction, J1, composed of four conventional strands of DNA. The strands are labeled with Arabic numerals and the double helical arms with Roman numerals. The 5′ ends of strands are indicated by filled green circles, and the 3′ ends are indicated by red arrowheads. Unlike a Holliday junction, there is no twofold sequence symmetry at the branch point, so the position of the crossover cannot relocate through branch migration. The potential fourfold symmetry of the backbone is indicated by the filled brown square at the center of the branch point. The lower drawing shows the same junction converted to a bowtie junction. The sequences of strands 1 and 3 have been retained. Strand 2 now has two 5′ ends and a 3′,3′ linkage at the branch point; likewise, strand 4 has two 3′ ends, and a 5′,5′ linkage at the branch point. The unusual linkages restrict the bowtie junction backbone to twofold symmetry, about the axis indicated by two brown arrows on the diagonal. (c) Conformations of conventional and bowtie junctions. The same conventions apply as in (b). This view corresponds to looking down the horizontal direction of (a), where the rear helix has been rotated to be ideally parallel or antiparallel. The top panel shows the strand structures of the antiparallel (left) and parallel (right) conventional branched junction if its arms stack to form two helical domains. The helical strands [strands 1 and 3 of (b)] are drawn with a thick line, and the crossover strands [strands 2 and 4 of (b)] are drawn with a thin line. Major (wide) and minor (narrow) grooves are indicated by ‘W’s and ‘N’s, respectively, on both sides of each helical domain; the abutting surface on the inside of the molecule has smaller characters for reasons of clarity. Note that the major groove abuts a minor groove in the antiparallel junction, but that minor grooves abut minor grooves and major grooves abut major grooves in the parallel junction. There is a dyad axis normal to the page in the antiparallel structure, indicated by the brown lens-shaped figure at its center. The dyad axis of the parallel conformation lies in the plane of the page, and is indicated by the two brown arrows at the center. The bottom panel shows bowtie junctions drawn the same way. There is a dyad axis normal to the antiparallel bowtie junction at its center, but it has been omitted for clarity. The parallel bowtie junction has a branch point structure similar to the antiparallel conventional junction in this projection.
Chemistry & Biology 2000 7, DOI: ( /S (00) )

3. Figure 2
Constructs built from conventional junctions. (a) A conventional junction. A two-domain junction is shown, with the red domain closer to the reader than the blue domain. The angle between the domains is about +60°, in agreement with previous studies [10–12]. (b) A parallelogram built from four junctions. Four junctions of the type shown in (a) are shown combined into a parallelogram. The red edges are about 2 nm closer to the reader than the blue edges. This particular parallelogram is equilateral. (c) A one-dimensional array built from DNA parallelograms. The red edges have been connected by sticky-ended self-association to produce a railroad-like arrangement. The separation of the blue ‘ties’ is shorter between parallelograms than within them. (d) A two-dimensional array build from DNA parallelograms. In this case, the parallelogram has self-associated in two dimensions to form an array. All of these structures have been reported previously [12].
Chemistry & Biology 2000 7, DOI: ( /S (00) )

4. Figure 3
Two-dimensional arrays of bowtie parallelograms. (a) 4+2×4+2 arrays. The upper left panel shows a distant view of an array, the upper center panel shows a zoom, the upper right panel illustrates a Fourier smoothing of the upper center, and the lower left panel shows the autocorrelation function of the upper right. The knobs visible in the upper right panel correspond to the small rhombi of the bowtie version of Figure 2d, which are not resolved. The angle between domains is emphasized in the lower left, and is re-drawn in the lower center. The sign of the angle is evident in the autocorrelation function, because one set of domains clearly is in front of the other. The predicted and observed periodicities in the autocorrelation function are indicated. (b) 4+4×4+4 arrays. The same conventions apply as in (a). The knobs now correspond to single intersections. The sign of the angle is less clear in the autocorrelation function, possibly because the array is less robust to contact mode scanning. The periodicity indicated is the half-periodicity of the individual repeat; the actual chemical periodicity is twice that indicated.
Chemistry & Biology 2000 7, DOI: ( /S (00) )

5. Figure 4
Schematic diagram representations of the experiment to demonstrate the parallelism of the bowtie junction. (a) The question and the components. The top portion shows a drawing of the bowtie junction in the parallel conformation (left) and the antiparallel conformation (right). The 5′ and 3′ ends of the helical strands are labeled. The 3′,3′ linkage is indicated by the pair of green opposed triangles, and the 5′,5′ linkage is indicated by the pair of juxtaposed blue circles. The central row shows four 4+2×4+2 rhombus figures drawn dark blue in the shape corresponding to the parallel conformation at the top left. The opposed triangle and juxtaposed circle convention is repeated here, but the symbols are removed from the strands for clarity. The figures are labeled with Roman numerals, I, II, III and IV, and the ends of their helices are labeled 0, to represent hairpins, or the letters A, B, C and D, to represent sticky ends, or A′, B′, C′ and D′ to represent their complements, respectively. The bottom row shows the same figures, but now drawn red in the antiparallel conformation of the upper right. (b) V-shaped arrays formed by combinations of the components in (a). The left side shows the V-shaped arrays that would be formed by the combination of parallelograms I, III and IV. The acute dark-blue V-shaped figure corresponds to the parallel structure and the obtuse red V-shaped figure corresponds to the antiparallel structure. The right side shows the V-shaped arrays that would be formed by the combination of parallelograms II, III and IV. The obtuse dark-blue V-shaped figure corresponds to the parallel structure and the acute red V-shaped figure corresponds to the antiparallel structure.
Chemistry & Biology 2000 7, DOI: ( /S (00) )

6. Figure 5
AFM images of the V-shaped arrays formed by bowtie parallelograms. (a) V-shaped arrays formed by combining parallelograms I, III and IV. All arrays have angles in the range 65–69°, in agreement with a parallel structure. (b) V-shaped arrays formed by combining parallelograms II, III and IV. All arrays have angles in the range 110–115°, again in agreement with a parallel structure. (c) Control images of individual components. The panels are labeled by the component visualized there. Little structure is shown for components I and II, and components III and IV form the linear arrays expected for them.
Chemistry & Biology 2000 7, DOI: ( /S (00) )

7. Figure 6
A combined conventional–bowtie parallelogram tile. The conventional parallelogram is closer to the reader, drawn with thicker lines, and the bowtie parallelogram is further from the reader, as indicated by the thin lines. The two parallelograms are connected by double crossover structures. The orientation of the double crossover plane is somewhat arbitrary. The planes here are meant recede from the reader in the order red, dark blue, green, light blue. Note that the inverse relationship in sign between the conventional and bowtie junction enables this structure to be built with the favored structures for each type of junction. In principle, this type of tile could be used to create a space-filling array.
Chemistry & Biology 2000 7, DOI: ( /S (00) )