Two‐Dimensional Ketone‐Driven Metal–Organic Coordination on Cu(111)

Two‐dimensional metal–organic nanostructures based on the binding of ketone groups and metal atoms were fabricated by depositing pyrene‐4,5,9,10‐tetraone (PTO) molecules on a Cu(111) surface. The strongly electronegative ketone moieties bind to either copper adatoms from the substrate or codeposited iron atoms. In the former case, scanning tunnelling microscopy images reveal the development of an extended metal–organic supramolecular structure. Each copper adatom coordinates to two ketone ligands of two neighbouring PTO molecules, forming chains that are linked together into large islands through secondary van der Waals interactions. Deposition of iron atoms leads to a transformation of this assembly resulting from the substitution of the metal centres. Density functional theory calculations reveal that the driving force for the metal substitution is primarily determined by the strength of the ketone–metal bond, which is higher for Fe than for Cu. This second class of nanostructures displays a structural dependence on the rate of iron deposition.     

Photocontrolled DNA Origami Assembly by Using Two Photoswitches

Stimuli-responsive switching molecules have been widely investigated for the purpose of the mechanical control of biomolecules. Recently developed arylazopyrazole (AAP) shows photoisomerization activity, displaying a faster response to light-induced conformational changes and unique absorption spectral properties compared with those of conventionally used azobenzene. Herein, it is demonstrated that AAP can be used as a photoswitching molecule to control photoinduced assembly and disassembly of DNA origami nanostructures. An AAP-modified DNA origami has been designed and constructed. It is observed that the repeated assembly and disassembly of AAP-modified X-shaped DNA origami and hexagonal origami with complementary strands can be achieved by alternating UV and visible-light irradiation. Closed and linear assemblies of AAP-modified X-shaped origami were successfully formed by photoirradiation, and more than 1 μm linear assemblies were formed. Finally, it is shown that the two photoswitches, AAP and azobenzene, can be used in tandem to independently control different assembly configurations by using different irradiation wavelengths. AAP can extend the variety of available wavelengths of photoswitches and stably result in the assembly and disassembly of various DNA origami nanostructures.     

A Case Study of the Likes and Dislikes of DNA and RNA in Self‐Assembly

Programmed self‐assembly of nucleic acids (DNA and RNA) is an active research area as it promises a general approach for nanoconstruction. Whereas DNA self‐assembly has been extensively studied, RNA self‐assembly lags much behind. One strategy to boost RNA self‐assembly is to adapt the methods of DNA self‐assembly for RNA self‐assembly because of the chemical and structural similarities of DNA and RNA. However, these two types of molecules are still significantly different. To enable the rational design of RNA self‐assembly, a thorough examination of their likes and dislikes in programmed self‐assembly is needed. The current work begins to address this task. It was found that similar, two‐stranded motifs of RNA and DNA lead to similar, but clearly different nanostructures.     

Self‐Assembly of DNA–Oligo(p‐phenylene‐ethynylene) Hybrid Amphiphiles into Surface‐Engineered Vesicles with Enhanced Emission

Surface‐addressable nanostructures of linearly π‐conjugated molecules play a crucial role in the emerging field of nanoelectronics. Herein, by using DNA as the hydrophilic segment, we demonstrate a solid‐phase “click” chemistry approach for the synthesis of a series of DNA–chromophore hybrid amphiphiles and report their reversible self‐assembly into surface‐engineered vesicles with enhanced emission. DNA‐directed surface addressability of the vesicles was demonstrated through the integration of gold nanoparticles onto the surface of the vesicles by sequence‐specific DNA hybridization. This system could be converted to a supramolecular light‐harvesting antenna by integrating suitable FRET acceptors onto the surface of the nanostructures. The general nature of the synthesis, surface addressability, and biocompatibility of the resulting nanostructures offer great promises for nanoelectronics, energy, and biomedical applications.     

Synchronization of Two Assembly Processes To Build Responsive DNA Nanostructures

Herein, we report a strategy for the synchronization of two self‐assembly processes to assemble stimulus‐responsive DNA nanostructures under isothermal conditions. We hypothesized that two independent assembly processes, when brought into proximity in space, could be synchronized and would exhibit positive synergy. To demonstrate this strategy, we assembled a ladderlike DNA nanostructure and a ringlike DNA nanostructure through two hybridization chain reactions (HCRs) and an HCR in combination with T‐junction cohesion, respectively. Such proximity‐induced synchronization adds a new element to the tool box of DNA nanotechnology. We believe that it will be a useful approach for the assembly of complex and responsive nanostructures.     

