Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, ...DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields. Herein, we review recent progress on the use of aptamers in the construction of smart DNA origami objects and MRI and PET imaging agents. We also describe advances in the use of aptamers in the field of neurosciences (with a particular emphasis on the treatment of neurodegenerative diseases) and as drug delivery systems. Lastly, the use of chemical modifications, modified nucleoside triphosphate particularly, to enhance the binding and stability of aptamers is highlighted.
Structural DNA nanotechnology utilizes DNA molecules as programmable information-coding polymers to create higher order structures at the nanometer scale. An important milestone in structural DNA ...nanotechnology was the development of scaffolded DNA origami in which a long single-stranded viral genome (scaffold strand) is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides (staple strands). The achievable dimensions of the DNA origami tile units are currently limited by the length of the scaffold strand. Here we demonstrate a strategy referred to as “superorigami” or “origami of origami” to scale up DNA origami technology. First, this method uses a collection of bridge strands to prefold a single-stranded DNA scaffold into a loose framework. Subsequently, preformed individual DNA origami tiles are directed onto the loose framework so that each origami tile serves as a large staple. Using this strategy, we demonstrate the ability to organize DNA origami nanostructures into larger spatially addressable architectures.
We demonstrate the single-molecule imaging of the catalytic reaction of a Zn(2+)-dependent DNAzyme in a DNA origami nanostructure. The single-molecule catalytic activity of the DNAzyme was examined ...in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high-speed atomic force microscopy (AFM). This nanostructure-based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single-molecule level.
It is often argued that DNA nanotechnology has a multitude of possible applications. However, despite great advances in the understanding of the fundamental principles of the field, to date, there ...has been comparatively little commercial activity. Analysis of patent applications and company case studies suggests that this is now starting to change. The number of patent application filings is increasing, and new companies are being formed to exploit technologies based on nanoscale structures and devices made from DNA. There are parallels between the commercial developments in this field and those observed in other areas of innovation. Further commercialization is expected and new players will emerge.
Plasmonic nanoantennas mediate far and near optical fields and confine the light to subwavelength dimensions. The spatial organization of nanoantenna elements is critical as it affects the ...interelement coupling and determines the resultant antenna mode. To couple quantum emitters to optical antennas, high precision on the order of a few nm with respect to the antenna is necessary. As an emerging nanofabrication technique, DNA origami has proven itself to be a robust nanobreadboard to obtain sub‐5 nm positioning precision for a diverse range of materials. Eliminating the need for expensive state‐of‐the‐art top‐down fabrication facilities, DNA origami enables cost‐efficient implementation of nanoscale architectures, including novel nanoantennas. The ability of DNA origami to deterministically position single quantum emitters into nanoscale hotspots further boosts the efficiency of light–matter interaction controlled via optical antennas. This review recapitulates the recent progress in plasmonic nanoantennas assisted by DNA origami and focuses on their various configurations. How those nanoantennas act on the emission and absorption properties of quantum emitters positioned in the hotspots is explicitly discussed. In the end, open challenges are outlined and future possibilities lying ahead are pointed out for this powerful triad of biotechnology, nanooptics, and photophysics.
DNA origami technology enables designable spatial arrangement of nanomaterials. This capability allows deterministically positioning single quantum emitters at the hotspots of plasmonic nanoantennas. When quantum emitters couple efficiently to plasmonic nanoantennas, their emission properties can be substantially modified, rendering DNA origami‐assisted plasmonic nanoantennas a promising platform for manipulating the emission of quantum emitters.
