Search

DNA composite materials are at the forefront, especially for biomedical science, as they can increase the efficacy and safety of current therapies and drug delivery systems. The specificity and predictability of the Watson-Crick base pairing make DNA an excellent building material for the production of programmable and multifunctional objects. In addition, the principle of nucleic acid hybridization can be applied to realize mobile nanostructures, such as those reflected in DNA walkers that sort and collect cargo on DNA tracks, DNA robots performing tasks within living cells and/or DNA tweezers as ultra-sensitive biosensors. In this review, we present the diversity of dynamic DNA nanostructures functionalized with different biomolecules/functional units, imaging smart biomaterials capable of sensing, interacting, delivery and performing complex tasks within living cells/organisms., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Surface enhanced Raman spectroscopy (SERS) measurements are conventionally performed using assemblies of metal nanostructures on a macro- to micro-sized substrate or by dispersing colloidal metal nanoparticles directly onto the sample of interest. Despite intense use, these methods allow neither the removal of the nanoparticles after a measurement nor a defined confinement of the SERS measurement position. So far, tip enhanced Raman spectroscopy is still the key technique in this regard but not adequate for various samples mainly due to diminished signal enhancement compared to other techniques, poor device fabrication reproducibility, and cumbersome experimental setup requirements. Here, we demonstrate that a rational combination of only four gold nanoparticles (AuNPs) on a DNA origami template, and single silicon nanowires (SiNWs) yield functional optical amplifier nanoprobes for SERS. These nanoscale SERS devices offer a spatial resolution below the diffraction limit of light and still a high electric field intensity enhancement factor ( EF) of about 10 5 despite of miniaturization.

Plasmonic waveguides consisting of metal nanoparticle chains can localize and guide light well below the diffraction limit, but high propagation losses due to lithography-limited large interparticle spacing have impeded practical applications. Here, we demonstrate that DNA-origami-based self-assembly of monocrystalline gold nanoparticles allows the interparticle spacing to be decreased to ∼2 nm, thus reducing propagation losses to 0.8 dB per 50 nm at a deep subwavelength confinement of 62 nm (∼λ/10). We characterize the individual waveguides with nanometer-scale resolution by electron energy-loss spectroscopy. Light propagation toward a fluorescent nanodiamond is directly visualized by cathodoluminescence imaging spectroscopy on a single-device level, thereby realizing nanoscale light manipulation and energy conversion. Simulations suggest that longitudinal plasmon modes arising from the narrow gaps are responsible for the efficient waveguiding. With this scalable DNA origami approach, micrometer-long propagation lengths could be achieved, enabling applications in information technology, sensing, and quantum optics.

The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions. This reduced the number of staple strands needed to determine the shape and size of the final structure after gap filling. For this, several DNA polymerases and single-stranded binding (SSB) proteins were tested, with T4 DNA polymerase being the best fit. The structures could be folded in as little as 6 min, and the subsequent optimized gap-filling reaction was completed in less than 3 min. The introduction of flexible gap regions results in fully collapsed or partially bent structures due to entropic spring effects. Finally, we demonstrated structural transformations of such deformed wireframe DNA origami structures with DNA polymerases including the expansion of collapsed structures and the straightening of curved tubes. We anticipate that this approach will become a powerful tool to build DNA wireframe structures more material-efficiently, and to quickly prototype and test new wireframe designs that can be expanded, rigidified, or mechanically switched. Mechanical force generation and structural transitions will enable applications in structural DNA nanotechnology, plasmonics, or single-molecule biophysics.

DNA nanotechnology enables the synthesis of nanometer-sized objects that can be site-specifically functionalized with a large variety of materials. For these reasons, DNA-based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)-polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs). This straightforward, cost-effective, and robust route to protect DNA-based structures could therefore enable applications in biology and nanomedicine where unprotected DNA origami would be degraded., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Plasmonic structures allow the manipulation of light with materials that are smaller than the optical wavelength. Such structures can consist of plasmonically active metal nanoparticles and can be fabricated through scalable bottom-up self-assembly on DNA origami templates. To produce functional devices, the precise and high-yield arrangement of each of the nanoparticles on a structure is of vital importance as the absence of a single particle can destroy the functionality of the entire device. Nevertheless, the parameters influencing the yield of the multistep assembly process are still poorly understood. To overcome this deficiency, we employed a test system consisting of a tubular six-helix bundle DNA origami with binding sites for eight oligonucleotide-functionalized gold nanoparticles. We systematically studied the assembly yield as a function of a wide range of parameters such as ionic strength, stoichiometric ratio, oligonucleotide linker chemistry, and assembly kinetics by an automated high-throughput analysis of electron micrographs of the formed heterocomplexes. Our optimized protocols enable particle placement yields up to 98.7% and promise the reliable production of sophisticated DNA-based multiparticle plasmonic devices for applications in photonics, optoelectronics, and nanomedicine.

