Assembly and structural analysis of a covalently closed nano-scale DNA cage

Abstract

The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson–Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA-interacting enzymes. More recently, strategies for synthesis of more complex two-dimensional (2D) and 3D DNA structures have emerged. However, the building of such structures is still in progress and more experiences from different research groups and different fields of expertise are necessary before complex DNA structures can be routinely designed for the use in basal science and/or biotechnology. Here we present the design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron, as defined by the double-stranded DNA helices that assembles from eight oligonucleotides with a yield of ∼30%. As demonstrated by Small Angle X-ray Scattering and cryo-Transmission Electron Microscopy analyses the eight-stranded DNA structure has a central cavity larger than the apertures in the surrounding DNA lattice and can be described as a nano-scale DNA cage, Hence, in theory it could hold proteins or other bio-molecules to enable their investigation in certain harmful environments or even allow their organization into higher order structures.

Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage

“…By quantification of the band representing fully assembled Cage hp (3T) relative to the higher and lower-mobility products the yield of the correctly assembled Cage hp (3T) was estimated to approximately 30À40%, which is comparable to the yield previously reported for Cage(3T)À Cage(7T). 20,21 The anticipated yield of a DNA nanostructure was previously demonstrated to correlate to the number of double-stranded helices in the structure with a decrease in yield as the number of duplexes increase. 44 Factors hampering yield are slight variations in DNA strand concentrations and potential topological 3T and OL2hp 3T ; OL1hp 3T ÀOL3hp 3T ; OL1hp 3T ÀOL4hp 3T ; OL1hp 3T ÀOL4hp 3T and OL5 3T ; OL1hp 3T ÀOL4hp 3T and OL5 3T ÀOL6 3T ; OL1hp 3T À OL4hp 3T and OL5 3T ÀOL7 3T ; OL1hp 3T ÀOL4hp 3T and OL5 3T ÀOL8 3T to analysis in a native polyacrylamide gel.…”

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

“…In particular, this means that in oxDNA, the AA and TT stacking interactions are the same, whereas it is well known that the AA stacking interaction is significantly stronger than the TT interaction, an important property for DNA nanotechnology, for example, where poly-T single-stranded regions are often used as flexible linkers. 61,62 To remedy this, we use new experimental data to reparameterise the AA and TT stacking interactions in the model.…”

Self-assembly of a nanoscale DNA box with a controllable lid

“…Several assembly strategies have been developed for building complex threedimensional (3D) DNA nanostructures [2][3][4][5][6][7][8] . Recently, the DNA 'origami' method was used to build two-dimensional addressable DNA structures of arbitrary shape 9 that can be used as platforms to arrange nanomaterials with high precision and specificity [9][10][11][12][13] .…”