DNA‐Tile‐Directed Self‐Assembly of Quantum Dots into Two‐Dimensional Nanopatterns

Self-Assembly of Semiconductor Quantum Dots using Organic Templates

Colloidal semiconductor nanocrystals, known as quantum dots (QDs), are regarded as brightly photoluminescent nanomaterials possessing outstanding photophysical properties, such as high photodurability and tunable absorption and emission wavelengths. Therefore, QDs have great potential for a wide range of applications, such as in photoluminescent materials, biosensors and photovoltaic devices. Since the development of synthetic methods for accessing high-quality QDs with uniform morphology and size, various types of QDs have been designed and synthesized, and their photophysical properties dispersed in solutions and at the single QD level have been reported in detail. In contrast to dispersed QDs, the photophysical properties of assembled QDs have not been revealed, although the structures of the self-assemblies are closely related to the device performance of the solid-state QDs. Therefore, creating and controlling the self-assembly of QDs into well-defined nanostructures is crucial but remains challenging. In this Minireview, we discuss the notable examples of assembled QDs such as dimers, trimers and extended QD assemblies achieved using organic templates. This Minireview should facilitate future advancements in materials science related to the assembled QDs.

DNA Nanoribbon-Templated Self-Assembly of Ultrasmall Fluorescent Copper Nanoclusters with Enhanced Luminescence

Fluorescent copper nanoclusters (CuNCs) have been widely used in chemical sensors, biological imaging, and light-emitting devices. However, individual fluorescent CuNCs have limitations in their capabilities arising from poor photostability and weak emission intensities. As one kind of aggregation-induced emission luminogen (AIEgen), the formation of aggregates with high compactness and good order can efficiently improve the emission intensity, stability, and tunability of CuNCs. Here, DNA nanoribbons, containing multiple specific binding sites, serve as a template for in situ synthesis and assembly of ultrasmall CuNCs (0.6 nm). These CuNC self-assemblies exhibit enhanced luminescence and excellent fluorescence stability because of tight and ordered arrangement through DNA nanoribbons templating. Furthermore, the stable and bright CuNC assemblies are demonstrated in the high-sensitivity detection and intracellular fluorescence imaging of biothiols.

Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex

The rational design of a well-defined protein-like tertiary structure formed by small peptide building blocks is still a formidable challenge. By using peptide-oligonucleotide conjugates (POC) as building blocks, we present the self-assembly of miniature coiled-coil α-helical peptides guided by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex under physiological pH, and to be capable of templating the three peptide sequences to constitute a small coiled-coil motif displaying remarkable α-helicity. The formed trimeric complex was characterized by ultraviolet thermal denaturation, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering (SAXS), and molecular modeling. Stabilizing cooperativity was observed between the trimeric peptide and the oligonucleotide triplex domains, and the overall molecular size (ca. 12 nm) in solution was revealed to be independent of concentration. The topological folding of the peptide moiety differed strongly from those of the individual POC strands and the unconjugated peptide, exclusively adopting the designed triple helical structure.

Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain

A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction.

Size-selective 2D ordering of gold nanoparticles using surface topography of self-assembled diamide template

Size-selective organization of ~2 nm dodecanethiol stabilized gold nanoparticles (AuNPs) into periodic 1D arrays by using the surface topographical features of a soft template is described. The template consists of micrometer length nanotapes organized into nanosheets with periodic valleys running along their length and is generated by the hierarchical self-assembly of a diamide molecule (BHPB) in cyclohexane. The AuNP ordering achieved simply by mixing the preformed template with the readily available ~2 nm dodecanethiol stabilized AuNPs is comparable to those obtained using programmable DNA and functional block copolymers. The observed periodicity of the AuNP arrays provided valuable structural clues about the organization of nanotapes into nanosheets. Self-assembling BHPB molecules in the presence of AuNPs by heating and cooling the two components led to a comparatively disordered organization because the template structure was changed under these conditions. Moreover, the template could not order larger AuNPs (~5 nm) into a similar 1D array, owing to the steric restriction imposed by the dimension of the valleys on the template. Interestingly, this geometric constraint led to AuNP size sorting when a polydisperse sample (2.5 ± 0.9 nm) was used for organization, with AuNPs attached to the template edges being larger (≥2.2 ± 0.9 nm) than those associated to the inner valleys (1.6 ± 0.8 nm). This is a unique example of size-sorting induced by the surface topographical features of a soft template.

DNA architectonics: towards the next generation of bio-inspired materials

The use of DNA in nanobiotechnology has advanced to a stage at which almost any two or three dimensional architecture can be designed with high precision. The choice of the DNA sequences is essential for successful self-assembly, and opens new ways of making nanosized monomolecular assemblies with predictable structure and size. The inclusion of designer nucleoside analogues further adds functionality with addressable groups, which have an influence on the function of the DNA nano-objects. This article highlights the recent achievements in this emerging field and gives an outlook on future perspectives and applications.

Targeted cell-cell interactions by DNA nanoscaffold-templated multivalent bispecific aptamers

Cell-cell interactions are essential for multicellular organisms, playing important roles in their development, function, and immunity. Herein a bottom-up strategy to construct self-assembled DNA nanostructures is reported, consisting of multivalent, bispecific, cell-targeting aptamers to specifically induce cell-cell interactions. Various DNA nanoscaffolds are rationally designed to assemble aptamers with different valencies and flexibilities, and their cellular binding capabilities are tested. Multivalent aptamers, assembled on more rigid scaffolds, display higher binding activities. Further, multivalent bispecific aptamer fusion molecules are constructed based on this configuration, and successfully link two types of cells. Using cell-targeting aptamers, the presented strategy eliminates the need to chemically modify cell surfaces and offers excellent cell specificity, binding efficiency, and stability. This proof-of-concept study establishes that multivalent bispecific aptamers linked on DNA-nanoscaffolds can mediate cellular engagement, which could lead to their use in directing or guiding cell-cell interactions in many biological events.

Semisynthetic DNA-protein conjugates for biosensing and nanofabrication

Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.

Chemical approaches to DNA nanotechnology

Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built up by self-assembly of the designed DNA strands. DNA nanotechnology has already reached the stage at which the organization of desired functional molecules and nanomaterials can be programmed on a defined DNA scaffold. In this review, we will focus on DNA nanotechnology and describe the potential of synthetic chemistry to contribute to the further development of DNA nanomaterials.