Custom-shaped metal nanostructures based on DNA origami silhouettes

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Superstructure-Dependent Loading of DNA Origami Nanostructures with a Groove-Binding Drug

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DNA‐Origami‐Templated Growth of Multilamellar Lipid Assemblies

Lipids are important building blocks in cellular compartments, and therefore their self‐assembly into well‐defined hierarchical structures has gained increasing interest. Cationic lipids and unstructured DNA can co‐assemble into highly ordered structures (lipoplexes), but potential applications of lipoplexes are still limited. Using scaffolded DNA origami nanostructures could aid in resolving these drawbacks. Here, we have complexed DNA origami together with a cationic lipid 1,2‐dioleoly‐3‐trimethylammonium‐propane (DOTAP) and studied their self‐assembly driven by electrostatic and hydrophobic interactions. The results suggest that the DNA origami function as templates for the growth of multilamellar lipid structures and that the DNA origami are embedded in the formed lipid matrix. Furthermore, the lipid encapsulation was found to significantly shield the DNA origami against nuclease digestion. The presented complexation strategy is suitable for a wide range of DNA‐based templates and could therefore find uses in construction of cell‐membrane‐associated components.acceptedVersionPeer reviewe

Nanoparticle release from anionic nanocellulose hydrogel matrix

Nanocellulose hydrogels have been shown to be excellent platforms for sustained delivery of drug molecules. In this study, we examine the suitability of anionic nanocellulose hydrogels for the sustained release of various nanoparticles. Systems releasing nanoparticles could produce applications especially for therapeutic nanocarriers, whose life-times in vivo might be limited. Micelles, liposomes and DNA origami nanostructures were incorporated into the nanocellulose hydrogels, and their release rates were measured. Two different hydrogel qualities (with 1% and 2% mass of fiber content) were used for each nanoparticle formulation. We showed that the drug release rates depend on nanoparticle size, shape, and charge. Smaller particles with neutral charge were released faster from 1% hydrogels than from 2% hydrogels. Nanoparticles with cationic labeling were retained in both hydrogels, whereas for the neutral nanoparticles, we were able to determine the cut-off size for released particles for both hydrogels. Rod-shaped DNA origami were released rapidly even though their length was above the cut-off size of spherical particles, indicating that their smaller radial dimension facilitates their fast release. Based on our results, anionic nanocellulose hydrogels are versatile platforms for the sustained release of the chosen model nanoparticles (liposomes, micelles, and DNA origami). Alternatively, for the tightly bound nanoparticles, this could lead to nanoparticle reservoirs within hydrogels, which could act as immobilized drug release systems.Peer reviewe

Plasmonic nanostructures through DNA-assisted lithography

Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties. DALI is a parallel, high-throughput fabrication method compatible with transparent substrates, thus providing an additional advantage for optical measurements, and yields structures with a feature size of ~10 nm. We demonstrate its feasibility by producing metal nanostructures with a chiral plasmonic response and bowtie-shaped nanoantennas for surface-enhanced Raman spectroscopy. We envisage that DALI can be generalized to large substrates, which would subsequently enable scale-up production of diverse metallic nanostructures with tailored plasmonic features.Peer reviewe

Genomic Shift in Population Dynamics of mcr - 1 -Positive Escherichia Coli in Human Carriage

Emergence of the colistin resistance gene, mcr-1, has attracted worldwide attention. Despite the prevalence of mcr-1-positive Escherichia coli (MCRPEC) strains in human carriage showing a significant decrease between 2016 and 2019, genetic differences in MCRPEC strains remain largely unknown. We therefore conducted a comparative genomic study on MCRPEC strains from fecal samples of healthy human subjects in 2016 and 2019. We identified three major differences in MCRPEC strains between these two time points. First, the insertion sequence ISApl1 was often deleted and the percentage of mcr-1-carrying IncI2 plasmids was increased in MCRPEC strains in 2019. Second, the antibiotic resistance genes (ARGs), aac(3)-IVa and blaCTX-M-1, emerged and coexisted with mcr-1 in 2019. Third, MCRPEC strains in 2019 contained more virulence genes, resulting in an increased proportion of extraintestinal pathogenic E. coli (ExPEC) strains (36.1%) in MCRPEC strains in 2019 compared to that in 2016 (10.5%), implying that these strains could occupy intestinal ecological niches by competing with other commensal bacteria. Our results suggest that despite the significant reduction in the prevalence of MCRPEC strains in humans from 2016 to 2019, MCRPEC exhibits increased resistance to other clinically important ARGs and contains more virulence genes, which may pose a potential public health threat

