DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA ...nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico-chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami-based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio-medical applications.
An essential motif for the assembly of biological materials such as actin at the scale of hundreds of nanometers and beyond is a network of one-dimensional fibers with well-defined geometry. Here, we ...demonstrate the programmed organization of DNA filaments into micron-scale architectures where component filaments are oriented at preprogrammed angles. We assemble L-, T-, and Y-shaped DNA origami junctions that nucleate two or three micron length DNA nanotubes at high yields. The angles between the nanotubes mirror the angles between the templates on the junctions, demonstrating that nanoscale structures can control precisely how micron-scale architectures form. The ability to precisely program filament orientation could allow the assembly of complex filament architectures in two and three dimensions, including circuit structures, bundles, and extended materials.
The application of three-dimensional DNA origami objects as rigid mechanical mediators or force sensing elements requires detailed knowledge about their complex mechanical properties. Using magnetic ...tweezers, we directly measure the bending and torsional rigidities of four- and six-helix bundles assembled by this technique. Compared to duplex DNA, we find the bending rigidities to be greatly increased while the torsional rigidities are only moderately augmented. We present a mechanical model explicitly including the crossovers between the individual helices in the origami structure that reproduces the experimentally observed behavior. Our results provide an important basis for the future application of 3D DNA origami in nanomechanics.
Super-resolution microscopies, such as single molecule localization microscopy (SMLM), allow the visualization of biomolecules at the nanoscale. The requirement to observe molecules multiple times ...during an acquisition has pushed the field to explore methods that allow the binding of a fluorophore to a target. This binding is then used to build an image via points accumulation for imaging nanoscale topography (PAINT), which relies on the stochastic binding of a fluorescent ligand instead of the stochastic photo-activation of a permanently bound fluorophore. Recently, systems that use DNA to achieve repeated, transient binding for PAINT imaging have become the cutting edge in SMLM. Here, we review the history of PAINT imaging, with a particular focus on the development of DNA-PAINT. We outline the different variations of DNA-PAINT and their applications for imaging of both DNA origamis and cellular proteins via SMLM. Finally, we reflect on the current challenges for DNA-PAINT imaging going forward.
DNA nanotechnology enables the precise construction of nanoscale devices that mimic aspects of natural biomolecular systems yet exhibit robustly programmable behavior. While many important biological ...processes involve dynamic interactions between components associated with phospholipid membranes, little progress has been made toward creating synthetic mimics of such interfacial systems. We report the assembly and characterization of cholesterol-labeled DNA origami “barges” capable of reversible association with and lateral diffusion on supported lipid bilayers. Using single-particle fluorescence microscopy, we show that these DNA barges rapidly and stably embed in lipid bilayers and exhibit Brownian diffusion in a manner dependent on both cholesterol labeling and bilayer composition. Tracking of individual barges rapidly generates super-resolution maps of the contiguous regions of a membrane. Addition of appropriate command oligonucleotides enables membrane-associated barges to reversibly exchange fluorescent cargo with bulk solution, dissociate from the membrane, or form oligomers within the membrane, opening up new possibilities for programmable membrane-bound molecular devices.
Design strategies for DNA and RNA nanostructures have developed along parallel lines for the past 30 years, from small structural motifs derived from biology to large 'origami' structures with ...thousands to tens of thousands of bases. With the recent publication of numerous RNA origami structures and improved design methods-even permitting co-transcriptional folding of kilobase-sized structures - the RNA nanotechnolgy field is at an inflection point. Here, we review the key achievements which inspired and enabled RNA origami design and draw comparisons with the development and applications of DNA origami structures. We further present the available computational tools for the design and the simulation, which will be key to the growth of the RNA origami community. Finally, we portray the transition from RNA origami structure to function. Several functional RNA origami structures exist already, their expression in cells has been demonstrated and first applications in cell biology have already been realized. Overall, we foresee that the fast-paced RNA origami field will provide new molecular hardware for biophysics, synthetic biology and biomedicine, complementing the DNA origami toolbox.
