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DNA Origami with Complex Curvatures in Three-Dimensional Space

Science  15 Apr 2011:
Vol. 332, Issue 6027, pp. 342-346
DOI: 10.1126/science.1202998

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  1. Fig. 1

    Design principles for DNA origami with complex curvatures in 3D space. (A) A parallel arrangement of DNA double helices to make multihelical DNA nanostructures. The distance between consecutive crossovers connecting adjacent helices (L1, L2, and L3) is constant and generally corresponds to 21 or 32 bps (about two or three full turns of B-form DNA). (B) Bending of DNA helices into concentric rings to generate in-plane curvature. The distance between crossovers in the outer rings are greater than in the inner rings (L3 > L2 > L1). This distance is not required to be regular, or exactly equal to a whole number of full turns of B-form DNA for every helix. (C) Schematic diagram of a three-ring concentric structure. The long single-stranded DNA scaffold is shown in cyan, and short oligonucleotide staple strands are shown in various colors. Two scaffold crossovers are required between adjacent rings to achieve the three-ring arrangement. They are located far apart, on opposite sides of the rings. Five periodic, staple-strand crossovers connect the outer and middle rings and the middle and inner rings, respectively, constraining the three bent double-helical DNA rings to the same 2D plane. (D) Helical and cylindrical view of the three-ring concentric structure. (E) A general method to introduce out-of-plane curvature in a multihelical DNA structure. All DNA helices exhibit a natural B-form conformation. There are 10 possible values of θ ranging from ~34° to ~343°. Due to steric hindrance, not all values are allowed. Only a few of these values are demonstrated here. (F) Various views of the structure shown in (E), viewed along the helical axes, tilted by 135°, and perpendicular to the helical axes.

  2. Fig. 2

    Curved 2D DNA nanostructures with various structural features. (Upper panels) Schematic designs. (Middle panels) Zoom-in AFM images with 50-nm scale bars. (Lower panels) Zoom-out AFM images with 100-nm scale bars. (A) Nine-layer concentric ring structure. Only 3600 of 7249 nucleotides of the scaffold strand are used in this structure, and the remaining single-stranded loop is left unpaired, attached to the outer ring (often visible due to formation of secondary structures). (B) Eleven-layer modified concentric square frame structure with rounded outer corners and sharp inner corners.

  3. Fig. 3

    DNA nanostructures with complex 3D curvatures. (A) Schematic representation of the hemisphere. (B) Schematic representation of the sphere. (C) Schematic representation of the ellipsoid. (D) TEM images of the hemisphere, randomly deposited on TEM grids. The concave surface is visible as a dark area. (E) TEM images of the sphere, randomly deposited on TEM grids. Due to the spherical symmetry, the orientation can not be determined. (F) TEM images of the ellipsoid. The outline of the ellipsoid is visible. Scale bar for the TEM images in (D), (E) and (F) is 50 nm. (G) Schematic representation of the nanoflask. (H) AFM images of the nanoflask. Scale bar is 75 nm. (I) TEM images of the nanoflask, randomly deposited on TEM grids. The cylindrical neck and rounded bottom of the flask are clearly visible in the images. Scale bar is 50 nm.