Growth of immobilized DNA by polymerase: bridging nanoelectrodes with individual dsDNA molecules

We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiol-modified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a procedure mimicking PCR, finally forming a complete dsDNA molecule bridging the gap between the electrodes. The technique opens up opportunities for building from the bottom-up, for detection and sensing applications, and also for molecular electronics.Comment: 5 pages, 3 figures; Nanoscale (2011

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Applications of DNA self-assembled structures in nanoelectronics and plasmonics

In this thesis, the potential applications of DNA self-assembled structures were explored in both nanoelectronics and plasmonics. The works can be divided into two parts: electrical characterization of unmodified multilayered DNA origami and DNA-gold-nanoparticle conjugates after they were trapped between gold nanoelectrodes by dielectrophoresis, and the development of a novel fabrication method using DNA origami as a template for smooth, high resolution metallic nanostructures as well as optical characterization of them. One of the biggest challenges in self-assembled nanoelectronic devices is to connect them to macroscopic circuits. Dielectrophoretic (DEP) trapping has been used extensively in manipulation of micro- and nanoscale objects in solution. We have demonstrated this technique by trapping four structurally distinct multilayered DNA origami between gold nanoelectrodes by DEP and electrically characterized some of the trapped structures at high relative humidity. Most of the samples showed insulating behavior in both DC I-V measurement and AC impedance spectroscopy. In the other experiment, an assembly of three gold nanoparticles (AuNPs) conjugated with a triple-cross-over-tile (TX-tile) structure were designed, synthesized, and trapped by DEP. At the beginning no current was observed, but after a few chemical gold growth steps, Coulomb blockade behavior was observed from the liquid helium temperature up to the room temperature. Although no gated measurement was carried out, the random switching at low temperature measurements highly resembled a similar behavior of single electron transistor (SET). The second half of this thesis is focused on the development of a DNA-assisted lithography (DALI) method, in which DNA origami was used to mask the growth of SiO2 on Si chips in order to generate a stencil mask with openings of the DNA origami shape. Then the stencil was used in conventional microfabrication processes to deposit metallic nanostructures with almost the same shape as DNA origami on different substrates. Three different DNA origami were used to fabricate metallic structures with various optical properties on sapphire substrates. The localized surface plasmon resonance (LSPR) of Seeman tile and a bowtie antenna was characterized by a dark-field microscope. The surface enhanced Raman spectroscopy (SERS) of two different marker molecules on gold bowtie antennas was characterized too. Finally, the chiral double-L samples landed on a surface with different orientation combinations showed distinct circular dichroism (CD) spectra. In addition, a method to deposit DNA origami on unmodified surface with large area by spray coating technique was reported

DNA Origami Nanophotonics and Plasmonics at Interfaces

DNA nanotechnology provides a versatile toolbox for creating custom and accurate shapes that can serve as versatile templates for nanopatterning. These DNA templates can be used as molecular-scale precision tools in, for example, biosensing, nanometrology, and super-resolution imaging, and biocompatible scaffolds for arranging other nano-objects, for example, for drug delivery applications and molecular electronics. Recently, increasing attention has been paid to their potent use in nanophotonics since these modular templates allow a wide range of plasmonic and photonic ensembles ranging from DNA-directed nanoparticle and fluorophore arrays to entirely metallic nanostructures. This Feature Article focuses on the DNA-origami-based nanophotonics and plasmonics - especially on the methods that take advantage of various substrates and interfaces for the foreseen applications.Peer reviewe