Infrared emitting quantum dots: DNA conjugation and DNA origami directed self-assembly

Aptamer-based targeted delivery systems for cancer treatment using DNA origami and DNA nanostructures

Due to the limitations of conventional cancer treatment methods, nanomedicine has appeared as a promising alternative, allowing improved drug targeting and decreased drug toxicity. In the development of cancer nanomedicines, among various nanoparticles (NPs), DNA nanostructures are more attractive because of their precisely controllable size, shape, excellent biocompatibility, programmability, biodegradability, and facile functionalization. Aptamers are introduced as single-stranded RNA or DNA molecules with recognize their corresponding targets. So, incorporating aptamers into DNA nanostructures led to influential vehicles for bioimaging and biosensing as well as targeted cancer therapy. In this review, the recent developments in the application of aptamer-based DNA origami and DNA nanostructures in advanced cancer treatment have been highlighted. Some of the main methods of cancer treatment are classified as chemo-, gene-, photodynamic- and combined therapy. Finally, the opportunities and problems for targeted DNA aptamer-based nanocarriers for medicinal applications have also been discussed.

Application and prospects of nucleic acid nanomaterials in tumor therapy

Cancer poses a great threat to human life, and current cancer treatments, such as radiotherapy, chemotherapy, and surgery, have significant side effects and limitations that hinder their application. Nucleic acid nanomaterials have specific spatial configurations and can be used as nanocarriers to deliver different therapeutic drugs, thereby enabling various biomedical applications, such as biosensors and cancer therapy. In recent decades, a variety of DNA nanostructures have been synthesized, and they have demonstrated remarkable potential in cancer therapy related applications, such as DNA origami structures, tetrahedral framework nucleic acids, and dynamic DNA nanostructures. Importantly, more attention is also being paid to RNA nanostructures, which play an important role in gene therapy. Therefore, this review introduces the developmental history of nucleic acid nanotechnology, summarizes the applications of DNA and RNA nanostructures for tumor treatment, and discusses the development opportunities for nucleic acid nanomaterials in the future.

One-Step Ligand-Exchange Method to Produce Quantum Dot-DNA Conjugates for DNA-Directed Self-Assembly

To address the current challenges in making bright, stable, and small DNA-functionalized quantum dots (QDs), we have developed a one-step ligand-exchange method to produce QD-DNA conjugates from commonly available hydrophobic QDs. We show that by systematically adjusting the reaction conditions such as ligand-to-nanoparticle molar ratio, pH, and solvent composition, stable and highly photoluminescent water-soluble QD-DNA conjugates with relatively high ligand loadings can be produced. Moreover, by site specifically binding these QD-DNA conjugates to a DNA origami template, we demonstrate that these bioconjugates have sufficient colloidal stability for DNA-directed self-assembly. Fluorescence quenching by an adjacent gold nanoparticle (AuNP) was demonstrated. Such QD-AuNP dimers may serve as biosensors with improved sensitivity and reproducibility. Moreover, our simple method can facilitate the assembly of QDs into more complex superlattices and discrete clusters that may enable novel photophysical properties.

Aqueous Synthesis of DNA-Functionalized Near-Infrared AgInS2/ZnS Core/Shell Quantum Dots

