Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

A DNA Nanotube Based on a Six-Helix Bundle Motif

DNA nanotechnology produces objects, arrays and devices that are based on unusual motifs. It is possible to use cohesive ('sticky') ends to generate large self-assemblies of these motifs. For example, we have reported previously 2D arrays constructed from DNA double crossover (DX) molecules, DNA triple crossover (TX) molecules, and DNA parallelograms, all of which are relatively simple motifs. Here, we have used sticky ends to self-assemble a complex motif, a six-helix DNA bundle, into a 1D array. The bundle consists of laterally joined helices, so that every adjacent pair of helices forms a DX motif. However, unlike the TX motif, the angle between any three adjacent helices is 120รป; this corresponds to a 14-nucleotide inter-helix phasing, assuming 10.5 nucleotide pairs per double helical turn. This arrangement produces a cavity at the center of the bundle, having a diameter similar to that of the individual helices. The schematic diagram below shows an unfolded view of the six-helix bundle motif. The two points labeled 'a' and 'b' on either side of the diagram label identical crossover points. The repeat length of each helix is 84 nucleotide pairs (8 turns), but the helices are staggered with respect to each other. The helices are tailed with 5'-sticky ends whose lengths vary from 2 to 8 nucleotides. This motif self-assembles into extended wire-like structures whose length can exceed 10 microns. The example shown in the atomic force micrograph is about 12 microns long. Few short tubes are seen in the self-assemblies, which are produced in ambient conditions.

This research supported by NIGMS, ONR, NSF/DARPA, USAF and NSF.

Frederick Mathieu, Chengde Mao and Nadrian C. Seeman*

Department of Chemistry, New York University, New York, NY 10003, USA Ph: 212-998-8395; fx: 212-260-7905; email: ned.seeman@nyu.edu.