Self-Assembly of Chiral DNA Nanotubes

“…Th e synthesis of programmed one-, two-and three-dimensional DNA nanostructures is a rapidly developing research topic 5 -7 , and the resulting DNA assemblies were used as templates for the precise positioning of nanoparticles 8 -10 and proteins 11 -14 . Diff erent methods have been used to assemble DNA nanotubes, and these include the self-assembly of triple-cross-over tiles 15 , the closure of two-dimensional tiles or circular arrays by complementary hybridization 16 , the self-assembly of a single DNA tile with internal complementarity 17 , or covalent bonds 18 . Also, the synthesis of geometrically defi ned single-stranded DNA, rigidifi ed with organic vertices that are longitudinally assembled into nanotubules 19 , the synthesis of DNA nanotubes of predetermined lengths 20 and the templated synthesis of nanotubes have been reported 21 .…”

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Self-assembly of DNA nanotubes with controllable diameters

et al. 2011

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The synthesis of DNA nanotubes is an important area in nanobiotechnology. Different methods to assemble DNA nanotubes have been reported, and control over the width of the nanotubes has been achieved by programmed subunits of DNA tiles. Here we report the selfassembly of DNA nanotubes with controllable diameters. The DNA nanotubes are formed by the self-organization of single-stranded DNAs, exhibiting appropriate complementarities that yield hexagon (small or large) and tetragon geometries. In the presence of rolling circle amplifi cation strands, that exhibit partial complementarities to the edges of the hexagonor tetragon-building units, non-bundled DNA nanotubes of controlled diameters can be formed. The formation of the DNA tubes, and the control over the diameters of the generated nanotubes, are attributed to the thermodynamically favoured unidirectional growth of the sheets of the respective subunits, followed subjected to the folding of sheets by elastic-energy penalties that are compensated by favoured binding energies.

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“…[1][2][3] This combination of structural and biochemical properties makes DNA nanotubes especially interesting for applications. For example, they might be metallized or functionalized by surface attachment of biomolecules or nanoparticles and so serve as interconnects in self-assembled networks.…”

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Sturdier DNA Nanotubes via Ligation

et al. 2006

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DNA nanotubes are crystalline self-assemblies of DNA tiles ∼10 nm in diameter that readily grow tens of micrometers in length. Easy assembly, programmability, and stiffness make them interesting for many applications, but DNA nanotubes begin to melt at temperatures below 40°C, break open when deposited on mica or scanned by AFM, and disintegrate in deionized water. These weaknesses can be traced to the presence of discontinuities in the phosphate backbone, called nicks. The nanotubes studied here have five nicks, one in the core of a tile and one at each corner. We report the successful ligation of all four corner nicks by T4 DNA ligase. Although ligation does not change the nanotubes' stiffness, ligated nanotubes withstand temperatures over 70°C, resist breaking during AFM, and are stable in pure water for over a month. Ligated DNA nanotubes are thus physically and chemically sturdy enough to withstand the manipulations necessary for many technological applications.Made entirely of DNA, but hundreds of times stiffer than ordinary double-stranded DNA (dsDNA), DNA nanotubes combine the binding specificity of nucleic acids with a rigid, linear structure. [1][2][3] This combination of structural and biochemical properties makes DNA nanotubes especially interesting for applications. For example, they might be metallized or functionalized by surface attachment of biomolecules or nanoparticles and so serve as interconnects in self-assembled networks. [4][5][6][7][8] Alternatively, DNA nanotubes might be used, like actin filaments, 9 as mechanical magnifiers of the nanoscopic motion of biomolecules, but with greater chemical stability and versatility. However, the practical realization of these and many other applications will require DNA nanotubes that withstand considerable mechanical and chemical manipulation. Therefore, to enhance the technological relevance of DNA nanotubes, we sought to increase their stability via ligation.Ligation is commonly used to establish the topology of programmed DNA nanostructures. 10-13 However, its effectiveness within a two-dimensional DNA tile array has never been well characterized. 14 Crystal structures of ligase enzymes suggest that ligation requires the enzyme to access a large portion of the double helical surface. 15 One might therefore expect ligation among the potentially close-packed double helices of the nanotube tile lattice to be particularly inhibited.In this paper, we report that DNA nanotubes are viable substrates for T4 DNA ligase, quantify the extent of ligation at each of the five nicks, and show that ligated nanotubes are significantly more stable to practical manipulation than unligated nanotubes.The DNA nanotubes that we use self-assemble from a single DAE-E type 16 tile (Figure 1). The tile is made of five synthetic DNA oligomers that hybridize into a rigid rectangular core with a single-stranded five-base overhang (sticky end) at each corner. The core consists of two double helices joined at two four-way junctions (crossovers). Diagonally opposite corn...

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Self-Assembly of Chiral DNA Nanotubes

Cited by 205 publications

References 16 publications

Self-assembly of precisely defined DNA nanotube superstructures using DNA origami seeds

Self-assembly of precisely defined DNA nanotube superstructures using DNA origami seeds

Self-assembly of DNA nanotubes with controllable diameters

Sturdier DNA Nanotubes via Ligation

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