Directed Assembly of Nucleic Acid-Based Polymeric Nanoparticles from Molecular Tetravalent Cores

From Structure to Application: The Evolutionary Trajectory of Spherical Nucleic Acids

Since the proposal of the concept of spherical nucleic acids (SNAs) in 1996, numerous studies have focused on this topic and have achieved great advances. As a new delivery system for nucleic acids, SNAs have advantages over conventional deoxyribonucleic acid (DNA) nanostructures, including independence from transfection reagents, tolerance to nucleases, and lower immune reactions. The flexible structure of SNAs proves that various inorganic or organic materials can be used as the core, and different types of nucleic acids can be conjugated to realize diverse functions and achieve surprising and exciting outcomes. The special DNA nanostructures have been employed for immunomodulation, gene regulation, drug delivery, biosensing, and bioimaging. Despite the lack of rational design strategies, potential cytotoxicity, and structural defects of this technology, various successful examples demonstrate the bright and convincing future of SNAs in fields such as new materials, clinical practice, and pharmacy.

Efficient one-pot assembly of higher-order DNA nanostructures by chemically conjugated branched DNA

Chemically conjugated branched DNA was successfully synthesized by a copper-free click reaction to construct sophisticated and higher-order polyhedral DNA nanostructures with pre-defined units in one pot, which can be used as an efficient nanoplatform to precisely organize multiple gold nanoparticles in predesigned patterns.

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.

Original Synthesis of a Nucleolipid for Preparation of Vesicular Spherical Nucleic Acids

Spherical nucleic acids (SNAs)-nanostructures, consisting of a nanoparticle core densely functionalized with a shell of short oligonucleotide strands-are a rapidly emerging class of nanoparticle-based therapeutics with unique properties and specific applications as drug and nucleic acid delivery and gene regulation materials. In this contribution, we report on the preparation of hollow SNA nanoconstructs by co-assembly of an originally synthesized nucleolipid-a hybrid biomacromolecule, composed of a lipidic residue, covalently linked to a DNA oligonucleotide strand-with other lipids. The nucleolipid was synthesized via a click chemistry approach employing initiator-free, UV light-induced thiol-ene coupling of appropriately functionalized intermediates, performed in mild conditions using a custom-made UV light-emitting device. The SNA nanoconstructs were of a vesicular structure consisting of a self-closed bilayer membrane in which the nucleolipid was intercalated via its lipid-mimetic residue. They were in the lower nanometer size range, moderately negatively charged, and were found to carry thousands of oligonucleotide strands per particle, corresponding to a grafting density comparable to that of other SNA structures. The surface density of the strands on the bilayer implied that they adopted an unextended conformation. We demonstrated that preformed vesicular structures could be successfully loaded with either hydrophilic or hydrophobic dyes.

Hollow spherical nucleic acid structures based on polymer-coated phospholipid vesicles

A feasible one pot synthesis of hollow spherical nucleic acids (SNAs) using phospholipid liposomes is reported. These constructs are synthesized in a chemically straightforward process involving formation of unilamellar liposomes, coating the liposomes with a thin cross-linked polymeric layer, and grafting the latter with short (about 20 bases) DNA oligonucleotide strands. They consist of vesicular cores, composed of readily available phospholipid (1,2-dipalmitoyl-sn-glycero-phosphocholine), whereas the strands are deliberately arranged on the surface of the vesicular entities. The initial vesicular structure and morphology are preserved during the coating and grafting reactions. The novel hollow/vesicular SNAs are characterized with a hydrodynamic radius and radius of gyration of 78.3 and 88.5 nm, respectively, and moderately negative (-14.2 mV) ζ potential. They carry thousands (5868) of oligonucleotide strands per vesicle, which are not strongly radially oriented and adopt an unextended conformation as anticipated from the smaller value of the grafting density compared to the critical grafting density at the transition to brush conformation. The constructs are practically devoid of toxicity and exhibit high binding affinity to complementary nucleic acids. Unlike any other nucleic acid structural motif, they cross the cell membrane and enter cells without the need of transfection agents.

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.

