Functionalization of quantum rods with oligonucleotides for programmable assembly with DNA origami

Biomimetic recognition strategy for efficient capture and release of circulating tumor cells

Efficient capture and release of circulating tumor cells play an important role in cancer diagnosis, but the limited affinity of monovalent adhesion molecules in existing capture technologies leads to low capture efficiency, and the captured cells are difficult to be separated. Inspired by the phenomenon that the long tentacles of jellyfish contain multiple adhesion domains and can effectively capture moving food, we have constructed a biomimetic recognition strategy to capture and release tumor cells. In details, gold-coated magnetic nanomaterials (Au@Fe₃O₄ NPs) were first prepared and characterized by scanning electron microscopy, UV-vis absorption spectra, and Zeta potential. Then, the DNA primers modified on Au@Fe₃O₄ nanoparticles can be extended to form many radialized DNA products by rolling circle amplification. These long DNA products resemble jellyfish tentacles and contain multivalent aptamers that can be extended into three dimensions to increase the accessibility of target cells, resulting in efficient, simple, rapid, and specific cells capture. The capture efficiencies are no less than 92% in PBS buffer and 77% in blood. Subsequently, DNase I was selected to degrade biomimetic tentacles to release the captured tumor cells with high viability. This release strategy can not only improve cell viability, but also reduce a tedious release process and unnecessary costs. We believe that the proposed method can be expanded for the capture and release of various tumor cells and will inspire the development of circulating tumor cells analysis. A biomimetic recognition strategy for capture and release of circulating tumor cells has been developed. This method modified specific P1 DNA primers on Au@Fe₃O₄ NPs to form many radialized DNA products by rolling circle amplification. These products can efficiently capture CTCs since it contains multiple aptamers with a multivalent binding capacity. This make it a promising tool to capture and release of other tumor cells, and will inspire the development of CTC analysis.

In silico modelling of DNA nanostructures

The rise of material science and nanotechnology created a demand for a next generation of materials and procedures that can transcend the shaping of simple geometrical nano-objects. As a legacy of the technological progress made in the Human Genome Project, DNA was identified as a possible candidate. The low production costs of custom-made DNA molecules and the possibilities concerning the structural manipulation triggered significant advances in the field of DNA nanotechnology in the last decade. To facilitate the development of new DNA nanostructures and provide users an insight in less intuitive complexities and physical properties of the DNA folding, several in silico modelling tools were published. Here, we summarize the main characteristics of these specialised tools, describe the most common design principles and discuss tools and strategies used to predict the properties of DNA nanostructures.

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.

Systematic Investigation of Two-Dimensional DNA Nanoassemblies for Construction of a Nonspecific Sensor Array

We have performed a systematic study to analyze the effect of ssDNA length, nucleobase composition, and the type of two-dimensional nanoparticles (2D-nps) on the desorption response of 36 two-dimensional nanoassemblies (2D-NAs) against several proteins. The studies were performed using fluorescently labeled polyA, polyC, and polyT with 23, 18, 12, and 7 nucleotide-long sequences. The results suggest that the ssDNAs with polyC and longer sequences are more resistant to desorption, compared to their counterparts. In addition, 2D-NAs assembled using WS₂ were least susceptible to desorption by the proteins tested, whereas nGO 2D-NAs were the most susceptible nanoassemblies. Later, the results of these systematic studies were used to construct a sensor array for discrimination of seven model proteins (BSA, lipase, alkaline phosphatase, acid phosphatase, protease, β-galactosidase, and Cytochrome c). Neither the ssDNAs nor the 2D-nps have any specific interaction with the proteins tested. Only the displacement of the ssDNAs from the 2D-np surface was measured upon the disruption of the existing forces within 2D-NAs. A customized sensor array with five 2D-NAs was developed as a result of a careful screening/filtering process. The sensor array was tested against 200 nM of protein targets, and each protein was discriminated successfully. The results suggest that the systematic studies performed using various ssDNAs and 2D-nps enabled the construction of a sensor array without a bind-and-release sensing mechanism. The studies also demonstrate the significance of systematic investigations in the construction of two-dimensional DNA nanoassemblies for functional studies.

(Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures

DNA nanostructures hold immense potential to be used for biological and medical applications. However, they are extremely vulnerable towards salt depletion and nucleases, which are common under physiological conditions. In this contribution, we used chitosan and linear polyethyleneimine for coating and long-term stabilization of several three-dimensional DNA origami nanostructures. The impact of the degree of polymerization and the charge density of the polymer together with the N/P charge ratio (ratio of the amines in polycations to the phosphates in DNA) on the stability of encapsulated DNA origami nanostructures in the presence of nucleases and in low-salt media was examined. The polycation shells were compatible with enzyme- and aptamer-based functionalization of the DNA nanostructures. Additionally, we showed that despite being highly vulnerable to salt depletion and nucleolytic digestion, self-assembled DNA nanostructures are stable in cell culture media up to a week. This was contrary to unassembled DNA scaffolds that degraded in one hour, showing that placing DNA strands into a spatially designed configuration crucially affect the structural integrity. The stability of naked DNA nanostructures in cell culture was shown to be mediated by growth media. DNA origami nanostructures kept in growth media were significantly more resistant towards low-salt denaturation, DNase I and serum-mediated digestion than when in a conventional buffer. Moreover, we confirmed that DNA origami nanostructures remain not only structurally intact but also fully functional after exposure to cell media. Agarose gel electrophoresis and negative stain transmission electron microscopy analysis revealed the hybridization of DNA origami nanostructures to their targets in the presence of serum proteins and nucleases. The structural integrity and functionality of DNA nanostructures in physiological fluids validate their use particularly for short-time biological applications in which the shape and structural details of DNA nanodevices are functionally critical.

