Backbone-branched DNA building blocks for facile angular control in nanostructures

Chemically Conjugated Branched Staples for Super-DNA Origami

DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.

Multidimensional Honeycomb-like DNA Nanostructures Made of C-Motifs

Thanks to its remarkable properties of self-assembly and molecular recognition, DNA can be used in the construction of various dimensional nanostructures to serve as templates for decorating nanomaterials with nanometer-scale precision. Accordingly, this study discusses a design strategy for fabricating such multidimensional DNA nanostructures made of simple C-motifs. One-dimensional (1D) honeycomb-like tubes (1HTs) and two-dimensional (2D) honeycomb-like lattices (2HLs) were constructed using a C-motif with an arm length of 14 nucleotides (nt) at an angle of 240° along the counterclockwise direction. We designed and fabricated four different types of 1HTs and three different 2HLs. The study used atomic force microscopy to characterize the distinct topologies of the 1D and 2D DNA nanostructures (i.e., 1HTs and 2HLs, respectively). The width deviation of the 1HTs and height suppression percentage of the 2HLs were calculated and discussed. Our study can be provided to construct various dimensional DNA nanostructures easily with high efficiency.

A covalently conjugated branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery

Targeted delivery of therapeutic drugs is essential for precise treatment of various diseases to reduce possible serious side-effects. A screened DNA aptamer has been widely developed for active targeting delivery. Herein, we report a facile strategy for the construction of a branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery. In our design, the terminal-modified DNA aptamer can be covalently conjugated to form a branched aptamer cluster by click reaction easily. The branched aptamer cluster-modified DNA tetrahedron (TET) demonstrates highly targeted cellular uptake with the modification of only one site. After loading the chemotherapeutic drug (doxorubicin, DOX), the DNA aptamer cluster-based nanoplatform elicits a remarkable and selective inhibition of tumor cell proliferation by much-enhanced targeted delivery. This covalently conjugated branched DNA aptamer cluster-based nanoplatform provides a new strategy for the development of targeted drug delivery.

Enhanced Immunostimulatory Activity of Covalent DNA Dendrons

The present study focused on the design and synthesis of covalent DNA dendrons bearing multivalent cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODNs) that can stimulate the immune system through the activation of TLR9. These dendrons were synthesized using branching trebler phosphoramidite containing three identical protecting groups that enabled the simultaneous synthesis of multiple strands on a single molecule. Compared with linear ODNs, covalent DNA dendrons were found to be more resistant to nuclease degradation and were more efficiently taken up by macrophage-like RAW264.7 cells. Cellular uptake was suggested to be mediated by macrophage scavenger receptors. The covalent DNA dendrons composed of multivalent immunostimulatory branches enhanced the secretion of proinflammatory cytokines TNF-α and IL-6 from RAW264.7 cells, and 9-branched DNA dendrons showed the highest enhancement. Given their enhanced efficacy, we expect covalent DNA dendrons to be useful structures of oligonucleotide medicines.

Hierarchical Assembly of Super-DNA Origami Based on a Flexible and Covalent-Bound Branched DNA Structure

DNA origami technique provides a programmable way to construct nanostructures with arbitrary shapes. The dimension of assembled DNA origami, however, is usually limited by the length of the scaffold strand. Herein, we report a general strategy to efficiently organize multiple DNA origami tiles to form super-DNA origami using a flexible and covalent-bound branched DNA structure. In our design, the branched DNA structures (B_n: with a certain number of 2-6 branches) are synthesized by a copper-free click reaction. Equilateral triangular DNA origamis with different numbers of capture strands (T_n: T₁, T₂, and T₃) are constructed as the coassembly tiles. After hybridization with the branched DNA structures, the super-DNA origami (up to 13 tiles) can be efficiently ordered in the predesigned patterns. Compared with traditional DNA junctions (J_n: J₂-J₆, as control groups) assembled by base pairing between several DNA strands, a higher yield and more compact structures are obtained using our strategy. The highly ordered and discrete DNA origamis can further precisely organize gold nanoparticles into different patterns. This rationally developed DNA origami ordering strategy based on the flexible and covalent-bound branched DNA structure presents a new avenue for the construction of sophisticated DNA architectures with larger molecular weights.