Amplification of the Fluorescence Signal with Clustered Regularly Interspaced Short Palindromic Repeats-Cas12a Based on Au Nanoparticle-DNAzyme Probe and On-Site Detection of Pb2+ Via the Photonic Crystal Chip

Although great headway has been made in DNAzyme-based detection of Pb²⁺, its adaptability, sensitivity, and accessibility in complex media still need to be improved. For this, we introduce new ways to surmount these hurdles. First, a spherical nucleic acid (SNA) fluorescence probe (Au nanoparticles-DNAzyme probe) is utilized to specifically identify Pb²⁺ and its suitability for precise detection of Pb²⁺ in complex samples due to its excellent nuclease resistance. Second, the sensitivity of Pb²⁺ detection is greatly enhanced via the use of a clustered regularly interspaced short palindromic repeats-Cas12a with target recognition accuracy to amplify the fluorescent signal upon the trans cleavage of the SNA (signal probe), and the limit of detection reaches as low as 86 fM. Third, we boost the fluorescence on photonic crystal chips with a bionic periodic arrangement by employing a straightforward detection device (smartphone and portable UV lamp) to achieve on-site detection of Pb²⁺ with the limit of detection as low as 24 pM. Based on the abovementioned efforts, the modified Pb²⁺ fluorescence sensor has the advantages of higher sensitivity, better specificity, accessibility, less sample consumption, and so forth. Moreover, it can be applied to accurately detect Pb²⁺ in complex biological or environmental samples, which is of great promise for widespread applications.

Chemically Modified DNA Nanostructures for Drug Delivery

Based on predictable, complementary base pairing, DNA can be artificially pre-designed into versatile DNA nanostructures of well-defined shapes and sizes. With excellent addressability and biocompatibility, DNA nanostructures have been widely employed in biomedical research, such as bio-sensing, bio-imaging, and drug delivery. With the development of the chemical biology of nucleic acid, chemically modified nucleic acids are also gradually developed to construct multifunctional DNA nanostructures. In this review, we summarize the recent progress in the construction and functionalization of chemically modified DNA nanostructures. Their applications in the delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted. Furthermore, the remaining challenges and future prospects in drug delivery by chemically modified DNA nanostructures are discussed.

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With excellent addressability and biocompatibility, DNA nanostructures are promising candidates for bio-sensing, bio-imaging, and drug delivery

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The recent progress in chemical modifications of DNA nanostructures is summarized

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Chemically modified DNA nanostructures for efficient delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted

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Challenges and prospects of future development toward chemically modified DNA nanostructures for drug delivery are discussed

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.

Chemotherapeutic drug-DNA hybrid nanostructures for anti-tumor therapy

Compared to traditional drug delivery systems, DNA nanostructure-based drug delivery systems have several advantages including programmable sequences, precise size and shape, high drug payloads, excellent biocompatibility and biodegradability. To date, a wide range of chemotherapeutic drug-DNA hybrid nanostructures have been developed for anti-tumor therapy. In this review, the constructions of various DNA nanostructures for anticancer drug delivery are firstly summarized. Next, the anticancer drug loading methods for DNA nanostructures are presented. Then, the recent applications of chemotherapeutic drug-DNA hybrid nanostructures for drug delivery are highlighted. In the end, the challenges and opportunities of the chemotherapeutic drug-DNA hybrid nanostructure-based delivery system are discussed. The designs of drug-DNA hybrid systems, including the constructions of nanostructures and the strategies for drug loading, largely influence the efficiency of drug delivery. Recent studies have focused on the development of novel drug-DNA hybrid systems to acquire more precise and efficient therapy for various diseases. A systematic review of the design strategies of chemotherapeutic drug-DNA hybrid nanostructures will benefit the innovation and development of the chemotherapeutic drug-based chemotherapy in clinics.

One-pot synthesis of oligonucleotide-grafted polymeric nanoparticles

A feasible one-pot approach for constructing oligonucleotide-grafted polymeric nanoparticles is reported. The approach involves formation of mesoglobules from a thermoresponsive polymer, coating of the mesoglobules with a cross-linked polymeric shell, and grafting the latter with oligonucleotide strands. Dynamic and static light scattering are used to parameterize the novel constructs. They are relatively large structures with hydrodynamic radii and molar masses reaching 200 nm and 150.0 × 10⁶ g mol^-1, respectively. The oligonucleotide-grafted polymeric nanoparticles are of spherical morphology and moderately negative (-12.4 to -19.1 mV) ζ potential as revealed by AFM, TEM, and electrophoretic light scattering. In accordance with their large size, they are found to carry thousands of oligonucleotide strands per particle. The novel constructs are thermoresponsive. They undergo reversible collapse upon heating and swelling upon cooling, which is associated with changes in the grafting density and, hence, the conformation of the oligonucleotide strands from unextended at room temperature to a more extended one at elevated temperatures. The versatility of the approach is demonstrated by varying the type of the cross-linked shell and content of the oligonucleotide strands and, hence, the grafting density. Appropriate diversification and modifications are suggested as well.

Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein

By combining both chemical and enzymatic ligation with procedures guiding the self-assembly of nanotubular tobacco mosaic virus (TMV)-like particles (TLPs), novel nucleoprotein structures based on DNA-terminated branching elements, RNA scaffolds and TMV coat protein (CP) are made accessible. Tetrahedral tetrakis(hydroxybiphenyl)adamantane cores with four 5'-phosphorylated dinucleotide arms were coupled to DNA linkers by chemical ligation. The resulting three-dimensional (3D) branching elements were enzymatically ligated to the 3' termini of RNA scaffolds either prior to or after the RNAs' incorporation into TLPs. Thus, architectures with interconnected nanotube domains in two different length classes were generated, each containing 70 CP subunits per 10 nm length. Short TMV origin-of-assembly-containing RNA scaffolds ligated to the DNA allowed the growth of protein-coated 34 nm tubes on the terminal RNA strands in situ. Alternatively, 290 nm pre-fabricated tubes with accessible RNA 3' termini, attained by DNA blocking elements hybridized to the RNAs, were ligated with the branched cores. Both approaches resulted in four-armed nanoobjects, demonstrating a so far unique combination of organic synthesis of branching elements, enzymatic modifications, nucleic acid-based scaffolding and RNA-guided and DNA-controlled assembly of tubular RNA-encapsidating protein domains, yielding a novel class of 3D nucleoprotein architectures with polyvalent protein elements. In the long term, the production route might give rise to supramolecular systems with complex functionalities, installed via the orthogonal coupling of effector molecules to TLP domains.

Construction and structure studies of DNA-bipyridine complexes as versatile scaffolds for site-specific incorporation of metal ions into DNA

The facile construction of metal-DNA complexes using 'Click' reactions is reported here. A series of 2'-propargyl-modified DNA oligonucleotides were initially synthesized as structure scaffolds and were then modified through 'Click' reaction to incorporate a bipyridine ligand equipped with an azido group. These metal chelating ligands can be placed in the DNA context in site-specific fashion to provide versatile templates for binding various metal ions, which are exchangeable using a simple EDTA washing-and-filtration step. The constructed metal-DNA complexes were found to be thermally stable. Their structures were explored by solving a crystal structure of a propargyl-modified DNA duplex and installing the bipyridine ligands by molecular modeling and simulation. These metal-DNA complexes could have wide applications as novel organometallic catalysts, artificial ribonucleases, and potential metal delivery systems.

The competing effects of core rigidity and linker flexibility in the nanoassembly of trivalent small molecule-DNA hybrids (SMDH3s)-a synergistic experimental-modeling study

The nanoassembly behavior of trivalent small molecule-DNA hybrids (SMDH3s) was investigated as a function of core geometry and supramolecular flexibility through a synergistic experimental-modeling study. While complementary SMDH3s possessing a highly flexible tetrahedral trivalent core primarily assemble into nanoscale caged dimers, the nanoassemblies of SMDH3 comonomers with rigid pyramidal and trigonal cores yield fewer caged dimers and more large-oligomer networks. Specifically, the rigid pyramidal SMDH3 comonomers tend to form smaller nanosized aggregates (dimers, tetramers, and hexamers) upon assembly, attributable to the small (<109°) branch-core-branch angle of the pyramidal core. In contrast, the more-rigid trigonal planar SMDH3 comonomers have a larger (∼120°) branch-core-branch angle, which spaces their DNA arms farther apart, facilitating the formation of larger nanoassemblies (≥nonamers). The population distributions of these nanoassemblies were successfully captured by coarse-grained molecular dynamics (CGMD) simulations over a broad range of DNA concentrations. CGMD simulations can also forecast the effect of incorporating Tn spacer units between the hydridizing DNA arms and the rigid organic cores to increase the overall flexibility of the SMDH3 comonomers. Such "decoupling" of the DNA arms from the organic core was found to result in preferential formation of nanoscale dimers up to an optimal spacer length, beyond which network formation takes over due to entropic factors. This excellent agreement between the simulation and experimental results confirms the versatility of the CGMD model as a useful and reliable tool for elucidating the nanoassembly of SMDH-based building blocks.

