Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Pseudohexagonal 2D DNA Crystals from Double Crossover Cohesion

The control of the structure of matter on the finest possible scale requires the successful design of both stiff intramolecular motifs and robust intermolecular interactions. Previous motifs used in our lab to design 2D crystalline arrays have included the double crossover (DX), triple crossover (TX), and the DNA parallelogram. These motifs have been used to produce 2D crystalline arrays lacking symmetry or with twofold symmetry. By contrast, all previous attempts to produce trigonal or hexagonal arrays have met with failure. Given the inherent rigidity of triangles and the importance of trigonal motifs in nature it is key to solve this problem. The flexibility of 3-arm junctions was discovered in the first attempt to assemble a hexagonal lattice. Triangles built from bulged 3-arm junctions demonstrated cyclic closure with trimers and above, not just from the hexamers one would have expected. Triangles whose edges were flanked by coplanar helices derived from DX molecules behaved in a similar fashion.

We have overcome these problems by the development of a new motif, the DX triangle. This motif is derived by combining the DX motif with the bulged triangle motif (Left, below). The DX molecule has been shown to be about twice as stiff as conventional linear duplex DNA (1). Thus, one might expect that this doubly-thick triangle would be more rigid than the simple bulged junction triangle. In addition, the DX triangle is capable of a double intermolecular interaction that may be more robust than the single helical interactions used previously, because it is less sensitive to errors in twist. Here, we report the self-assembly of a trigonal array from this motif. We demonstrate that improving the intermolecular contacts is the key feature of the DX triangle motif that enables formation of trigonal arrays.

Two triangles were designed to produce a pseudohexagonal trigonal lattice arrangement when combined. They are identical, except for their sticky ends. When assembled, they form hexagonal honey-comb-like arrays. A long view of such an array is shown in the middle below, and a zoom is shown to its right. This is the first trigonal array to be designed and formed from DNA motifs. Despite the beauty of these arrays, the importance of this work extends beyond the results presented here. When one of the sticky ends is removed from the DX linkages, no arrays are seen. It appears that DX cohesion is able to accommodate structural design errors that remain present when cohesion is restricted to individual sticky ends. This principle has now been used successfully to produce numerous 2D arrays that previously were unobtainable with simple sticky-ended cohesion.

Baoquan Ding
Ruojie Sha
Nadrian C. Seeman*

Department of Chemistry
New York University
New York, NY 10003, USA

Fax: 212-260-7905
Email: ned.seeman@nyu.edu


This research supported by NIGMS, ONR, NSF and Nanoscience Technologies, Inc.

References and Footnotes
  1. Sa-Ardyen, P., Vologodskii, A. V., and Seeman, N.C. Biophys. J. 84, 3829-3837 (2003).