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Biophys. J. BioFAST: First Published March 31, 2006. doi:10.1529/biophysj.105.080390
© 2006 by the Biophysical Society.

A more recent version of this article appeared on June 15, 2006.
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NUCLEIC ACIDS

Design of Minimally Strained Nucleic Acid Nanotubes

William B. Sherman 1 and Nadrian C. Seeman 1*

1 New York University

* To whom correspondence should be addressed. E-mail: ned.seeman{at}nyu.edu.

Submitted on December 27, 2005
Revised on March 3, 2006
Accepted on 15 March 2006


  Abstract
A practical theoretical framework is presented for designing and classifying minimally strained nucleic acid nanotubes. The structures are based on the double crossover motif where each double helical domain is connected to each of its neighbors via two or more Holliday junction-like reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a 5-parameter characterization of the segmented double-helical structure. Once the constraint equations have been derived, the primary design problem for a minimally strained N-domain structure is reduced to solving 3 simultaneous equations in 2N+2 variables. Symmetry analysis and tube merging then allow for the design of a wide variety of tubes, which can be tailored to satisfy requirements such as specific inner-and-outer radii, or multiple lobed structures. The general form of the equations allows similar techniques to be applied to various nucleic acid helices: B-DNA, A-DNA, RNA, DNA-PNA, or others. Possible applications for such tubes include nano-scale scaffolding as well as custom shaped enclosures for other nano-objects.

Key Words: DNA Crossovers, DNA Tubes, Geometrical Molecular Modeling, Molecular Architecture, Self-Assembly, Structural DNA Nanotechnology




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Copyright © 2006 by the Biophysical Society.