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Growing millimeter-sized DNA crystals

Synthetic oligonucleotides, engineered to self-assemble into periodic 2D arrays, could serve as templates for the fabrication of nanostructures.
3 April 2006, SPIE Newsroom. DOI: 10.1117/2.1200602.0098

Conventional top-down techniques are able to produce patterns at the micrometer scale, but have limited capability to produce features at the nanometer scale. Bottom-up approaches, on the other hand, are more promising for building nanoscale patterns by self-assembly. DNA is among the top candidates for molecules that can serve as ‘building blocks’ for constructing well-defined nanostructures.1 DNA has an excellent ability to recognize molecules and has a predictable double-helix structure.

Two key elements of DNA self-assembly are the molecule's sticky ends and its ability to form branched structures or motifs. Sticky ends are complementary single-stranded overhangs at the ends of DNA duplexes. Hybridization between sticky ends associates two DNA molecules together. Besides naturally-linear DNA molecules, many branched DNA motifs have been rationally designed in the last two decades to produce diverse and complex nanostructures. These motifs, when carrying sticky ends, have been self-assembled into well-defined periodic 2D crystals.

All existing DNA 2D crystals are too small (at most several micrometers) to be useful for many technological applications. To increase 2D crystal sizes, we introduced ‘sequence symmetry’ to design DNA nanostructures.2,3 Conventionally, sequence symmetry has been strictly avoided in designing DNA nanostructures because only specific and unique sequences are believed to reliably lead to predictable DNA self-assembly. If the predictability of DNA nanostructures is preserved, however, introduction of sequence symmetry may provide several advantages: it simplifies the sequence design; it reduces the number of different DNA strands and thus lowers the cost; it simplifies the experimental operations; and it cancels some unpredictable distortions in DNA nanostructures. In our work, we successfully applied sequence symmetry and produced two kinds of 2D DNA crystals with sizes of larger than 1mm.

The DNA motifs used in our work are a simplified cross motif and a newly designed three-point-star motif (see Figure 1). Each motif contains only three different kinds of DNA single strands (different colored lines). As a result, all branches in the motifs are identical: so are all sticky ends. The identical branches remove potential curvatures associated with nonsymmetrical motifs. Identical sticky ends also provide identical cohesion strength in all directions. Consequently, large isotropic 2D crystals were expected, and these were confirmed by studying images of the crystals obtained by atomic force microscopy and fluorescence microscopy. The atomic force microscope images showed the well-ordered tetragonal and hexagonal patterns assembled from the cross motif and the three-point-star motif, respectively. The DNA arrays were often larger than the microscope's scanning field. To study the large sizes of the DNA crystals, we stained the DNA crystals with a dye—YOYO-1—and imaged them with fluorescence microscopy. The results showed that these two kinds of crystals both are larger than 1mm.

Figure. 1. Two symmetric DNA nanomotifs and the crystals grown using them: (a) and (d) show a symmetric cross motif and a three-point-star motif, respectively. Images (b) and (e) are atomic force micrographs showing the crystal structure, and (c) and (f) are fluorescence microscopy images of DNA 2D crystals assembled from the DNA motifs.

DNA 2D crystals have already been demonstrated to be suited to nanofabrication tasks such as organizing nanoscale objects, and to serving as masks in nanopatterning. We expect they will have a bright future in nanoscience and nanotechnology.

Chengde Mao and He Yu
Department of Chemistry, Purdue University
West Lafayette, IN