Orientation Of Dye Research Articles

Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage.

PNA is hybrid molecule ideally suited for bridging the functional landscape of polypeptides with the structural diversity that can be engineered with DNA nanostructures. However, PNA can be more challenging to work with in aqueous solvents due to its hydrophobic nature. A solution phase method using strain promoted, copper free click chemistry was developed to conjugate the fluorescent dye Cy5 to 2 bifunctional PNA strands as a first step toward building cyclic PNA-polypeptides that can be arranged within 3D DNA nanoscaffolds. A 3D DNA nanocage was designed with binding sites for the 2 fluorescently labeled PNA strands in close proximity to mimic protein active sites. Denaturing polyacrylamide gel electrophoresis (PAGE) is introduced as an efficient method for purifying charged, dye-labeled PNA conjugates from large excesses of unreacted dye and unreacted, neutral PNA. Elution from the gel in water was monitored by fluorescence and found to be more efficient for the more soluble PNA strand. Native PAGE shows that both PNA strands hybridize to their intended binding sites within the DNA nanocage. Förster resonance energy transfer (FRET) with a Cy3 labeled DNA nanocage was used to determine the dissociation temperature of one PNA-Cy5 conjugate to be near 50°C. Steady-state and time resolved fluorescence was used to investigate the dye orientation and interactions within the various complexes. Bifunctional, thermostable PNA molecules are intriguing candidates for controlling the assembly and orientation of peptides within small DNA nanocages for mimicking protein catalytic sites.

Resonance energy transfer in DNA duplexes labeled with localized dyes.

The growing maturity of DNA-based architectures has raised considerable interest in applying them to create photoactive light harvesting and sensing devices. Toward optimizing efficiency in such structures, resonant energy transfer was systematically examined in a series of dye-labeled DNA duplexes where donor-acceptor separation was incrementally changed from 0 to 16 base pairs. Cyanine dyes were localized on the DNA using double phosphoramidite attachment chemistry. Steady state spectroscopy, single-pair fluorescence, time-resolved fluorescence, and ultrafast two-color pump-probe methods were utilized to examine the energy transfer processes. Energy transfer rates were found to be more sensitive to the distance between the Cy3 donor and Cy5 acceptor dye molecules than efficiency measurements. Picosecond energy transfer and near-unity efficiencies were observed for the closest separations. Comparison between our measurements and the predictions of Förster theory based on structural modeling of the dye-labeled DNA duplex suggest that the double phosphoramidite linkage leads to a distribution of intercalated and nonintercalated dye orientations. Deviations from the predictions of Förster theory point to a failure of the point dipole approximation for separations of less than 10 base pairs. Interactions between the dyes that alter their optical properties and violate the weak-coupling assumption of Förster theory were observed for separations of less than four base pairs, suggesting the removal of nucleobases causes DNA deformation and leads to enhanced dye-dye interaction.

Elucidation of photophysical changes and orientation of acridine orange dye on the surface of borate capped gold nanoparticles using multi-spectroscopic techniques.

In the present work, we have carried out a detailed investigation on the binding interaction of acridine orange (AO) with borate capped gold nanoparticles (Au NPs) by absorption spectroscopy, steady state emission spectroscopy, time resolved fluorescence spectroscopy, high resolution transmission electron microscopy (HR-TEM), dynamic light scattering (DLS), zeta potential measurements, Fourier transform infrared (FT-IR) and Raman spectroscopy. The phenomena of hypochromism and the appearance of coupled localized surface plasmon resonance (LSPR) bands in the absorption spectral studies of the AO-Au NP system suggested the vital role of electrostatic interactions between AO dye and Au NPs. The results from HR-TEM and DLS measurements confirmed the formation of aggregated clusters of nanoparticles. The zeta potential studies of Au NPs and AO coated Au NPs suggested the occurrence of partial surface charge neutralization of negatively charged Au NPs by cationic AO dye. The interparticle edge to edge separation distance of adjacent Au NPs revealed the presence of AO molecules between the nano-gaps of Au NPs. Emission spectral studies of AO in the presence of increasing concentrations of Au NPs indicated the existence of a static quenching mechanism. Time resolved fluorescence spectroscopic study further validated the findings of steady state emission measurements. The comparison of experimental emission quenching data with the theoretically calculated value suggested the probable multi-layered assembly of AO on the surface of Au NPs. FT-IR and Raman spectral studies further revealed the existence of electrostatic interactions and possible horizontal orientation of AO dye molecules on Au NP surfaces.