Biocompatibility, biofunctionality, and chemical stability are essential criteria to be fulfilled by quantum dot (QD) emitters for bio-imaging and -sensing applications. In addition to these criteria, achieving efficient near-infrared (NIR) emission with nontoxic QDs remains very challenging. In this perspective, we developed water-soluble NIR-emitting AgInS₂/ZnS core/shell (AIS/ZnS) QDs functionalized with DNA. The newly established aqueous route relying on a two-step hot-injection synthesis led to highly luminescent chalcopyrite-type AIS/ZnS core/shell QDs with an unprecedented photoluminescence quantum yield (PLQY) of 55% at 700 nm and a long photoluminescence (PL) decay time of 900 ns. Fast and slow hot injection of the precursors were compared for the AIS core QD synthesis, yielding a completely different behavior in terms of size, size distribution, stoichiometry, and crystal structure. The PL peak positions of both types of core QDs were 710 (fast) and 760 nm (slow injection) with PLQYs of 36 and 8%, respectively. The slow and successive incorporation of the Zn and S precursors during the subsequent shell growth step on the stronger emitting cores promoted the formation of a three-monolayer thick ZnS shell, evidenced by the increase of the average QD size from 3.0 to 4.8 nm. Bioconjugation of the AIS/ZnS QDs with hexylthiol-modified DNA was achieved during the ZnS shell growth, resulting in a grafting level of 5-6 DNA single strands per QD. The successful chemical conjugation of DNA was attested by UV-vis spectroscopy and agarose gel electrophoresis. Importantly, surface plasmon resonance imaging experiments using complementary DNA strands further corroborated the successful coupling and the stability of the AIS/ZnS-DNA QD conjugates as well as the preservation of the biological activity of the anchored DNA. The strong NIR emission and biocompatibility of these AIS/ZnS-DNA QDs provide a high potential for their use in biomedical applications.

DNA-Mediated Self-Assembly and Metallization of Semiconductor Nanorods for the Fabrication of Nanoelectronic Interfaces

DNA nanostructures provide a powerful platform for the programmable assembly of nanomaterials. Here, this approach is extended to semiconductor nanorods that possess interesting electrical properties and could be utilized for the bottom-up fabrication of nanoelectronic building blocks. The assembly scheme is based on an efficient DNA functionalization of the nanorods. A complete coverage of the rod surface with DNA ensures a high colloidal stability while maintaining the rod size and shape. It furthermore supports the assembly of the nanorods at defined docking positions of a DNA origami platform with binding efficiencies of up to 90 % as well as the formation of nanorod dimers with defined relative orientations. By incorporating orthogonal binding sites for gold nanoparticles, defined metal-semiconductor heterostructures can be fabricated. Subsequent application of a seeded growth procedure onto the gold nanoparticles (AuNPs) allows for to establish a direct metal-semiconductor interface as a crucial basis for the integration of semiconductors in self-assembled nanoelectronic devices.

Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler

DNA-nanoparticle conjugates are important tools in nanobiotechnology. Knowing the orientation, function, and length of DNA on nanoparticle surfaces at low nanomolar concentrations under physiological conditions is therefore of great interest. Here, we investigate the conformation of a 31 nucleotides (nt) long DNA attached to a semiconductor quantum dot (QD) via Förster resonance energy transfer (FRET) from Tb-DNA probes hybridized to different positions on the QD-DNA. Precise Tb-to-QD distance determination from 7 to 14 nm along 26 nt of the peptide-appended QD-DNA was realized by time-resolved FRET spectroscopy. The FRET nanoruler measured linear single-stranded (ssDNA) and double-stranded (dsDNA) extensions of ∼0.15 and ∼0.31 nm per base, reflecting the different conformations. Comparison with biomolecular modeling confirmed the denser conformation of ssDNA and a possibly more flexible orientation on the QD surface, whereas the dsDNA was fully extended with radial orientation. The temporally distinct photoluminescence decays of the different DNA-FRET configurations were used for prototypical DNA hybridization assays that demonstrated the large potential for extended temporal multiplexing. The extensive experimental and theoretical analysis of 11 different distances/configurations of the same QD-DNA conjugate provided important information on DNA conformation on nanoparticle surfaces and will be an important benchmark for the development and optimization of DNA-nanobiosensors.

Supra-Nanoparticle Functional Assemblies through Programmable Stacking

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. Here, we report a general method of assembling nanoparticles in a linear "pillar" morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization. By controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.

