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Originally published as Biophys J. BioFAST on March 31, 2006.
doi:10.1529/biophysj.105.080390
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Biophysical Journal 90:4546-4557 (2006)
© 2006 The Biophysical Society

Design of Minimally Strained Nucleic Acid Nanotubes

William B. Sherman and Nadrian C. Seeman

Department of Chemistry, New York University, New York, New York

Correspondence: Address reprint requests to Nadrian C. Seeman, Fax: 212-260-7905; E-mail: ned.seeman{at}nyu.edu.

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-junctionlike reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a five-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 three 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 nanoscale scaffolding as well as custom-shaped enclosures for other nano-objects.




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B. Ding and N. C. Seeman
Operation of a DNA Robot Arm Inserted into a 2D DNA Crystalline Substrate
Science, December 8, 2006; 314(5805): 1583 - 1585.
[Abstract] [Full Text] [PDF]


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Copyright © 2006 by the Biophysical Society.