Design of minimally strained nucleic acid nanotubes

William B. Sherman, Nadrian C. Seeman

Research output: Contribution to journalArticle

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-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.

Original languageEnglish (US)
Pages (from-to)4546-4557
Number of pages12
JournalBiophysical journal
Volume90
Issue number12
DOIs
StatePublished - Jun 2006

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ASJC Scopus subject areas

  • Biophysics

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