Another Method for 3 Dimensional DNA Structures

Douglas et al. report a method for designing and constructing three-dimensional nanostructures from DNA. a, The computer-aided design process begins with a block of tubes arranged in a honeycomb lattice. b, A template for the desired DNA structure is designed by removing sections of the tubes, just like carving a sculpture from a block. The remaining tubes will become DNA duplexes in the final object. The DNA structure is designed by routing a single-stranded scaffold DNA (a virus genome) through every section of the tube template. Hundreds of short strands of DNA are then designed to bind to the folded scaffold, cross-linking between different tubes and ‘stapling’ together the overall structure. When the staple molecules are synthesized and mixed with the scaffold DNA in solution under appropriate conditions, they direct the folding of the scaffold into the desired nanostructure. The structure shown here is more complex than those prepared by the authors

Self-assembly of DNA into nanoscale three-dimensional shapes using nanotubes of DNA has been proven. Note: On Jan 31, 2008 this site had declared that we had moved into the age of DNA Nanotechnology. Clearly the recent work in three dimensions with DNA is clearly screaming “Age of DNA Nanotechnology”.

This is the abstract

Shawn M. Douglas, Hendrik Dietz, Tim Liedl, Björn Högberg, Franziska Graf & William M. Shih1

Department of Cancer Biology, Dana-Farber Cancer Institute
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School
Wyss Institute for Biologically Inspired Engineering, Harvard University

Molecular self-assembly offers a ‘bottom-up’ route to fabrication with subnanometre precision of complex structures from simple components. DNA has proved to be a versatile building block for programmable construction of such objects, including two-dimensional crystals, nanotubes, and three-dimensional wireframe nanopolyhedra. Templated self-assembly of DNA into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase ‘scaffold strand’ that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide ‘staple strands’. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes—monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross—with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometre scale.

a, Double helices comprised of scaffold (grey) and staple strands (orange, white, blue) run parallel to the z-axis to form an unrolled two-dimensional schematic of the target shape. Phosphate linkages form crossovers between adjacent helices, with staple crossovers bridging different layers shown as semicircular arcs. b, Cylinder model of a half-rolled conceptual intermediate. Cylinders represent double helices, with loops of unpaired scaffold strand linking the ends of adjacent helices. c, Cylinder model of folded target shape. The honeycomb arrangement of parallel helices is shown in cross-sectional slices (i–iii) parallel to the x–y plane, spaced apart at seven base-pair intervals that repeat every 21 base pairs. All potential staple crossovers are shown for each cross-section. d, Atomistic DNA model of shape from c.

a, Left panel, Cylinder model of stacked-cross monomer (Fig. 2e), with dotted line indicating direction of assembly. Right panels, typical TEM micrographs showing stacked-cross polymers. Purified stacked-cross samples were mixed with a fivefold molar excess of connector staple strands in the presence of 5 mM Tris + 1 mM EDTA (pH 7.9 at 20 °C), 16 mM MgCl2 at 30 °C for 24 h. Monomers were folded in separate chambers, purified, and mixed with connector staple strands designed to bridge separate monomers. b, Cylinder model (left) and transmission electron micrograph (right) of a double-triangle shape comprised of 20 six-helix bundle half-struts. c, Heterotrimerization of the icosahedra was done with a 1:1:1 mixture of the three unpurified monomers at 50 °C for 24 h. d, Orthographic projection models and TEM data of four icosahedron particles. Scale bars in a, b and d: 100 nm.

Lincoln logs of DNA

26 pages of supplemental information that describe exactly how the DNA fits together