By exploiting the unique structural motifs and self-recognition properties of DNA, it is possible to generate self-assembled DNA nanostructures of specific shapes. Here, a previously described DNA 'origami' method has been extended into three dimensions to create an addressable DNA box on the nanometre scale that can be opened by an externally supplied DNA key'.

/pdf/self-assembly-of-a-nanoscale-dna-box-with-a-controllable-lid-4t0vka6sln.pdf

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

Small Angle Scattering of X-Rays

DNA cages are nanometer-scale polyhedral structures formed by self-assembly from synthetic DNA oligonucleotides. Potential applications include in vivo imaging and the targeted delivery of macromolecules into living cells. We report an investigation of the ability of a model cage, a DNA tetrahedron, to enter live cultured mammalian cells. Cultured human embryonic kidney cells were treated with a range of fluorescently labeled DNA tetrahedra and subsequently examined using confocal microscopy and flow cytometry. Substantial uptake of tetrahedra into cells was observed both when the cells were treated with tetrahedra alone and when the cells were treated with a mixture of tetrahedra and a transfection reagent. Analysis of the subcellular localization of transfected tetrahedra using confocal microscopy and organelle staining indicates that the cages are located in the cytoplasm. FRET experiments indicate that the DNA cages remain substantially intact within the cells for at least 48 h after transfection. Thi...

DNA Cage Delivery to Mammalian Cells

We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson–Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an “average base” description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bas...

/pdf/structural-mechanical-and-thermodynamic-properties-of-a-4tcm4n3t5i.pdf

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Three-dimensional nanoscale scaffolds can be self-assembled from RNA with precise control over their shape, size and composition.

/pdf/in-vitro-assembly-of-cubic-rna-based-scaffolds-designed-in-2lpqjt3izj.pdf

In vitro assembly of cubic RNA-based scaffolds designed in silico

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 approximately 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.

/pdf/assembly-and-structural-analysis-of-a-covalently-closed-nano-4aibbpuv2f.pdf

Dinna Krüger

Papers

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

Resolution of Holliday junction substrates by human topoisomerase I.