A study of the anti-reflection efficiency of natural nano-arrays of varying sizes

The dependence of optical reflectivity and wettability on the surface topography of 32 species of cicada wing membranes has been investigated using UV-visible spectrophotometry, contact angle measurements and environmental scanning electron microscopy. The nanoscale hexagonally close packed protrusions have been shown to exhibit an anti-reflection and in some cases an anti-wetting function. The parameters of the structures were measured to be 77-148 nm in diameter, 44-117 nm in spacing and 159-481 nm in height. The transmittance spectrum and static contact angles were measured. At a wavelength range of 500-2500 nm, only minor differences in the anti-reflection performance were observed for each cicada species ascribed to the mechanism of impedance matching between cuticle and air. The transmittance properties of cicada wings were altered successfully through the scanning probe microscope-based manipulation by reducing the protrusion height via the contact mode. A near linear dependence was found between a decrease in protuberance height and a resulting increase in reflectance intensity. A diversity of wettability was observed with contact angles varying from 56.5° to 146.0°. Both effects of anti-reflection and wettability are dependent on the height of protrusions. The anti-reflection is insensitive when the wavelength is larger than the lateral feature size of the nanostructure. The stronger hydrophobic properties are generally associated with a larger diameter, closer spacing and greater height of protrusions when the wing membrane is intact.     

Nanostructures of complexes formed by calf thymus DNA interacting with cationic surfactants

Synchrotron small-angle X-ray scattering was used to study the nanostructures of the complexes formed by calf thymus DNA interacting with cationic lipids (or surfactants) of didodecyldimethylammonium bromide (DDAB), cetyltrimethylammonium bromide (CTAB), and their mixture with a zwitterionic lipid of 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (PHGPC). The effects of lipid/DNA ratios, DNA chain flexibility, lipid topology, and neutral lipid mixing on the nanostructures of DNA-lipid complexes were investigated. The complexes between double-stranded DNA (dsDNA) and double-tailed DDAB formed a bilayered lamellar structure, whereas the complexes between dsDNA and single-tailed CTAB preferred a structure of 2D hexagonal close packing of cylinders. With single stranded DNA (ssDNA) interacting with CTAB, the complexes showed a Pm3n cubic structure due to the different chain flexibility between dsDNA and ssDNA. The lipid molecules bound by rigid dsDNA like to form cylindrical micelles, whereas lipids bound to flexible ssDNA could form spherical or short cylindrical micelles. The addition of the neutral single-chained PHGPC lipids to the CTAB lipids could induce a structural transition of dsDNA-lipid complexes from a 2D hexagonal to a multi-bilayered lamellar structure. The parallel DNA strands were intercalated in the water layers of lamellar stacks of the mixed lipid bilayers. The DNA-DNA spacing depended on the ratios of charged lipid to neutral lipid, and charged lipid to DNA, respectively.     

DNA四面体纳米结构及其在生物技术领域的应用进展

DNA四面体纳米结构是一种通过精确巧妙的DNA序列设计,应用碱基互补配对的原则,由4条单链自动杂交结合而成的具有四面体形状的DNA三维纳米结构。其具有良好的生物相容性和优异的细胞膜通透性,同时制备较为简单且产率高、尺寸以及动态性均可调节,因而在微生物鉴定、医学诊断和生物传感器等领域得到了广泛的研究与应用。基于此,介绍了DNA四面体纳米结构及其功能化修饰,综述了DNA四面体纳米结构在生物技术领域的应用进展,以期为推动DNA四面体纳米结构的研究、拓宽其应用领域提供参考。     

Folding of deoxyribonucleic acid in chromatin]

A structural model for the folding of deoxyribonucleic acid (DNA) in chromatin has been evolved on the basis of the X-ray diffraction patterns of deoxyribonucleoproteids (DNP). The DNA is oriented in the direction of DNP fibres and does not exhibit a superhelical structure. In the nu-bodies the DNA is folded 7 times to and fro on the envelope of a cylinder 10 nm in diameter. The height of the DNA-hairpins is 9 nm - 10 nm. The spacing between the refolded DNA segments is 3,6 nm. This supramolecular folding crystalization of the DNA is a general principle of organization and, through different types of morphological growth of the folding crystals, leads to the chromatin, to psi-DNA, to DNA monocrystals, and to DNA packing in some phage heads.     