Universal sensor array for highly selective system identification using two-dimensional nanoparticles

A typical lock-and-key sensing strategy, relying only on the most dominant interactions between the probe and target, could be too limiting. In reality, the information received upon sensing is much richer. Non-specific events due to various intermolecular forces contribute to the overall received information with different degrees, and when analyzed, could provide a much more powerful detection opportunity. Here, we have assembled a highly selective universal sensor array using water-soluble two-dimensional nanoparticles (nGO, MoS2 and WS2) and fluorescent DNA molecules. The array is composed of 12 fluorescently silent non-specific nanoreceptors (2D-nps) and used for the identification of three radically different systems; five proteins, three types of live breast cancer cells and a structure-switching event of a macromolecule. The data matrices for each system were processed using Partial Least Squares (PLS) discriminant analysis. In all of the systems, the sensor array was able to identify each object or event as separate clusters with 95% confidence and without any overlap. Out of 15 unknown entities with unknown protein concentrations tested, 14 of them were predicted successfully with correct concentration. 8 breast cancer cell samples out of 9 unknown entities from three cell types were predicted correctly. During the assembly of each nanoprobe, the intrinsic non-covalent interactions between unmodified 2D nanoparticles and ssDNAs were exploited. The unmodified 2D materials offer remarkable simplicity in the layout and the use of ssDNAs as probes provides limitless possibilities because the natural interaction of a ssDNA and 2D surface can be fine-tuned with the nucleobase composition, oligonucleotide length and type of 2D nanomaterial. Therefore, the approach described here can be advanced and fine-tuned indefinitely for meeting a particular sensing criterion. Though we have only studied three distinct elements, this approach is universal enough to be applied to a wide-range of systems.

Nanoparticle Functionalization and Its Potentials for Molecular Imaging

Functionalization enhances the properties and characteristics of nanoparticles through surface modification, and enables them to play a major role in the field of medicine. In molecular imaging, quality functional images are required with proper differentiation which can be seen with high contrast to obtain viable information. This review article discusses how functionalization enhances molecular imaging and enables multimodal imaging by which images with combination of functions particular to each modality can be obtained. This also explains how nanoparticles interacting at molecular level, when functionalized with molecules can target the cells of interest or substances with high specificity, reducing background signal and allowing simultaneous therapies to be carried out while imaging. Functionalization allows imaging for a prolonged period and enables to track the cells over a period of time. Recent researches and progress in functionalizing the nanoparticles to specifically enhance bioimaging with different modalities and their applications are reviewed in this article.

An ion-controlled four-color fluorescent telomeric switch on DNA origami structures

The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K(+) ions even in the presence of high Na(+) concentrations. Here, we demonstrate that the K(+)-selective G-quadruplex formation is reversible when using a cryptand to remove K(+) from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Förster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.

Probing Bioluminescence Resonance Energy Transfer in Quantum Rod-Luciferase Nanoconjugates

We describe the necessary design criteria to create highly efficient energy transfer conjugates containing luciferase enzymes derived from Photinus pyralis (Ppy) and semiconductor quantum rods (QRs) with rod-in-rod (r/r) microstructure. By fine-tuning the synthetic conditions, CdSe/CdS r/r-QRs were prepared with two different emission colors and three different aspect ratios (l/w) each. These were hybridized with blue, green, and red emitting Ppy, leading to a number of new BRET nanoconjugates. Measurements of the emission BRET ratio (BR) indicate that the resulting energy transfer is highly dependent on QR energy accepting properties, which include absorption, quantum yield, and optical anisotropy, as well as its morphological and topological properties, such as aspect ratio and defect concentration. The highest BR was found using r/r-QRs with lower l/w that were conjugated with red Ppy, which may be activating one of the anisotropic CdSe core energy levels. The role QR surface defects play on Ppy binding, and energy transfer was studied by growth of gold nanoparticles at the defects, which indicated that each QR set has different sites. The Ppy binding at those sites is suggested by the observed BRET red-shift as a function of Ppy-to-QR loading (L), where the lowest L results in highest efficiency and furthest shift.

Hybrid, multiplexed, functional DNA nanotechnology for bioanalysis

DNA nanotechnology allows for the realization of novel multiplexed assays in bioanalytical sciences.