Metal–DNA Coordination-Driven Self-Assembly: A Conceptual Methodology to Expand the Repertoire of DNA Nanobiotechnology

The past several decades have witnessed a rapid revolution of DNA nanotechnology. DNA nanostructures are mainly synthesized with two approaches, by assembly of purely DNA-based nanostructures through complementary base pairing or grafting DNA onto nanoparticles (NPs). Despite the progress made, developing simple and universal methods for the synthesis of DNA nanoarchitectures with specific morphologies and functionalities is still a challenge. This article introduces the reader to a new biomimetic methodology that leads to the controlled synthesis of DNA nanoarchitectures based on metal–DNA coordination chemistry and, furthermore, demonstrates the broad biomedical applications of these functional materials. In particular, we highlight the coordination-driven 1) surface-functionalization of NPs with DNA molecules and 2) direct self-assembly of metal–DNA nanostructures. Finally, challenges and opportunities of this approach to develop nanobiotechnology are provided.     

DNA-templated three-branched nanostructures for nanoelectronic devices

Three-branched DNA molecules have been designed and assembled from oligonucleotide components. These nucleic acid constructs contain double- and single-stranded regions that control the hybridization behavior of the assembly. Specific localization of a single streptavidin molecule at the center of the DNA complex has been investigated as a model system for the directed placement of nanostructures. Highly selective silver and copper metallization of the DNA template has also been characterized. Specific hybridization of these DNA complexes to oligonucleotide-coupled nanostructures followed by metallization should provide a bottom-up self-assembly route for the fabrication and characterization of discrete three-terminal nanodevices.     

Small molecule self‐assembly in polymer matrices

Using small molecules in polymer matrices is common in applications such as (i) plasticizing polymers to modify the glass transition and mechanical properties and (ii) dispersion of photoactive or electroactive small molecules in polymer matrices in organic‐electronic devices Aggregation of these small molecules and phase separation leading to crystallization often cannot be morphologically controlled. If these are designed with self‐assembling codes such as hydrogen bonding or aromatic interactions, their phase separation behavior would be distinctly different. This review summarizes the studies on morphologies in such situations, such as (i) sub‐surface assembly in polymer matrices, (ii) controlled polymerization‐induced phase separation to create polymer blends, (iii) using the polymer to direct the assembly of small molecules in liquid crystalline devices, (iv) functionalizing a polymer with self‐assembling small molecules to cause organo‐gelation which the polymer itself would not by itself, and (v) using such systems as templates to create porous polymer structures. Organic–inorganic hybrids using polymers as templates for nanostructures and imprinted porous membranes is an emerging area. Since self‐assembly is one of the dominating area of research with respect to both small molecules, polymers as well as the combination of the two, this review summarizes the studies on the aforementioned topics. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 451–478     

Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures.     

Self‐Assembly of Wireframe DNA Nanostructures from Junction Motifs

Wireframe frameworks have been investigated for the construction of complex nanostructures from a scaffolded DNA origami approach; however, a similar framework is yet to be fully explored in a scaffold‐free “LEGO” approach. Herein, we describe a general design scheme to construct wireframe DNA nanostructures entirely from short synthetic strands. A typical edge of the resulting structures in this study is composed of two parallel duplexes with crossovers on both ends, and three, four, or five edges radiate out from a certain vertex. By using such a self‐assembly scheme, we produced planar lattices and polyhedral objects.     

Reconfigurable Bioinspired Framework Nucleic Acid Nanoplatform Dynamically Manipulated in Living Cells for Subcellular Imaging

In nature, the formation of spider silk fibers begins with dimerizing the pH‐sensitive N‐terminal domains of silk proteins (spidroins) upon lowering pH, and provides a natural masterpiece for programmable assembly. Inspired by the similarity of pH‐dependent dimerization behaviors, introduced here is an i‐motif‐guided model to mimic the initial step of spidroin assembly at the subcellular level. A framework nucleic acid (FNA) nanoplatform is designed using two tetrahedral DNA nanostructures (TDNs) with different branched vertexes carrying a bimolecular i‐motif and a split ATP aptamer. Once TDNs enter acidic lysosomes within living cells, they assemble into a heterodimeric architecture, thereby enabling the formation of a larger‐size framework and meanwhile subcellular imaging in response to endogenous ATP, which can be dynamically manipulated by adjusting intracellular pH and ATP levels with external drug stimuli.     

Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.     

The Assembly of Supramolecular Boxes and Coordination Polymers Based on Bis‐Zinc‐Salphen Building Blocks

We report the assembly of supramolecular boxes and coordination polymers based on a rigid bis‐zinc(II)‐salphen complex and various ditopic nitrogen ligands. The use of the bis‐zinc(II)‐salphen building block in combination with small ditopic nitrogen ligands gave organic coordination polymers both in solution as well as in the solid state. Molecular modeling shows that supramolecular boxes with small internal cavities can be formed. However, the inability to accommodate solvent molecules (such as toluene) in these cavities explains why coordination polymers are prevailing over well‐defined boxes, as it would lead to an energetically unfavorable vacuum. In contrast, for relatively longer ditopic nitrogen ligands, we observed the selective formation of supramolecular box assemblies in all cases studied. The approach can be easily extended to chiral analogues by using chiral ditopic nitrogen ligands.     