Search of Extremely Sensitive Near-Infrared Plasmonic Interfaces: A Theoretical Study

The sensitivity of the wavelength position of localized surface plasmon resonance (LSPR) in metal nanostructures to local changes in the refractive index has been widely used for label-free detection strategies. Tuning the optical properties of the nanostructures from the visible to the infrared region is expected to have a drastic effect on the refractive index sensitivity. Here, we theoretically investigate the optical response of a newly designed plasmonic interface to changes in the bulk refractive index by the finite difference time domain method. It consists of a structured interface, where the planar interface is superposed with dielectric pillars 30 nm in height and 125 nm in length with a separation distance of 15 nm. The pillars are covered with U-shaped gold nanostructures of 50 nm in height, 125 nm in length, and 5 nm of gold base thickness. The whole structure is finally covered with a 5-nm thick dielectric layer of n ₂?=?2.63. This plasmonic structure shows bulk refractive index sensitivities up to 1750 nm/RIU (RIU : refractive index unit) in the near infrared (λ?=?2621 nm). The enhanced sensitivity is a consequence of the extremely enhanced electrical field between the gold nanopillars of the plasmonic interface.     

CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells

DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.     

Investigations into the polymorphism of rat tail tendon fibrils using atomic force microscopy

Collagen type I displays a typical banding periodicity of 67 nm when visualized by atomic force or transmission electron microscopy imaging. We have investigated collagen fibers extracted from rat tail tendons using atomic force microscopy, under different ionic and pH conditions. The majority of the fibers reproduce the typical wavy structure with 67 nm spacing and a height difference between the peak and the grooves of at least 5 nm. However, we were also able to individuate two other banding patterns with 23+/-2 nm and 210+/-15 nm periodicities. The small pattern showed height differences of about 2 nm, whereas the large pattern seems to be a superposition of the 67 nm periodicity showing height differences of about 20 nm. Furthermore, we could show that at pH values of 3 and below the fibril structure gets dissolved whereas high concentrations of NaCl and CaCl(2) could prevent this effect.     

Triangular Au�CAg Nanoframes with Tunable Surface Plasmon Resonance Signal from Visible to Near-Infrared Region

In recent years, metal hollow nanostructures are intriguing to be synthesized and studied because they exhibit unique surface plasmonic properties. Although many methods for tuning the surface plasmonic absorption peaks of silver nanostructures have been reported, it still remains a great challenge to produce hollow Ag nanostructure with controllable surface plasmon resonance (SPR) via a facile method. In this paper, triangular Au–Ag nanoframes were successfully fabricated using triangular silver nanoplates as templates, through galvanic replacement reaction between the silver nanoplates and HAuCl₄, exhibiting tuneable SPR response from visible (605 nm) to near-infrared region (1,235 nm).     

Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment

Enzymatic ligation is a popular method in DNA nanotechnology for structural enforcement. When employed as stability switch for chosen components, ligation can be applied to induce DNA nanostructure reconfiguration. In this study, we investigate the reinforcement effect of ligation on addressable DNA nanostructures assembled entirely from short synthetic strands as the basis of structural reconfiguration. A careful calibration of ligation efficiency is performed on structures with programmable nicks. Systematic investigation using comparative agarose gel electrophoresis enables quantitative assessment of enhanced survivability with ligation treatment on a number of unique structures. The solid ligation performance sets up the foundation for the ligation-based structural reconfiguration. With the capability of switching base pairing status between permanent and transient (ON and OFF) by a simple round of enzymatic treatment, ligation induced reconfiguration can be engineered for DNA nanostructures accordingly.     

