Self-assembly of DNA nanotubes with controllable diameters

Abstract

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.

Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds

“…As shown in Fig. 1c, the same pentameric A-B-A-B-A pattern ( [5] AP , 248 bp) was easily generated in fairly high yield (B45% based on weighted band intensity) with this in situ ligation strategy. Note that we use the nomenclature [N] to represent products with N alternating sequence domains.…”

“…As shown in Fig. 1c (lane 6), denaturing [5] AP to observe the component strand sizes reveals a distribution of products from the intended pentamer all the way down to monomers. This is likely due to a combination of failed phosphorylation and ligation steps during growth, as neither process is expected to proceed quantitatively.…”

“…This explains the apparent contrast between lanes 5 and 6 in Fig. 1c, and shows that [5] AP is composed of both fully covalent and partially nicked products. As discussed below, however, we have developed a strategy to enrich and isolate the full-length target strands from this mixture.…”

“…By growing [5] AP and [5] BP in parallel and then combining them, the decameric product [10] could be produced rapidly (30 min, room temperature) and in reasonable yield (B30% based on weighted band intensity, Fig. 2c).…”

“…From customized genes 1 to high-density data storage tools 2 to backbones for structurally diverse nanostructures [3][4][5][6] , there is a tremendous interest in developing synthetic protocols for the production of sequence-defined DNA that is longer than what conventional solid phase synthesis can achieve (4200 bp). For many applications, the entire product must be completely sequenceunique to maximize information density.…”