“Precipitation on Nanoparticles”: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles

Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self‐assembled monolayers obtained by co‐adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on‐nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well‐defined hybrid organic–inorganic nanostructures.     

DNA nanostructures as models for evaluating the role of enthalpy and entropy in polyvalent binding

DNA nanotechnology allows the design and construction of nanoscale objects that have finely tuned dimensions, orientation, and structure with remarkable ease and convenience. Synthetic DNA nanostructures can be precisely engineered to model a variety of molecules and systems, providing the opportunity to probe very subtle biophysical phenomena. In this study, several such synthetic DNA nanostructures were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility, will affect their association equilibrium. This approach has yielded a quantitative identification of the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect.     

In situ Surface Charge Density Visualization of Self-assembled DNA Nanostructures after Ion Exchange

The charge density of DNA is a key parameter in strand hybridization and for the interactions occurring between DNA and molecules in biological systems. Due to the intricate structure of DNA, visualization of the surface charge density of DNA nanostructures under physiological conditions was not previously possible. Here, we perform a simultaneous analysis of the topography and surface charge density of DNA nanostructures using atomic force microscopy and scanning ion conductance microscopy. The effect of in situ ion exchange using various alkali metal ions is tested with respect to the adsorption of DNA origami onto mica, and a quantitative study of surface charge density reveals ion exchange phenomena in mica as a key parameter in DNA adsorption. This is important for structure-function studies of DNA nanostructures. The research provides an efficient approach to study surface charge density of DNA origami nanostructures and other biological molecules at a single molecule level.     

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site-specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.     

NMR in paramagnetic complexes of radicals with organic ligands. II. Method of identification of electronic structure of complexes — Theory

A method of identification of the electronic structure of stable nitroxide radical complexes with organic ligands is developed. The idea of this approach is that the concentration dependences of the paramagnetic shifts and line widths of the NMR spectra of two ligands in solution depend on whether these ligands form complexes with the same radical orbital or with different orbitals. In the latter case the complexation of one ligand should not influence the paramagnetic shift and line broadening of another ligand molecule present in the solution. In contrast, in the former case such influence should exist since both ligands are in competition. On this basis different schemes of complexation are considered and theoretical expressions for paramagnetic shifts and line widths are derived that show what kind of experimental data is required to identify the structure of the complex. The theory developed can be generalized to other paramagnetic complexes of radicals, ions and molecules.     

pH-Responsive Reversible DNA Self-assembly Mediated by Zwitterion

pH-Responsive DNA assembles have drawn growing attentions owing to their great potential in diverse areas.However,pH-responsive motifs are limited to specific DNA sequences and annealing is usually needed for DNA assemblies;therefore,sequence-independent pH-responsive DNA assembly at room temperature is highly desired as a more general way.Here,we propose a reversible pH-responsive DNA assembly strategy at room-temperature using zwitterion,glycine betaine(GB),as charge-regulation molecules.The reversible assembly and disassembly of DNA nanostructures could be achieved by alternatively regulating the acidic and basic environments in the presence of GB,respectively.In an acidic environment,carboxylate group in GB was protonated and GB was positively charged,which facilitated to shield the inherent electrostatic repulsion of DNA strands.Molecular simulation showed that the newly formed carboxyl group in protonated GB could form hydrogen bonds with bases in DNA to promote the assembly of DNA strands.In a basic solution,carboxylate group in GB was deprotonated and GB was neutral,thus inducing the dissociation of DNA assembly.     

Designed Intercalators for Modification of DNA Origami Surface Properties

The modification of the backbone properties of DNA origami nanostructures through noncovalent interactions with designed intercalators, based on acridine derivatized with side chains containing esterified fatty acids or oligo(ethylene glycol) residues is reported. Spectroscopic analyses indicate that these intercalators bind to DNA origami structures. Atomic force microscopy studies reveal that intercalator binding does not affect the structural intactness but leads to altered surface properties of the highly negatively charged nanostructures, as demonstrated by their interaction with solid mica or graphite supports. Moreover, the noncovalent interaction between the intercalators and the origami structures leads to alteration in cellular uptake, as shown by confocal microscopy studies using two different eukaryotic cell lines. Hence, the intercalator approach offers a potential means for tailoring the surface properties of DNA nanostructures.