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

DNA nanotechnology enables the programmed synthesis of intricate nanometer-scale structures for diverse applications in materials and biological science. Precise control over the 3D solution shape and mechanical flexibility of target designs is important to achieve desired functionality. Because experimental validation of designed nanostructures is time-consuming and cost-intensive, predictive physical models of nanostructure shape and flexibility have the capacity to enhance dramatically the design process. Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.-N., Shiao,E.L., Wauer,T., Wortmann,P., Bathe,M., Dietz,H. (2011) A primer to scaffolded DNA origami. Nat. Meth., 8, 221-229.]. 3D solution shape and flexibility are predicted from basepair connectivity maps now accounting for nicks in the DNA double helix, entropic elasticity of single-stranded DNA, and distant crossovers required to model wireframe structures, in addition to previous modeling (Castro,C.E., et al.) that accounted only for the canonical twist, bend and stretch stiffness of double-helical DNA domains. Systematic experimental validation of nanostructure flexibility mediated by internal crossover density probed using a 32-helix DNA bundle demonstrates for the first time that our model not only predicts the 3D solution shape of complex DNA nanostructures but also their mechanical flexibility. Thus, our model represents an important advance in the quantitative understanding of DNA-based nanostructure shape and flexibility, and we anticipate that this model will increase significantly the number and variety of synthetic nanostructures designed using nucleic acids.     

Mechanisms and control of silk-based electrospinning

Silk fibroin (SF) nanofibers, formed through electrospinning, have attractive utility in regenerative medicine due to the biocompatibility, mechanical properties, and tailorable degradability. The mechanism of SF electrospun nanofiber formation was studied to gain new insight into the formation and control of nanofibers. SF electrospinning solutions with different nanostructures (nanospheres or nanofilaments) were prepared by controlling the drying process during the preparation of regenerated SF films. Compared to SF nanospheres in solution, SF nanofilaments had better spinnability with lower viscosity when the concentration of silk protein was below 10%, indicating a critical role for SF morphology, and in particular, nanostructures, for the formation of electrospun fibers. More interesting, the diameter of electrospun fibers gradually increased from 50 to 300 nm as the concentration of SF nanofilaments in the solution increased from 6 to 12%, implying size control by simply adjusting SF nanostructure and concentration. Aside from process parameters investigated in previous studies, such as SF concentration, viscosity, and electrical potential, the present mechanism emphasizes significant influence of SF nanostructure on spinnability and diameter control of SF electrospun fibers, providing a controllable option for the preparation of silk-based electrospun scaffolds for biomaterials, drug delivery, and tissue engineering needs.     

Chitosan and Glyceryl Monooleate Nanostructures Containing Gemcitabine: Potential Delivery System for Pancreatic Cancer Treatment

The objectives of this study are to enhance cellular accumulation of gemcitabine with chitosan/glyceryl monooleate (GMO) nanostructures, and to provide significant increase in cell death of human pancreatic cancer cells in vitro. The delivery system was prepared by a multiple emulsion solvent evaporation method. The nanostructure topography, size, and surface charge were determined by atomic force microscopy (AFM), and a zetameter. The cellular accumulation, cellular internalization and cytotoxicity of the nanostructures were evaluated by HPLC, confocal microscopy, or MTT assay in Mia PaCa-2 and BxPC-3 cells. The average particle diameter for 2% and 4% (w/w) drug loaded delivery system were 382.3 ± 28.6 nm, and 385.2 ± 16.1 nm, respectively with a surface charge of +21.94 ± 4.37 and +21.23 ± 1.46 mV. The MTT cytotoxicity dose-response studies revealed the placebo at/or below 1 mg/ml has no effect on MIA PaCa-2 or BxPC-3 cells. The delivery system demonstrated a significant decrease in the IC50 (3 to 4 log unit shift) in cell survival for gemcitabine nanostructures at 72 and 96 h post-treatment when compared with a solution of gemcitabine alone. The nanostructure reported here can be resuspended in an aqueous medium that demonstrate increased effective treatment compared with gemcitabine treatment alone in an in vitro model of human pancreatic cancer. The drug delivery system demonstrates capability to entrap both hydrophilic and hydrophobic compounds to potentially provide an effective treatment option in human pancreatic cancer.     

