Six-helix bundles designed from DNA

Abstract

We present a designed cyclic DNA motif that consists of six DNA double helices that are connected to each other at two crossover sites. DNA double helices with 10.5 nucleotide pairs per turn facilitate the programming of DNA double crossover molecules to form hexagonally symmetric arrangements when the crossover points are separated by seven or fourteen nucleotide pairs. We demonstrate by atomic force microscopy well-formed arrays of hexagonal six-helix bundle motifs both in 1D and in 2D.

Figure 1

Schematic Drawings of the Six-Helix Bundle Motif. (a) The strand sequences are shown for a version of this motif with 14 nucleotide pairs between crossovers. Points A and B are the places where the cyclic bundle closes. Strand numbering is indicated. There are six helical strands, shown in black, and the other strands perform the crossovers. (b) A cross-sectional geometrical view of a six helix bundle in which the helices are indicated by Roman numerals. (c) A geometrical side view of a six helix bundle in which the crossovers are separated by seven nucleotide pairs. The back and front are indicated as the ends to be used in self-assembly.

Figure 2

Autoradiograms of 5% Non-Denaturing Gels that Establish the Robustness and Proper Stoichiometry of the Six Helix Bundle Motif. Every lane contains the complete blunt-ended 6HB molecule. The lanes are labeled with the radioactive strand that is contained in that complex; strand numbering is as shown in Figure 1. The marker lanes contain a 100-base pair ladder. Note that every strand is incorporated into the motif, and that there are neither multimers nor breakdown products in this gel, demonstrating the robust character of the motif.

Figure 3

One-Dimensional 6HB Self-Assembled Arrays. The images are obtained by contact mode atomic force microscopy. (a) A series of 6HB wire-like images. (b) A long nanotube. (c) A zoomed view showing a large nanotube. (d) A bundle of nanotubes from which some have been separated. Note that the molecules in all panels are relatively unbent.

Figure 4

Two dimensional arrays obtained from six helix bundle motifs. The three different paired sets of helical sticky ends have been blunted to produce a 2D array. A schematic where the vertices of hexagons represent helix axes is shown in (a); the red layer is closer to the reader than the blue layer. From the first set, a zoom is shown in panel (b), its autocorrelation function is shown in (c), and a long view is shown in (d). The zoom in (b) shows how the individual 6HB motifs form a corrugated arrangement. Note that the autocorrelation function indicates 2D order. A long view of each of the other two directions is shown in (e) and (f). Neither of their autocorrelation functions indicates good order in more than one direction. (g) shows that the image in (f) has clear vacancies, but that they do not appear to destroy the periodicity of the array.