The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals.

Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnology. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addition of the Watson-Crick complement to a TFO containing a short toehold, and (c) the addition of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.

A device that operates within a self-assembled 3D DNA crystal.

Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

An Organic Semiconductor Organized into 3D DNA Arrays by "Bottom-up" Rational Design.

A 3D array of organic semiconductors was assembled using a DNA scaffold. An octameric aniline molecule ("octaniline") was incorporated into a DNA building block based on a dimeric tensegrity triangle. The construct self-assembled to form a 3D crystal. Reversible redox conversion between the pernigraniline and leucoemeraldine states of the octaniline is retained in the crystal. Protonic doping gave emeraldine salt at pH 5, corresponding to the conductive form of polyaniline. Redox cycling within the crystal was visualized by color changes and Raman microscopy. The ease of conversion between the octaniline states suggests that it is a viable electronic switch within a unique 3D structure.

Thermal-induced surface plasmon band shift of gold nanoparticle monolayer: morphology and refractive index sensitivity.

In this paper, thermal-induced behaviors of a gold nanoparticle monolayer on glass slides are investigated. First, through horizontal lifting, gold nanoparticle monolayers are transferred from a water/hexane interface to glass slides. Then thermal treatment is carried out in air, after which an apparent color change of the obtained samples is noticed, depending on the annealing temperature, reflecting a shift of the surface plasmon band (SPB). Depending on the trend of SPB shift, the overall thermal process is divided into three stages. In the first stage, SPB shows a redshift trend with concomitant band broadening. Further increase of the annealing temperature in the second stage results in an increase of interparticle distance. Thus an apparent decrease in absorbance takes place with SPB shift to shorter wavelengths. In the third stage, the SPB redshifts again. Bulk refractive index sensitivity (RIS) measurements are taken by immersing the obtained samples in solutions of various refractive indices and a linear dependence of RIS(λ) and RIS(ext) on refractive index is concluded. In particular, the influences of parameters such as particle sizes, location of SPB, substrate effect and morphology effect on RIS are discussed in detail. The corresponding performance of each sample as a localized surface plasmon resonance-based sensor is evaluated by a figure of merit (FOM) represented as FOM(λ) and FOM(ext). It is found that the optimum annealing temperature is 500 °C. In terms of nanoparticle sizes, samples with a 35 nm gold nanoparticle monolayer perform better than those with 15 nm. The current strategy is simple and facile to achieve fine control of the SPB, in which large-size precision instruments or complex chemosynthesis are unnecessary. Therefore, this method has not only significance for theory but also usefulness in practical applications.

Elliptical silicon arrays with anisotropic optical and wetting properties.

We demonstrate a facile etching method to fabricate silicon elliptical pillar arrays (Si-EPAs) with unique anisotropic optical and wetting characters using polystyrene elliptical hemisphere arrays (EHAs) as mask. The EHAs were fabricated via a modified micromolding method. By varying the experimental conditions in the fabrication process, the morphology of the resulting microstructures can be controlled exactly. Because of the anisotropic morphology of the elliptical pillar, the Si-EPA shows unique anisotropic properties, such as anisotropic surface reflection and anisotropic wetting property. Additionally, through oblique evaporation deposition of Au and selective chemical modification to turn the elliptical pillars into "Janus" elliptical pillars, the "Janus" Si-EPA shows more peculiar anisotropic properties owing to the further increased asymmetry. We believe that the Si-EPAs will have potential applications in anisotropic optical and electronic devices.

Device based in-chip critical dimension and overlay metrology.

The use of optical metrology techniques in process control for microelectronic manufacturing has become widespread. These techniques are fast and non-destructive, allowing a higher sampling rate than non-optical methods like scanning electron or atomic force microscopy. One drawback of most optical metrology tools is the requirement that special measurement structures be fabricated in the scribe line between chips. This poses significant limitations regarding the characterization of lithography processes that may be overcome via in-chip measurements. In this paper we present experimental results for an in-chip optical metrology technique that allows direct measurement of both critical dimensions and overlay displacement errors in the DRAM manufacturing process. This technique does not require special target structures and is performed on the actual semiconductor devices.

Passive stiffness in Drosophila indirect flight muscle reduced by disrupting paramyosin phosphorylation, but not by embryonic myosin S2 hinge substitution.

High passive stiffness is one of the characteristic properties of the asynchronous indirect flight muscle (IFM) found in many insects like Drosophila. To evaluate the effects of two thick filament protein domains on passive sarcomeric stiffness, and to investigate their correlation with IFM function, we used microfabricated cantilevers and a high resolution imaging system to study the passive IFM myofibril stiffness of two groups of transgenic Drosophila lines. One group (hinge-switch mutants) had a portion of the endogenous S2 hinge region replaced by an embryonic version; the other group (paramyosin mutants) had one or more putative phosphorylation sites near the N-terminus of paramyosin disabled. Both transgenic groups showed severely compromised flight ability. In this study, we found no difference (compared to the control) in passive elastic modulus in the hinge-switch group, but a 15% reduction in the paramyosin mutants. All results were corroborated by muscle fiber mechanics experiments performed on the same lines. The fact that myofibril elasticity is unaffected by hinge switching implies alternative S2 hinges do not critically affect passive sarcomere stiffness. In contrast, the mechanical defects observed upon disrupting paramyosin phosphorylation sites in Drosophila suggests that paramyosin phosphorylation is important for maintaining high passive stiffness in IFM myofibrils, probably by affecting paramyosin's interaction with other sarcomeric proteins.

Passive stiffness of Drosophila IFM myofibrils: a novel, high accuracy measurement method.

As the smallest muscle-cell substructure that retains the intact contractile apparatus, the single myofibril is considered the optimal specimen for muscle mechanics, although its small size also poses some technical difficulties. Myofibrils from Drosophila indirect flight muscle (IFM) are particularly difficult to study because their high passive stiffness makes them hard to handle, and too resistant to stretch to produce enough elongation for the accurate measurement of sarcomere length change. In this study, we devised a novel method for accurate stiffness measurement of single relaxed myofibrils using microfabricated cantilevers and phase contrast microscopy. A special experimental protocol was developed to minimize errors, and some data analysis strategies were used to identify and exclude spurious data. Remarkably consistent results were obtained from Drosophila IFM myofibrils. This novel, high accuracy method is potentially an effective tool for detecting small passive stiffness change in muscle mutants.