An autonomously self-assembling dendritic DNA nanostructure for target DNA detection

There is a growing need for sensitive and reliable nucleic acid detection methods that are convenient and inexpensive. Responsive and programmable DNA nanostructures have shown great promise as chemical detection systems. Here, we describe a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. The detection protocol is executed autonomously without external intervention. Detection begins when a specific, single-stranded target DNA strand (T) triggers a hybridization chain reaction (HCR) between two, distinct DNA hairpins (α and β). Each hairpin opens and hybridizes up to two copies of the other. In the absence of T, α and β are stable and remain in their poised, closed-hairpin form. In the presence of T, α hairpins are opened by toe-hold mediated strand-displacement, each of which then opens and hybridizes two β hairpins. Likewise, each opened β hairpin can open and hybridize two α hairpins. Hence, each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a high molecular weight nanostructure. This HCR system has minimal sequence constraints, allowing reconfiguration for the detection of arbitrary target sequences. Here, we demonstrate detection of unique sequence identifiers of HIV and Chlamydia pathogens.     

Fabrication of Acrylonitrile-Butadiene-Styrene Nanostructures with Anodic Alumina Oxide Templates,Characterization and Biofilm Development Test for Staphylococcus epidermidis

Medical devices can be contaminated by microbial biofilm which causes nosocomial infections. One of the strategies for the prevention of such microbial adhesion is to modify the biomaterials by creating micro or nanofeatures on their surface. This study aimed (1) to nanostructure acrylonitrile-butadiene-styrene (ABS), a polymer composing connectors in perfusion devices, using Anodic Alumina Oxide templates, and to control the reproducibility of this process; (2) to characterize the physico-chemical properties of the nanostructured surfaces such as wettability using captive-bubble contact angle measurement technique; (3) to test the impact of nanostructures on Staphylococcus epidermidis biofilm development. Fabrication of Anodic Alumina Oxide molds was realized by double anodization in oxalic acid. This process was reproducible. The obtained molds present hexagonally arranged 50 nm diameter pores, with a 100 nm interpore distance and a length of 100 nm. Acrylonitrile-butadiene-styrene nanostructures were successfully prepared using a polymer solution and two melt wetting methods. For all methods, the nanopicots were obtained but inside each sample their length was different. One method was selected essentially for industrial purposes and for better reproducibility results. The flat ABS surface presents a slightly hydrophilic character, which remains roughly unchanged after nanostructuration, the increasing apparent wettability observed in that case being explained by roughness effects. Also, the nanostructuration of the polymer surface does not induce any significant effect on Staphylococcus epidermidis adhesion.     

Gel electrophoretic mobility evaluation of a necklace-like DNA nanostructure

DNA nanotechnologies have been highlighted as a promising synthetic tool for the creation of new shaped materials. They have developed a variety of materials in different shapes and sizes [1]. Inspired by these advancements, we sought to design a ring-shaped DNA nanostructure connected by X-DNA blocks. Six XDNA blocks were ligated together to form a circular nanostructure with a diameter of approximately 30 nm. Each DNA block possesses different overhang sequences in its terminal. It was sequentially built up onto each block platform in the line and later clipped into a necklace shape via enzymatic ligation. It was finally evaluated by a gel electrophoretic migration shift assay. It was concluded that the complete set of the necklace shaped DNA nanostructure was the most slowly retarded relative to other forms of incompleteness.     

Fine Structures of Cell Envelopes of Chlamydia Organisms as Revealed by Freeze-Etching and Negative Staining Techniques