DNA origami has emerged as a versatile platform for diverse applications, namely, photonics, electronics, (bio) sensing, smart actuator, and drug delivery. In the last decade, DNA origami has been ...extensively pursued for efficient anticancer therapy. However, challenges remain to develop strategies that improve the targeting efficiency and drug delivery capability of the DNA origami nanostructures. In this direction, we developed folate-functionalized DNA origami that effectively targets and delivers doxorubicin (DOX), a well-known anticancer drug to the folate receptor alpha (FOLR1) expressing triple-negative breast cancer (TNBC) cells
in vitro
. We show that folate-functionalized DNA origami structure targets and kills FOLR1 overexpressing cells with better efficacy than nontargeted origami. We envision that this study will open up the possibility of target specific delivery of anticancer drug combinations using the versatile DNA origami nanostructures to the drug resistant cancer cells.
Effect of DNA Origami Nanostructures on Bacterial Growth Garcia‐Diosa, Jaime Andres; Grundmeier, Guido; Keller, Adrian
Chembiochem : a European journal of chemical biology,
April 2, 2024, Letnik:
25, Številka:
7
Journal Article
Recenzirano
Odprti dostop
DNA origami nanostructures are a powerful tool in biomedicine and can be used to combat drug‐resistant bacterial infections. However, the effect of unmodified DNA origami nanostructures on bacteria ...is yet to be elucidated. With the aim to obtain a better understanding of this phenomenon, the effect of three DNA origami shapes, i.e., DNA origami triangles, six‐helix bundles (6HBs), and 24‐helix bundles (24HBs), on the growth of Gram‐negative Escherichia coli and Gram‐positive Bacillus subtilis is investigated. The results reveal that while triangles and 24HBs can be used as a source of nutrients by E. coli and thereby promote population growth, their effect is much smaller than that of genomic single‐ and double‐stranded DNA. However, no effect on E. coli population growth is observed for the 6HBs. On the other hand, B. subtilis does not show any significant changes in population growth when cultured with the different DNA origami shapes or genomic DNA. The detailed effect of DNA origami nanostructures on bacterial growth thus depends on the competence signals and uptake mechanism of each bacterial species, as well as the DNA origami shape. This should be considered in the development of antimicrobial DNA origami nanostructures.
Bacteria can use DNA origami nanostructures as a nutrient source, leading to increased population growth. This process depends not only on the competence signal and uptake mechanisms of each species, but also on DNA origami shape and superstructure. It should thus be considered in the design and development of antimicrobial DNA origami nanostructures.
Nanoscale structures demonstrate considerable potential utility in the construction of nanorobots, nanomachines, and many other devices. In this study, a hexagonal DNA origami ring was assembled and ...visualized via atomic force microscopy. The DNA origami shape could be programmed into either a hexagonal or linear shape with an open or folded pattern. The flexible origami was robust and switchable for dynamic pattern recognition. Its edges were folded by six bundles of DNA helices, which could be opened or folded in a honeycomb shape. Additionally, the edges were programmed into a concave-convex pattern, which enabled linkage between the origami and dipolymers. Furthermore, biotin-streptavidin labels were embedded at each edge for nanoscale calibration. The atomic force microscopy results demonstrated the stability and high-yield of the flexible DNA origami ring. The polymorphous nanostructure is useful for dynamic nano-construction and calibration of structural probes or sensors.
•A MUC1-specific DNA nanosphere was constructed via the DNA origami technique.•MUC1-Apt-Sphere selectively delivers doxorubicin to MCF-7 cells.•MUC1-Apt-Sphere enhances the cytotoxicity of ...doxorubicin in MCF-7 cells.
Targeted drug delivery systems have attracted much attention as they can enhance treatment efficiency and minimize cytotoxicity of chemotherapeutic drugs. Several nanomaterials with biological advantages have been explored for novel drug carrier invention. Here, a DNA origami nanosphere modified with a specific aptamer was developed for selective doxorubicin delivery. The specificity of the targeted nanocarrier was investigated against three cell lines with different levels of Mucin 1 (MUC1) expression. Our data showed that the doxorubicin-loaded, MUC1 aptamer-functionalized nanosphere (Dox-Apt-sphere) preferentially delivered drugs and exhibited cytotoxic effects at low Dox concentration in MUC1-high MCF-7 cells. These results also proved that the aptamer-modified DNA nanostructure may serve as a promising candidate for targeted drug delivery.
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