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures

Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.

Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite

Branched DNAs (bDNAs) having comb-like structures have found wide utility in molecular diagnostics and DNA nanotechnology. bDNAs can be generated either by designing and assembling linear DNA molecules into rigid non-covalent structures or by using an orthogonally protected branching unit to synthesize covalently linked structures. Despite the advantages of the covalently linked structures, use of this motif has been hampered by the challenging synthesis of appropriately protected branching monomers. We report the facile synthesis of a branching monomer having orthogonal DMT and Lev protecting groups using readily available δ-velarolactone and 1,3-diaminopropan-2-ol. Using this branching monomer, a comb-shaped bDNA was synthesized having three different DNA arms. The synthesis and hybridization capability of the bDNA was assessed by fluorescence microscopy using fluorescently labeled complementary and mismatched DNA probes. Convenient access to an orthogonally protected branching monomer is anticipated to accelerate applications of bDNAs in applications including diagnostics, biosensing, gene-profiling, DNA computing, multicolor imaging, and nanotechnology.

Click-based functionalization of a 2'-O-propargyl-modified branched DNA nanostructure

DNA has emerged as a versatile building block for programmable self-assembly. DNA-based nanostructures have been widely applied in biosensing, bioimaging, drug delivery, molecular computation and macromolecular scaffolding. A variety of strategies have been developed to functionalize these nanostructures. In this study, we report a facile click-based strategy to incorporate a metal chelating ligand and a fluorescent tag into a three-point-star DNA tile containing 2'-O-propargyl groups. Such a strategy opens up the possibility of functionalizing pre-assembled DNA strands to construct platforms for metal or drug delivery.

Pseudo-Ligandless Click Chemistry for Oligonucleotide Conjugation

Particularly for its use in bioconjugations, the copper-catalyzed (or copper-promoted) azide-alkyne cycloaddition (CuAAC) reaction or 'click chemistry', has become an essential component of the modern chemical biologist's toolbox. Click chemistry has been applied to DNA, and more recently, RNA conjugations, and the protocols presented here can be used for either. The reaction can be carried out in aqueous buffer, and uses acetonitrile as a minor co-solvent that serves as a ligand to stabilize the copper. The method also includes details on the analysis of the reaction product. © 2016 by John Wiley & Sons, Inc.

Flexibility of C3h -Symmetrical Linkers in Tris-oligonucleotide-Based Tetrahedral Scaffolds

Flexibility of tris-oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris-oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C3h -symmetrical linker core at these chains. Four tris-oligonucleotides hybridise into a tetrahedral nanocage by sequence-determined self-assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris-oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene-chain linkers were too rigid. Tris-oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate-based linkers was established.

Nucleotidyl transferase assisted DNA labeling with different click chemistries

Here, we present a simple, modular and efficient strategy that allows the 3′-terminal labeling of DNA, regardless of whether it has been chemically or enzymatically synthesized or isolated from natural sources. We first incorporate a range of modified nucleotides at the 3′-terminus, using terminal deoxynucleotidyl transferase. In the second step, we convert the incorporated nucleotides, using either of four highly efficient click chemistry-type reactions, namely copper-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, Staudinger ligation or Diels-Alder reaction with inverse electron demand. Moreover, we create internal modifications, making use of either ligation or primer extension, after the nucleotidyl transferase step, prior to the click reaction. We further study the influence of linker variants on the reactivity of azides in different click reactions. We find that different click reactions exhibit distinct substrate preferences, a fact that is often overlooked, but should be considered when labeling oligonucleotides or other biomolecules with click chemistry. Finally, our findings allowed us to extend our previously published RNA labeling strategy to the use of a different copper-free click chemistry, namely the Staudinger ligation.