The cell walls of Chlamydia psittaci (meningopneumonitis strain) were examined by the freeze-etching and negative staining techniques. It was observed that the cleaved convex surface of the developmental, reticulate body was covered with numerous non-etchable particles 9 to 10 nm in diameter, these particles being rarely seen on the concave surface. Similarly, the convex surface of the mature, elementary body (EB) was covered with many particles but the concavity lacked these particles. After etching, the smooth concave surface of the EB appeared to have a hexagonally arrayed subunit structure, on which the button structure (B structure) was observed. Each B structure had a diameter of 27 nm and several B structures were grouped together in a hexagonal arrangement with a center-to-center spacing of 45 nm. In a limited area of the negatively stained EB cell wall, hexagonally arrayed rosette structures were present, with a center-to-center spacing similar to the B structures seen in the freeze-etched preparation. Each rosette, about 19 to 20 nm in diameter, appeared to be composed of a radial arrangement of nine subunits. The freeze-fractured cell wall-cytoplasmic membrane complexes indicated that the outer surface of the cytoplasmic membrane which appeared as the convex surface was covered with the fine particles, and thus it was likely that frozen EB was cleaved at the gap between the cell wall and ctyoplasmic membrane. On the cleaved inclusion, several groups of fine particles were observed. In each group, the particles were arranged hexagonally with the spacing ranging from 20 to 50 nm.     

Temperature dependence of the ripple structure in dimyristoylphosphatidylcholine studied by synchrotron X-ray small-angle diffraction

The ripple structure of 1,2-dimyristoyl-L-phosphatidylcholine (DMPC) multibilayer containing excess water (60 wt%) was studied by synchrotron X-ray small-angle diffraction. The (0,1) spacing which corresponds to the ripple repeat distance depends on temperature: At 13 degrees C the (0,1) spacing is 14.15 nm, the spacing decreases at higher temperatures and reaches 12.1 nm at 23.5 degrees C, just below the main transition temperature. The spacing is in good agreement between heating process and cooling process except for the supercooling region. The result suggests that the rearrangement of the ripple structure takes place during temperature change successively. The Landau-de Gennes free energy equation explains well the temperature dependence of the ripple repeat distance.     

Structure-based model for light-harvesting properties of nucleic acid nanostructures

Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.     

Polyvalent interactions of HIV-gp120 protein and nanostructures of carbohydrate ligands

This paper presents the initial effort in anti-HIV infection using glycosphingolipid-based nanostructures. HIV infection of CD4 negative cells is initiated by the binding of the viral envelope glycoprotein gp120 to galactosylceramide (GalCer), a glycosphingolipid that serves as the cellular receptor for viral recognition. A series of nanostructures of GalCer are designed and produced using an AFM-based lithography method known as nanografting. The geometry dependence of recombinant gp120 binding to these nanostructures is monitored using high-resolution AFM imaging. Gp120 molecules are found to favor binding sites that allow for polyvalent interactions. Increased adsorption at the intersection of two lines, or between two parallel lines with matching separation for trimeric binding, strongly suggests that trivalent interactions are dominant in gp120-GalCer nanostructure interactions. Systematic distance-dependence studies, using parallel nanolines with various separations, reveal a separation of 4.8 nm, matching the separation of V3 loops in gp120 trimers. This investigation demonstrates that nanotechnology provides a powerful tool for investigating and guiding polyvalent interactions among biological systems.     

Ag Nanostructures Produced by Glancing Angle Deposition with Remarkable Refractive Index Sensitivity

Glancing angle deposition is a powerful method for direct fabrication of nanostructures on various substrates. In this research, GLAD method has been used to fabricate Ag nanostructures with columnar morphology for refractive index sensing applications. The morphology and plasmonic properties of the nanostructures are controlled by changing deposition parameters such as glancing angle, speed of azimuthal rotation of the substrate, and the height of deposited nanostructures. The results show that increasing the deposition thickness from 200 to 500 nm leads to narrowing the plasmonic peak, which mainly relates to increment of the distance between larger nanostructures. By changing the glancing angle between 86° to 80°, the narrowest plasmonic peak corresponding to the greatest sensitivity has been obtained for the film deposited at the angle of 82°. Also, increment of the rotation speed of the samples leads to narrowing of the plasmonic peaks. By measuring the refractive index sensitivity (RIS) of the nanostructures, a best sensitivity of 154 nm/RIU has been obtained. Finally, we investigated the stability of Ag nanostructures in deionized water by introducing a new stabilizing technique in which a thin Au layer is coated on the Ag nanostructures. This technique has the merits of simultaneously protecting the Ag nanostructures against oxidation and keeping their refractive index sensitivity high enough for long time usages.