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

  title={Self-assembly of a nanoscale DNA box with a controllable lid},
  author={Ebbe Sloth Andersen and Mingdong Dong and Morten M Nielsen and Kasper Jahn and Ramesh Subramani and Wael Mamdouh and Monika M. Golas and Bjoern Sander and Holger Stark and Cristiano Luis Pinto Oliveira and Jan Skov Pedersen and Victoria Birkedal and Flemming Besenbacher and Kurt Vesterager Gothelf and J{\o}rgen Kjems},
The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a ‘bottom-up’ approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA ‘origami’ method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity… 
Self-assembly of three-dimensional nucleic acid nanostructures
This work addresses the challenges in structural DNA nanotechnology by developing a modular DNA "brick" approach that can self-assemble in a single-pot reaction to a prescribed 3D shape, and represents a simple, modular, and versatile method for 3D nanofabrication.
Engineering DNA self-assemblies as templates for functional nanostructures.
It is shown that DNA nanostructures can guide the assembly of achiral, spherical, metallic nanoparticles into nature-mimicking chiral geometries through hybridization between complementary DNA strands on the surface of nanoparticles and DNA scaffolds, to generate circular dichroism response in the visible light region.
Multilayer DNA origami packed on a square lattice.
A more compact design for 3D origami, with layers of helices packed on a square lattice that can be folded successfully into structures of designed dimensions in a one-step annealing process, despite the increased density of DNA helices.
Self-assembly of complex two-dimensional shapes from single-stranded DNA tiles.
Detailed protocols on how to fabricate sophisticated 2D shapes through the self-assembly of uniquely addressable single-stranded DNA tiles which act as molecular pixels on a molecular canvas are described.
Synergistic self-assembly of RNA and DNA molecules
A simple, general strategy for the de novo design of nanostructures in which the self-assembly of RNA strands is programmed by DNA strands to enable the integration of the precise programmability of DNA with the rich functionality of RNA.
Self-Assembled DNA Origami Templates for the Fabrication of Electronic Nanostructures
Self-Assembled DNA Origami Templates for the Fabrication of Electronic Nanostructures Elisabeth P. Gates Department of Chemistry and Biochemistry, BYU Doctor of Philosophy An important goal of
DNA Origami: Scaffolds for Creating Higher Order Structures.
This review provides a comprehensive survey of recent developments in DNA origami structure, design, assembly, and directed self-assembly, as well as its broad applications.
Bottom-Up Self-Assembly Based on DNA Nanotechnology
This review introduces three typical DNA self-assembly strategies in this field and highlights the significant progress of each.
Encapsulation of a gold nanoparticle in a DNA origami container
A ‘box-shaped’ three-dimensional (3D) DNA origami of ~40-nm dimensions was selectively formed by closing a symmetric open motif with three orthogonal faces by exploiting the flexibility at the hinge of an M13 scaffold.


Assembly and structural analysis of a covalently closed nano-scale DNA cage
The design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron that assembles from eight oligonucleotides with a yield of ∼30%.
Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
This work designs basic DNA building units in such a way that many copies of identical units assemble into larger three-dimensional structures, and tests this hierarchical self-assembly concept with DNA molecules that form three-point-star motifs, or tiles.
Reconfigurable, braced, three-dimensional DNA nanostructures.
This work demonstrates the operation of reconfigurable DNA tetrahedra whose shapes change precisely and reversibly in response to specific molecular signals.
DNA origami design of dolphin-shaped structures with flexible tails.
A user-friendly software package for designing DNA origami structures is presented and it is shown that the addition of specific attachment sites promotes dimerization between two independently self-assembled dolphin structures, and that these interactions stabilize the flexible tail.
A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron
The design and synthesis of a 1,669-nucleotide, single-stranded DNA molecule that is readily amplified by polymerases and that, in the presence of five 40-mer synthetic oligodeoxynucleotides, folds into an octahedron structure by a simple denaturation–renaturation procedure is reported.
An Overview of Structural DNA Nanotechnology
  • N. Seeman
  • Biology, Chemistry
    Molecular biotechnology
  • 2007
Structural DNA Nanotechnology uses unusual DNA motifs to build target shapes and arrangements, leading to branched systems with many strands and multiple helical domains and the use of periodic arrays.
Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding.
This work shows that distance-dependent multivalent binding effects can be systematically investigated by incorporating multiple-affinity ligands into DNA nanostructures with precise nanometre spatial control and illustrates the potential of using designer DNA nanoscaffolds to engineer more complex and interactive biomolecular networks.
Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication
A family of DNA tetrahedra, less than 10 nanometers on a side, that can self-assemble in seconds with near-quantitative yield of one diastereomer are reported that can be connected by programmable DNA linkers.
Operation of a DNA Robot Arm Inserted into a 2D DNA Crystalline Substrate
A cassette is developed that enables the placement of a robust, sequence-dependent DNA robot arm within a two-dimensional (2D) crystalline DNA array and is used to demonstrate that the rotary device is fully functional after insertion.
Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold.
Atomic force microscopy imaging reveals a dramatically improved yield of the AuNPs on DNA tile structure compared to the ensembles using monothiolate AuNP-DNA conjugates.