Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT

Protein structure networks are constructed for the identification of long-range signaling pathways in cysteinyl tRNA synthetase (CysRS). Molecular dynamics simulation trajectory of CysRS-ligand complexes were used to determine conformational ensembles in order to gain insight into the allosteric signaling paths. Communication paths between the anticodon binding region and the aminoacylation region have been identified. Extensive interaction between the helix bundle domain and the anticodon binding domain, resulting in structural rigidity in the presence of tRNA, has been detected. Based on the predicted model, six residues along the communication paths have been examined by mutations (single and double) and shown to mediate a coordinated coupling between anticodon recognition and activation of amino acid at the active site. This study on CysRS clearly shows that specific key residues, which are involved in communication between distal sites in allosteric proteins but may be elusive in direct structure analysis, can be identified from dynamics of protein structure networks.

Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

Readout of a real-time hologram in bacteriorhodopsin film with high diffraction efficiency and intensity

A scheme for the readout of a hologram recorded in bacteriorhodopsin film with high diffraction efficiency and intensity is suggested and demonstrated. Two weak coherent continuous beams function as the recording beams, and a strong light pulse is used to read the real-time hologram. The width of the readout light pulse is modulated to be short compared with the erase time of the reading beam; the time space between two adjacent pulses is ensured to be longer than the time the beams take to recover the hologram, and high diffraction efficiency and intensity (similar to 11 mW/cm(2)) can be obtained. (C) 1996 Optical Society of America.

Wavefront conversion by local volume holograms between cylindrical and plane waves with reconstruction at a different readout wavelength

Based on the two-dimensional coupled-wave theory, the wavefront conversion between cylindrical and plane waves by local volume holograms recorded at 632.8 nm and reconstructed at 800 nm is investigated. The proposed model can realize the 90 degrees holographic readout at a different readout wavelength. The analytical integral solutions for the amplitudes of the space harmonics of the field inside the transmission geometry are presented. The values of the off-Bragg parameter at the reconstructed process and the diffracted beam's amplitude distribution are analysed. In addition, the dependences of diffraction efficiency on the focal length of the recording cylindrical wave and on the geometrical dimensions of the grating are discussed. Furthermore, the focusing properties of this photorefractive holographic cylindrical lens are analysed.

Diffraction properties of volume holographic gratings for an ultrashort pulsed beam with different polarization states readout

The diffraction properties of volume holographic gratings are studied when the gratings are illuminated by an ultrashort pulsed beam with different polarization states. The developed coupled wave theory of Kogelnik is used. Considering the dispersion effect of the grating media, solutions for the diffracted and transmitted intensities, diffraction efficiencies and the bandwidths of the gratings are given in transmission volume holographic gratings and reflection volume holographic gratings. The bandwidths of the gratings are reduced by the dispersion effect of the grating media. They also have different influences on the diffraction of an ultrashort pulsed beam with different polarization states. For different values of the ratio of the spectral bandwidth of the input pulse to that of the grating, the changes of the spectral and temporal distributions of the diffracted intensities, as well as the diffraction efficiencies of the gratings are shown.

Three-dimensional coupled wave study for finite-sized anisotropic volume holographic gratings under ultrashort pulsed beam readout

The three-dimensional coupled wave theory is extended to systematically investigate the diffraction properties of finite-sized anisotropic volume holographic gratings (VHGs) under ultrashort pulsed beam (UPB) readout. The effects of the grating geometrical size and the polarizations of the recording and readout beams on the diffraction properties are presented, in particular under the influence of grating material dispersion. The wavelength selectivity of the finite-sized VHG is analyzed. The wavelength selectivity determines the intensity distributions of the transmitted and diffracted pulsed beams along the output face of the VHG. The distortion and widening of the diffracted pulsed beams are different for different points on the output face, as is numerically shown for a VHG recorded in a LiNbO3 crystal. The beam quality is analyzed, and the variations of the total diffraction efficiency are shown in relation to the geometrical size of the grating and the temporal width of the readout UPB. In addition, the diffraction properties of the finite-sized and one-dimensional VHG for pulsed and continuous-wave readout are compared. The study shows the potential application of VHGs in controlling spatial and temporal features of UPBs simultaneously. (C) 2007 Optical Society of America

