Self‐Assembly of a DNA Dodecahedron from 20 Trisoligonucleotides with C_3h Linkers

Abstract

Since Seemans pioneering work, [1a-c] DNA has been recognized as a building material for programmable hollow 3D nanoobjects. DNA nanoconstruction benefits from the structural rigidity of short DNA double strands, scalability, good accessibility of synthetic and chemically modified DNA, and the option for enzymatic amplification and processing. Four strategies for the construction of nanoobjects such as polyhedra exist so far. Strategy I is vertex-centered and goes from noncovalent junctions to covalent objects: Noncovalent three-way junctions are assembled from three linear oligonucleotides. Each arm contains a sticky end sequence which is hybridized to its complement in another junction and then covalently connected by DNA ligases.[1] Strategy II is the reverse of strategy I and makes use of trisoligonucleotides, in other words covalent junctions are noncovalently assembled to give the target nanoobjects.[2d, e] Non-natural modes of copying [2a] and amplifying [2b] were proposed to enable the replication of junctions and nanoconstructs from the latter.[2c]Strategy III is a face-centered approach, employing as many oligonucleotides as there are faces on the object while each oligonucleotide is composed of as many segments as there are edges surrounding the faces.[3a-d] Strategy IV first defines the longest path through the object by connecting all vertices using a very long DNA single strand; a set of shorter oligonucleotides generates suitable rigid motifs such as double crossovers, while additional connectivities are expressed by means of paranemic crossover motifs. [4] Recently the assembly of triangular prisms, cubes, pentameric and hexameric prisms, heteroprisms, and biprisms was reported. A set of single-stranded linear and cyclic DNA building blocks was used, and in the latter case rigid organic linker molecules were used as vertices.[5]Herein we report on a new generation of trisoligonucleotides and their employment in benchmark experiments to evaluate strategy II. We selected a dodecahedron, as polyhedra with a smaller number of vertices have been described already. [1][2][3][4][5] The feasibility of constructing a dodecahedron that reflects the basic symmetry of a virus was forseen for strategy III, [1d] but so far this has not been achieved by any strategy.Previously prepared trisoligonucleotides with three different arms were based on asymmetric linker constructs, [2a, e, f, 6] so that in principle a set of three different sequences could be connected in three different ways. Linker scaffolds with C 3h symmetry are thought to be advantageous because all vertices are expected to be subject to the same conformational constraints. Moreover, diastereomeric mixtures obtained by the utilization of commercially available racemic linker amidites [6b, 7] are avoided here. Until now trisoligonucleotides with C 3h linkers were synthesized by chemical copying of connectivity, that is the usage of a 3'-connected trisoligonucleotide template for the trislinking of suitable 5'-functionalized linear oligonucleo...

A synthetic icosahedral DNA-based host–cargo complex for functional in vivo imaging

“…Recently, bio-inspired peptide scaffolds, based on viral proteins that mimic naturally occurring hosts like viruses, have emerged as promising synthetic hosts 10 . Controlled oligomerization of DNA motifs into well-defined polyhedra enclosing well-defined cavities has been also recently demonstrated [11][12][13][14][15][16][17][18][19][20] . However, the potential of DNA polyhedra as synthetic molecular hosts for encapsulating functional cargo has remained unexplored, despite the internal cavity being utilizable [21][22][23] .…”

Conformational flexibility facilitates self-assembly of complex DNA nanostructures

“…DNA, in particular, shows great potential to be a superb molecular system (4). In the last 20 years, DNA has been explored as building blocks for nanoconstructions, including preparation of periodic and aperiodic 2D nanopatterns (5)(6)(7)(8) and 3D polyhedra (9)(10)(11)(12)(13)(14). Most of the branched DNA structures are intrinsically flexible and are not suitable building blocks for construction of well defined geometric structures.…”

Supramolecular Wireframe DNA Polyhedra: Assembly and Applications

“…[23] Kiedrowski et al developed a method to synthesize a trisoligonucleotide in which three distinct DNA single-strands were covalently linked to a C 3h -symmetric molecular linker. [24] Based on 20 different trisoligonucleotides, a DNA dodecahedron with double helix edges has been assembled. [24] The polyhedral structures with organic molecules as branch vertices should have improved stabilities in low salt buffers.…”

“…[24] Based on 20 different trisoligonucleotides, a DNA dodecahedron with double helix edges has been assembled. [24] The polyhedral structures with organic molecules as branch vertices should have improved stabilities in low salt buffers.…”