Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

The Design of Nucleic Acid Nanotubes

Nucleic acids are extraordinarily versatile components for nano-scale construction. Base sequence programming of individual strands can precisely specify the interactions necessary for the self-assembly of a broad variety of complex structures and devices. We present techniques for designing molecules which are rigid, hollow tubes formed out of linked nucleic acid helices.

Figure 1. a) Depictions of the cross sections of an assortment of nanotubes which can be built from B-DNA . b) An illustration of the relationship between the 2D pictures and the 3D structure of the phosphate backbone.

Typically, nucleic acid structures less than 5nm thick have been designed using numerous straightforward methods. Extending those techniques, previous work took advantage of the symmetry in a regular hexagon, and the ability to form 120° angles with B-DNA to design and build a six-helix DNA tube (1). In general, designing such thick and rigid molecules proves difficult for two reasons. First, representing such structures in a convenient visual format is problematical. Second, with each helical domain rigidly held at a specific orientation with respect to its two neighbors the interplay of local and global geometries presents very tight constraints that must be satisfied. We have developed a set of analysis tools that facilitate overcoming these difficulties. Key features include systematic identification of possible (minimally stressed) structures; the detailed assignment of strand paths; and clear, graphical representations of the salient design features.

Once the construction techniques are developed, symmetry analysis, or simple exhaustive computer search yields a rich set of tubes with a wide variety of possible structures. Detailed analysis of solution B-DNA nanotubes reveals:
  1. Polygons can be designed for all even numbers of vertices, N, except 4.
  2. The only regular polygons are for N=6,14, or 42.
  3. Any closed curve on a regular hexagonal lattice can be the cross section of a tube.
Such tubes can be designed to satisfy a variety of different nanoengineering needs, with potential uses as robust construction motifs as well as easily manipulated, water-soluble scaffolds for nano-scale objects such as nano-crystals, and other species of nanotubes.

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

William B. Sherman
Nadrian C. Seeman*

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

References and Footnotes
  1. F. Mathieu, C. Mao, N. C. Seeman, Journal of Biomolecular Structure & Dynamics, 18, p.907 (2001).