DNA nanotechnology offers unique control over matter on the nanoscale. Here, we extend the DNA origami method to cover a range of wireframe truss structures composed of equilateral triangles, which use less material per volume than standard multiple-helix bundles. From a flat truss design, we folded tetrahedral, octahedral, or irregular dodecahedral trusses by exchanging few connector strands. Other than standard origami designs, the trusses can be folded in low-salt buffers that make them compatible with cell culture buffers. The structures also have defined cavities that may in the future be used to precisely position functional elements such as metallic nanoparticles or enzymes. Our graph routing program and a simple design pipeline will enable other laboratories to make use of this valuable and potent new construction principle for DNA-based nanoengineering.

The synthesis, purification, and structure characterization of a seven-ring interlocked DNA catenane is described. The design of the seven-ring catenane allows the dynamic reconfiguration of any of the four rings (R1, R3, R4, and R6) on the catenane scaffold, or the simultaneous switching of any combination of two, three, or all four rings to yield 16 different isomeric states of the catenane. The dynamic reconfiguration across the states is achieved by implementing the strand-displacement process in the presence of appropriate fuel/antifuel strands and is probed by fluorescence spectroscopy. Each of the 16 isomers of the catenane can be transformed into any of the other isomers, thus allowing for 240 dynamic transitions within the system.

The assembly of double-stranded (ds) DNA nanocircles both by hybridization with branched oligodeoxynucleotides (ODNs) and by intercalation was analyzed by atomic force microscopy (AFM). Branched ODNs ligated to single-stranded (ss) gap regions of dsDNA nanocircles led to defined, dumbbell-shaped architectures. ODNs containing an aromatic intercalator yielded oligomeric aggregates.

G-quadruplexes are becoming reliable alternative interaction modules for the construction of DNA nanoarchitectures due to their prompt inducibility by salts. In this Full Paper, we report the design and synthesis of two different DNA minicircles equipped with G-rich appendixes that can self-hybridize into a G-quadruplex, which acts as a DNA recruiter and glue. Both minicircles, one containing a hairpin-like G-rich region and the other an open tuning-fork-like G-rich region, have the potential to form DNA G-nanoconstructs but only the tuning-fork minicircle does so. Incubation of the tuning-fork minicircle with Na(+) and Ni(2+) results in the formation of minicircle dimers, while K(+) and Sr(2+) unexpectedly induce the formation of multimers. Moreover, a catenated DNA nanoconstruct is obtained when the components of the hairpin minicircle are incubated with K(+) or Na(+) and assembled in a stepwise sequence. All nanoconstructs are visualized by atomic force microscopy.

Mechanically interlocked molecules such as rotaxanes and catenanes have potential as components of molecular machinery. Rotaxanes consist of a dumb-bell-shaped molecule encircled by a macrocycle that can move unhindered along the axle, trapped by bulky stoppers. Previously, rotaxanes have been made from a variety of molecules, but not from DNA. Here, we report the design, assembly and characterization of rotaxanes in which both the dumb-bell-shaped molecule and the macrocycle are made of double-stranded DNA, and in which the axle of the dumb-bell is threaded through the macrocycle by base pairing. The assembly involves the formation of pseudorotaxanes, in which the macrocycle and the axle are locked together by hybridization. Ligation of stopper modules to the axle leads to the characteristic dumb-bell topology. When an oligonucleotide is added to release the macrocycle from the axle, the pseudorotaxanes are either converted to mechanically stable rotaxanes, or they disassemble by means of a slippage mechanism to yield a dumb-bell and a free macrocycle. Our DNA rotaxanes allow the fields of mechanically interlocked molecules and DNA nanotechnology to be combined, thus opening new possibilities for research into molecular machines and synthetic biology.

We have recently constructed a "DNA strut" consisting of two DNA-binding hairpin polyamides of Dervan-type connected via a long flexible linker and were able to show that this strut can be used to sequence-selectively connect DNA helices. This approach provides a second structural element (besides the Watson-Crick base pairing) for the assembly of higher-order DNA nanoarchitectures from smaller DNA building blocks. Since none of the existing analytical techniques for studying this kind of system were found suitable for detection and quantification of the formation of the resulting complexes, we chose fluorescence correlation spectroscopy (FCS). In the present study we show that FCS allowed us in a versatile and fast way to investigate the binding of Dervan polyamides to DNA. In particular it also shows its power in the quantitative detection of the formation of multimeric complexes and the in investigation of binding under nonphysiological conditions.