Introduction of the solid phase method to synthesize biopolymers has revolutionized the field of biological research by enabling efficient production of peptides and oligonucleotides. One of the ...advantages of this method is the ease of removal of excess production materials from the desired product, as it is immobilized on solid substrate. The DNA origami method utilizes the nature of nucleotide base‐pairing to construct well‐defined objects at the nanoscale, and has become a potent tool for manipulating matter in the fields of chemistry, physics, and biology. Here, the development of an approach to synthesize DNA nanostructures directly on magnetic beads, where the reaction is performed in heavy liquid to maintain the beads in suspension is reported. It is demonstrated that the method can achieve high folding yields of up to 90% for various DNA shapes, comparable to standard folding. At the same time, this establishes an easy, fast, and efficient way to further functionalize the DNA origami in one‐pot, as well as providing a built‐in purification method for easy removal of excess by‐products such as non‐integrated DNA strands and residual functionalization molecules.
A new method is introduced to fold DNA origami in heavy liquid directly on magnetic beads for easy and fast purification and functionalization after folding. Then excessive material after folding and functionalization can be removed with the help of a magnet. The final product elutes with an invader strand in a strand displacement reaction. This one‐pot reaction achieves up to 90% yield.
Alongside other players, such as CpG methylation and the “histone code,” transcription factors (TFs) represent a key feature of gene regulation. TFs are implicated in critical cellular processes, ...ranging from cell death, growth, and differentiation, up to intranuclear signaling of steroid and other hormones, physical entities, and hypoxia regulation. Notwithstanding an extensive body of research in this field, several questions and therapeutic options remain unanswered and unexplored, respectively. Of note, many of these TFs represent therapeutic targets, which are either difficult to be pharmacologically tackled or are still not
drugged
via traditional approaches, such as small-molecule inhibition. Upon providing a brief overview of TFs, we focus herein on how synthetic biology/medicine could assist in their study as well as their therapeutic targeting. Specifically, we contend that DNA origami, i.e., a novel synthetic DNA nanotechnological approach, represents an excellent synthetic biology/medicine tool to accomplish the above goals, since it can harness several vital characteristics of DNA: DNA polymerization, DNA complementarity, DNA “programmability,” and DNA “editability.” In doing so, DNA origami can be applied to study TF dynamics during DNA transcription, to elucidate xeno-nucleic acids with distinct scaffolds and unconventional base pairs, and to use TFs as competitors of oncogene-engaged promoters. Overall, because of their potential for high-throughput design and their favorable pharmacodynamic and pharmacokinetic properties, DNA origami can be a novel armory for TF-related drug design. Last, we discuss future trends in the field, such as RNA origami and innovative DNA origami–based therapeutic delivery approaches.
The micrometer-scale assembly of various DNA nanostructures is one of the major challenges for further progress in DNA nanotechnology. Programmed patterns of 1D and 2D DNA origami assembly using ...specific DNA strands and micrometer-sized lattice assembly using cross-shaped DNA origami were performed on a lipid bilayer surface. During the diffusion of DNA origami on the membrane surface, the formation of lattices and their rearrangement in real-time were observed using high-speed atomic force microscopy (HS-AFM). The formed lattices were used to further assemble DNA origami tiles into their cavities. Various patterns of lattice–tile complexes were created by changing the interactions between the lattice and tiles. For the control of the nanostructure formation, the photo-controlled assembly and disassembly of DNA origami were performed reversibly, and dynamic assembly and disassembly were observed on a lipid bilayer surface using HS-AFM. Using a lipid bilayer for DNA origami assembly, it is possible to perform a hierarchical assembly of multiple DNA origami nanostructures, such as the integration of functional components into a frame architecture.
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.
Fluorescence microscopy has been one of the most discovery-rich methods in biology. In the digital age, the discipline is becoming increasingly quantitative. Virtually all biological laboratories ...have access to fluorescence microscopes, but abilities to quantify biomolecule copy numbers are limited by the complexity and sophistication associated with current quantification methods. Here, we present DNA-origami-based fluorescence brightness standards for counting 5–300 copies of proteins in bacterial and mammalian cells, tagged with fluorescent proteins or membrane-permeable organic dyes. Compared to conventional quantification techniques, our brightness standards are robust, straightforward to use, and compatible with nearly all fluorescence imaging applications, thereby providing a practical and versatile tool to quantify biomolecules via fluorescence microscopy.
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