Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

2D DNA Crystalline Sections as a Method to Test Structural Design in 3D

The steepest challenge of structural DNA nanotechnology is the construction of 3D arrays with high order. A number of designs have been self-assembled to yield 3D crystals, sometimes of dimensions that exceed 1 millimeter. However, the diffraction patterns of these crystals have been limited to 10 Å resolution.

It is extremely difficult to troubleshoot structural errors in 3D crystals, because the crystals do not themselves yield much information if they do not diffract. Some DNA motifs, such as the DX, TX, and PX motifs are inherently two-dimensional, because all of their helix axes are confined to a single plane. However, other motifs, such as the tensegrity triangle (1), the 6-helix bundle (2) or the skewed TX motif, are inherently 3-dimensional, because they contain three vectors that span 3-space. These three motifs are shown below (left to right, respectively), although the tensegrity triangle is modified for DX cohesion.

By blunting the sticky ends in one of the three linearly independent directcions, it is possible to produce get these motifs to self-assemble into three different 2D crystalline arrays. This is an excellent way to establish that there are no geometrical flaws in the design, at least to the accuracy of the method of observation, AFM. One successful 2D array from each motifs is shown below in the same order as the motifs. When all three directions form well-ordered arrays in two dimensions, it is then reasonable to consider self-assembly in three dimensions.

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

References and Footnotes
  1. Liu, D., Wang, M., Deng, Z., Walulu, R., and Mao, C. J. Am. Chem. Soc. 126, 2324-2325, (2004).

Pamela E. Constantinou
Tong Wang
Jens Kopatsch
Baoquan Ding
William B. Sherman
Jens J. Birktoft
Ruojie Sha
Chengde Maoa
Nadrian C. Seeman*

*Department of Chemistry
New York University
New York, NY 10003, USA
aDepartment of Chemistry
Purdue University
West Lafayette, IN 47907, USA

*Phone: 212-998-8395
Fax: 212-260-7905
Email: ned.seeman@nyu.edu