DNA origami applications in cancer therapy

Due to the complexity and heterogeneity of cancer, the development of cancer diagnosis and therapy is still progressing, and a complete understanding of cancer biology remains elusive. Recently, cancer nanomedicine has gained much interest as a promising diagnostic and therapeutic strategy, as a wide range of nanomaterials possess unique physical properties that can render drug delivery systems safer and more effective. Also, targeted drug delivery and precision medicine have now become a new paradigm in cancer therapy. With nanocarriers, chemotherapeutic drugs could be directly delivered into target cancer cells, resulting in enhanced efficiency with fewer side-effects. DNA, a biomolecule with molecular self-assembly properties, has emerged as a versatile nanomaterial to construct multifunctional platforms; DNA nanostructures can be modified with functional groups to improve their utilities as biosensors or drug carriers. Such applications have become possible with the advent of the scaffolded DNA origami method. This breakthrough technique in structural DNA nanotechnology provides an easier and faster way to construct DNA nanostructures with various shapes. Several experiments proved that DNA origami nanostructures possess abilities to enhance efficacies of chemotherapy, reduce adverse side-effects, and even circumvent drug resistance. Here, we highlight the principles of the DNA origami technique and its applications in cancer therapeutics and discuss current challenges and opportunities to improve cancer detection and targeted drug delivery.

Using CdTe/ZnSe core/shell quantum dots to detect DNA and damage to DNA

CdTe/ZnSe core/shell quantum dot (QD), one of the strongest and most highly luminescent nanoparticles, was directly synthesized in an aqueous medium to study its individual interactions with important nucleobases (adenine, guanine, cytosine, and thymine) in detail. The results obtained from the optical analyses indicated that the interactions of the QDs with different nucleobases were different, which reflected in different fluorescent emission maxima and intensities. The difference in the interaction was found due to the different chemical behavior and different sizes of the formed nanoconjugates. An electrochemical study also confirmed that the purines and pyrimidines show different interactions with the core/shell QDs. Based on these phenomena, a novel QD-based method is developed to detect the presence of the DNA, damage to DNA, and mutation. The QDs were successfully applied very easily to detect any change in the sequence (mutation) of DNA. The QDs also showed their ability to detect DNAs directly from the extracts of human cancer (PC3) and normal (PNT1A) cells (detection limit of 500 pM of DNA), which indicates the possibilities to use this easy assay technique to confirm the presence of living organisms in extreme environments.

Photoelectrochemical CaMV35S biosensor for discriminating transgenic from non-transgenic soybean based on SiO2@CdTe quantum dots core-shell nanoparticles as signal indicators

A methodology for detection of the Cauliflower Mosaic Virus 35S(CaMV35S) promoter was developed to distinguish transgenic from non-transgenic soybean samples by using photoelectrochemical (PEC) biosensor. In this PEC biosensing system, the as-prepared gold nanoparticles-reduced graphene oxide acted as a nanocarrier to immobilize the thiol-functional probe (probe1), and the SiO₂@CdTe quantum dots (QDs) core-shell nanoparticles tagged with the amino-functional probe (probe2) acted as signal indicators, respectively. In the presence of target DNA (tDNA) of CaMV35S, the binding of tDNA with probe1 and probe2 through the high specific DNA hybridization led to the fabrication of sandwich structure, and thus the high loading of the signal indicators SiO₂@CdTe QDs at the electrode surface, which increased the PEC signal. The increased PEC signal depended on the concentration of tDNA, and a wide linear range from 0.1pM to 0.5nM with low detection limit of 0.05pM was obtained. In addition, the PEC biosensor has been successfully used for discriminating transgenic soybean from non-transgenic samples, which was consistent with the polymerase chain reaction (PCR) results, suggesting the proposed PEC biosensor is a feasible tool for the further daily genetically modified organism detection.