Bragg diffraction of multilayer volume holographic gratings under ultrashort laser pulse readout

The multilayer coupled wave theory is extended to systematically investigate the diffraction properties of multilayer volume holographic gratings (MVHGs) under ultrashort laser pulse readout. Solutions for the diffracted and transmitted intensities, diffraction efficiency, and the grating bandwidth are obtained in transmission MVHGs. It is shown that the diffraction characteristics depend not only on the input pulse duration but also on the number and thickness of grating layers and the gaps between holographic layers. This analysis can be implemented as a useful tool to aid with the design of multilayer volume grating-based devices employed in optical communications, pulse shaping, and processing. (C) 2008 Optical Society of America

Novel approach to super-resolution pits readout

We proposed a novel method to realize the readout of super-resolution pits by using a super-resolution reflective film to replace the reflective layer of the conventional ROM. At the same time, by using Sb as the super-resolution reflective layer and SiN as a dielectric layer, the super-resolution pits with diameters of 380 nm were read out by a setup whose laser wavelength is 632.8 nm and numerical aperture is 0.40. In addition, the influence of the Sb thin film thickness on the readout signal was investigated, the results showed that the optimum Sb thin film thickness is 28 to 30 nm, and the maximum CNR is 38 to 40 dB. (C) 2002 Society of Photo-Optical Instrumentation Engineers.

Dynamic readout of subdiffraction-limited pit arrays with a silver superlens

Recent theoretical and experimental results suggested that the silver superlens could be constructed through controlling silver thin film thickness and preparation conditions, and applied in subdiffraction-limited optical imaging and optical lithography. In this work, we report another significant application of silver superlens-ultrahigh density optical data storage. With the silver superlens the subdiffraction-limited pit arrays on an optical disk are dynamically read out and the carrier-to-noise ratio can reach 25 dB for the thin film thickness of 46 nm. The readout laser power and readout velocity have little effect on the carrier-to-noise ratio. Additionally, in our experiment the silver thin film thickness needs to be controlled in the range from 20 to 80 nm.

On the dynamic readout of sub-diffraction-limit pit arrays with a silver thin film

Fast moving arrays of periodic sub-diffraction-limit pits were dynamically read out via a silver thin film. The mechanism of the dynamic readout is analysed and discussed in detail, both experimentally and theoretically. The analysis and experiment show that, in the course of readout, surface plasmons can be excited at the silver/air interface by the focused laser beam and amplified by the silver thin film. The surface plasmons are transmitted into the substrate/silver interface with a large enhancement. The surface waves at the substrate/silver interface are scattered by the sinusoidal pits of sub-diffraction-limit size. The scattered waves are collected by a converging lens and guided into the detector for the readout.

Study on readout durability of super-RENS disk

Characteristics essential for the readout durability of a superresolution near-field structure (super-RENS) disk are studied experimentally by using a home-built optical measuring setup and atomic force microscope, based on a simplified PtOx super-RENS disk. The experimental results show that for a super-RENS disk with constant structure and materials, readout signals including transmittance and reflectance vary with changes in bubble shape and size, indicating that the readout durability of the disk has a strong dependence on bubble stability, which is closely related to the thickness of the cover layer, the recording power and readout power, and the mechanical properties of the dielectric layer. Based on our experimental results, the main direction for improving readout durability is also proposed. (c) 2008 Optical Society of America.

Low-Power Super-resolution Readout with Antimony Bismuth Alloy Film as Mask layer

Sb-Bi alloy films are proposed as a new kind of super-resolution mask layer with low readout threshold power. Using the Sb-Bi alloy film as a mask layer and SiN as a protective layer in a read-only memory disc, the super-resolution pits with diameters of 380 nm are read out by a dynamic setup, the laser wavelength is 780 nm and the numerical aperture of pickup lens is 0.45. The effects of the Sb-Bi thin film thickness, laser readout power and disc rotating velocity on the readout signal are investigated. The results show that the threshold laser power of super-resolution readout of the Sb-Bi mask layer is about 0.5 mW, and the corresponding carrier-to-noise ratio is about 20 dB at the film thickness of 50 nm. The super-resolution mechanism of the Sb-Bi alloy mask layer is discussed based on its temperature dependence of reflection.