Small Circular DNA Molecules Act as Rigid Motifs To Build DNA Nanotubes

Abstract

Small circular DNA molecules with designed lengths, for example 64 and 96 nucleotides (nt), after hybridization with a few 32-nt staple strands respectively, can act as rigid motifs for the construction of DNA nanotubes with excellent uniformity in ring diameter. Unlike most native DNA nanotubes, which consist of longitudinal double helices, nanotubes assembled from circular DNAs are constructed from lateral double helices. Of the five types of DNA nanotubes designed here, four are built by alternating two different rings of the same ring size, while one is composed of all the same 96-nt rings. Nanotubes constructed from the same 96-nt rings are 10-100 times shorter than those constructed from two different 96-nt rings, because there are fewer hinge joints on the rings.

Circular DNA by “Bis‐Click” Ligation: Template‐Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides

“…These compounds also play a notable role in the bottom‐up construction of nanoscaled objects . Small, circular DNA molecules of defined lengths can act as rigid elements for the construction of DNA nanodevices, such as nanotubes …”

DNA nanochannels

“…The tile in this strategy, unlike the previous method, was only the DNA single strand. Another way to build the DNA nanotube was to use small circular DNA molecules as tiles and then introduce assisted staple strands to connect the circular DNA by forming crossover 13 . Owing to the designability and biological compatibility, the tile-based nanotubes were widely used as the one-dimensional templates 14 and nanowires 15 .…”

DNA nanostructures: a shift from assembly to applications

“…In a novel approach to nanotube assembly, Xiao and co-workers reported the use of small circular DNA (Figure 1d) [14]. This strategy allowed for the creation of rigid nanotubes with helices perpendicular to the direction of the tube, as opposed to most nanotubes whose helices run along the backbone of the tube.…”

“…(d) Nanotubes assembled from circular oligonucleotides connected by short staple strands. (Reprinted with permission from [14]. Copyright 2014 American Chemical Society.…”