Plasmonic Effect on Exciton and Multiexciton Emission of Single Quantum Dots

Quantum dots are nanoscale quantum emitters with high quantum yield and size-dependent emission wavelength, holding promises in many optical and electronic applications. When quantum dots are situated close to noble metal nanoparticles, their emitting behavior can be conveniently tuned because of the interaction between the excitons of the quantum dots and the plasmons of the metal nanoparticles. This interaction at the single quantum dot level gives rise to reduced or suppressed photoluminescence blinking and enhanced multiexciton emission, which is difficult to achieve in isolated quantum dots. However, the mechanism of how plasmonic structures cause the changes in the quantum dot emission remains unclear. Because of the complexity of the system, the interfaces between metal, semiconductor, and ligands must be considered, in addition to factors such as geometry, interparticle distance, and spectral overlap. The challenges in the design and fabrication of the hybrid nanostructures as well as in understanding the exciton-plasmon coupling mechanism can be overcome by a cooperative effort in synthesis, optical spectroscopy, and theoretical modeling.

Structural stability of DNA origami nanostructures in the presence of chaotropic agents

DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching.

Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology

Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.

The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex

While the self-assembly of different types of DNA origami into well-defined complexes could produce nanostructures on which thousands of locations can be independently functionalized with nanometer-scale precision, current assembly processes have low yields. Biomolecular complex formation requires relatively strong interactions and reversible assembly pathways that prevent kinetic trapping. To characterize how these issues control origami complex yields, the equilibrium constants for each possible reaction for the assembly of a heterotetrameric ring, the unit cell of a rectangular lattice, were measured using fluorescence colocalization microscopy. We found that origami interface structure controlled reaction free energies. Cooperativity, measured for the first time for a DNA nanostructure assembly reaction, was weak. Simulations of assembly kinetics suggest assembly occurs via parallel pathways with the primary mechanism of assembly being hierarchical: two dimers form that then bind to one another to complete the ring.

Site-Specific Surface Functionalization of Gold Nanorods Using DNA Origami Clamps

Precise control over surface functionalities of nanomaterials offers great opportunities for fabricating complex functional nanoarchitectures but still remains challenging. In this work, we successfully developed a novel strategy to modify a gold nanorod (AuNR) with specific surface recognition sites using a DNA origami clamp. AuNRs were encapsulated by the DNA origami through hybridization of single-stranded DNA on the AuNRs and complementary capture strands inside the clamp. Another set of capture strands on the outside of the clamp create the specific recognition sites on the AuNR surface. By means of this strategy, AuNRs were site-specifically modified with gold nanoparticles at the top, middle, and bottom of the surface, respectively, to construct a series of well-defined heterostructures with controlled "chemical valence". Our study greatly expands the utility of DNA origami as a tool for building complex nanoarchitectures and represents a new approach for precise tailoring of nanomaterial surfaces.

DNA nanotechnology for nanophotonic applications

DNA nanotechnology has touched the epitome of miniaturization by integrating various nanometer size particles with nanometer precision. This enticing bottom-up approach has employed small DNA tiles, large multi-dimensional polymeric structures or more recently DNA origami to organize nanoparticles of different inorganic materials, small organic molecules or macro-biomolecules like proteins, and RNAs into fascinating patterns that are difficult to achieve by other conventional methods. Here, we are especially interested in the self-assembly of nanomaterials that are potentially attractive elements in the burgeoning field of nanophotonics. These materials include plasmonic nanoparticles, quantum dots, fluorescent organic dyes, etc. DNA based self-assembly allows excellent control over distance, orientation and stoichiometry of these nano-elements that helps to engineer intelligent systems that can potentially pave the path for future technology. Many outstanding structures have been fabricated that are capable of fine tuning optical properties, such as fluorescence intensity and lifetime modulation, enhancement of Raman scattering and emergence of circular dichroism responses. Within the limited scope of this review we have tried to give a glimpse of the development of this still nascent but highly promising field to its current status as well as the existing challenges before us.

Controlled formation of nanoparticle clusters mediated by electrostatic interaction

A general strategy for high yield fabrication of homo- and hetero-nanoparticle clusters with controlled configuration and inter-particle gap through a self-assembly process mediated by electrostatic interaction was reported.