Nanoparticle-Programmed Surface for Drug Release and Cell Regulation via Reversible Hybridization Reaction

A surface directly connects the bulk of a material to its surroundings. The ability to dynamically regulate the surface without affecting the bulk of a material holds great potential for new applications. The purpose of this work was to demonstrate that the surface can be dynamically changed using nanoparticles and oligonucleotides (ODNs) in a reversible and reiterative manner. A dual-functional nanogel was synthesized as the model of nanoparticles using miniemulsion polymerization and click chemistry. The nanogel can not only adsorb drugs for sustained drug release but also bind a surface functionalized with complementary ODNs. Importantly, hybridization reaction and ODN degradation can drive reversible and reiterative nanogel binding to the surface for dynamic change, which in principle is unlimited. Moreover, nanogel-mediated dynamic change offers the surface with the drug-releasing function for inhibiting the growth of surrounding cells. Because nanogels can be replaced by any functional nanoparticles with a diverse array of properties, nanoparticle-programmed surface change constitutes a promising platform for various applications such as drug delivery and stent implantation.

DNA micelles as nanoreactors: efficient DNA functionalization with hydrophobic organic molecules

We report a micelle-templated method to enhance the reactivity of DNA with highly hydrophobic molecules. Lipids, chromophores and polymers can be conjugated to DNA in high yield and under mild conditions. This method expands the range of DNA-templated reactions for DNA-encoded libraries, oligonucleotide and drug delivery, nanopore mimetics and DNA nanotechnology.

Branch-PCR Constructed Stable shRNA Transcription Nanoparticles Have Long-Lasting RNAi Effect

RNA interference (RNAi) is a cellular process for gene silencing. Because of poor serum stability, transferring dsRNA directly into the target cells is a challenge. We report a facile and universal strategy to construct short hairpin RNA (shRNA) transcription nanoparticles with multiple shRNA transcription templates by PCR with flexible branched primers (branch-PCR). Compared with conventional linear shRNA transcription templates, these shRNA transcription nanoparticles show excellent stability against digestion by exonuclease III. Importantly, we found that our highly stable shRNA transcription nanoparticles can also be transcribed and thus induce efficient and long-lasting RNAi with picomolar activity in living mammalian cells. These chemically well-defined branch-PCR-generated stable shRNA transcription nanoparticles might facilitate RNAi delivery with a long-lasting RNAi effects.

A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra

A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures.

Smart Magnetic Nanosensors Synthesized through Layer-by-Layer Deposition of Molecular Beacons for Noninvasive and Longitudinal Monitoring of Cellular mRNA

Noninvasive and longitudinal monitoring of gene expression in living cells is essential for understanding and monitoring cellular activities. Herein, a smart magnetic nanosensor is constructed for the real-time, noninvasive, and longitudinal monitoring of cellular mRNA expression through the layer-by-layer deposition of molecular beacons (MBs) and polyethylenimine on the iron oxide nanoparticles. The loading of MBs, responsible for the signal intensity and the tracking time, was easily tuned with the number of layers incorporated. The idea was first demonstrated with the magnetic nanosensors for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA, which was efficiently internalized into the cells under the influence of magnetic field. This nanosensor allowed the continuous monitoring of the cellular GAPDH mRNA expression for 1 month. Then this platform was further utilized to incorporate two kinds of MBs for alkaline phosphatase (ALP) and GAPDH mRNAs, respectively. The multifunctional nanosensors permitted the simultaneous monitoring of the reference gene (GAPDH mRNA) and the early osteogenic differentiation marker (ALP mRNA) expression. When the fluorescence signal ratio between ALP mRNA MBs and GAPDH mRNA MBs was taken, the dynamic osteogenic differentiation process of MSCs was accurately monitored.

Effects of Complementary DNA and Salt on the Thermoresponsiveness of Poly(N-isopropylacrylamide)-b-DNA

The thermoresponsive structural transition of poly(N-isopropylacrylamide) (PNIPAAm)-b-DNA copolymers was explored. Molecular assembly of the block copolymers was facilitated by adding salt, and this assembly was not nucleated by the association between DNA strands but by the coil-globule transition of PNIPAAm blocks. Below the lower critical solution temperature (LCST) of PNIPAAm, the copolymer solution remained transparent even at high salt concentrations, regardless of whether DNA was hybridized with its complementary partner to form a double-strand (or single-strand) structure. At the LCST, the hybridized copolymer assembled in spherical nanoparticles, surrounded by double-stranded DNA; subsequently, the non-cross-linking aggregation occurred, while the nanoparticles were dispersed if the salt concentration was low or DNA blocks were unhybridized. When the DNA duplex was denatured to a single-stranded state by heating, the aggregated nanoparticles redispersed owing to the recovery of the steric repulsion of the DNA strands. The changes in the steric and electrostatic effects by hybridization and the addition of salt did not result in any specific attraction between DNA strands but merely decreased the repulsive interactions. The van der Waals attraction between the nanoparticles overcame such repulsive interactions so that the non-cross-linking aggregation of the micellar particles was mediated.