Molecular design strategy toward diarylethenes that photoswitch with visible light.

Photoactive molecules that reversibly switch upon visible light irradiation are one of the most attractive targets for biological as well as imaging applications. One possible approach to prepare such photoswitches is to extend π-conjugation length of molecules and shift the absorption bands to longer wavelengths. Although several attempts have been demonstrated based on this approach for diarylethene (DAE) photoswitches, photoreactivity of the DAE derivatives is dramatically suppressed when the conjugation length is extended by connecting aromatic dyes at the side positions of aryl groups in the DAE unit. In this study, we successfully prepared a visible-light reactive DAE derivative by introducing an aromatic dye at the reactive carbon atom of the DAE unit, optimizing orbital level of each component, and controlling the mutual orientation of the aromatic dye and the DAE unit. The DAE derivative (3) undergoes a photocyclization reaction upon irradiation with 560 nm light and the closed-isomer converts to the open-ring isomer upon irradiation with 405 nm light. The high photoconversion yields (>90%) were achieved for both photocyclization and photocycloreversion reactions. The photoreactivity induced by visible light irradiation and the molecular design strategy were discussed based on theoretical calculations.

Complementary surface second harmonic generation and molecular dynamics investigation of the orientation of organic dyes at a liquid/liquid interface.

The second-order nonlinear response of two dyes adsorbed at the dodecane/water interface was investigated by surface second harmonic generation (SSHG). These dyes consist of the same chromophoric unit, 2-pyridinyl-5-phenyloxazole, with an alkyl chain located at the two opposite ends. The analysis of the polarization dependence of the SSHG intensity as usually performed points to similar tilt angles of the two dyes with respect to the interface but does not give information on the absolute direction. Molecular dynamics (MD) simulations reveal that both dyes lie almost flat at the interface but have opposite orientations. A refined SSHG data analysis with the width of the orientational distribution yields tilt angles that are in very satisfactory agreement with the MD simulations.

Thermodynamic Driving Forces for Dye Molecule Position and Orientation in Nanoconfined Solvents.

The results of replica exchange molecular dynamics simulations of a coumarin 153 (C153) dye molecule dissolved in ethanol confined within a 2.4 nm hydrophilic amorphous silica pore are presented. The C153 dye position and orientation distributions provide insight into time-dependent fluorescence measurements in nanoconfined solvents as well as general features of chemistry in mesoporous materials. In addition to the distributions themselves, the free energy, internal energy, and entropic contributions have been calculated to explore the factors determining the distributions. The most likely location of C153 is found to be near the pore surface, but two possible hydrogen-bonding structures lead to differing orientations. Internal energy and entropy are found to be competing forces within the pore, with entropy playing a significant role with unexpected consequences. These results represent a crucial step in determining how the nanoconfining framework can affect measurements of solvation dynamics.

Effect of Molecular Fluctuations on Hole Diffusion within Dye Monolayers

Measured hole diffusion coefficients in dye monolayers are larger than can be explained by a charge hopping model with a static distribution of parameters describing intermolecular hole transfer. We show that large amplitude fluctuations of the tethered dye configurations on the surface could explain the observed diffusion rates by enabling charges trapped in particular configurations to escape as the dye orientation changes. We present a multiscale model of hole transport that includes the effect of dynamic rearrangement of the monolayer of anchored dyes. Conformations of pairs of indolene dye molecules (both D102 and D149) were generated by a rigid molecular packing algorithm and Car–Parrinello molecular dynamics to mimic the conformational and configurational disorder of a dye monolayer adsorbed to an anatase (101) titanium dioxide surface. The electronic coupling (Jij) for each pair of neighboring dyes was calculated to build distributions representing the disorder in a real system. These values were used as inputs to Marcus’ non-adiabatic equation for charge transfer to calculate the rate of hole hopping for each pair. Hole diffusion was simulated with a continuous time random walk, accounting for different time scales of molecular rearrangement (changes in the dye geometry). The dynamic nature of configurational disorder was captured by reassigning the values of Jij, drawn from the aforementioned distributions, after a fixed renewal time. We found hole diffusion coefficients of 3.3 × 10–8 and 9.2 × 10–8 cm2 s–1 for D102 and D149, respectively, for a renewal time of 10–7 s. This is in good agreement with the corresponding measured coefficients for D102 and D149 of 9.6 × 10–8 and 2.5 × 10–7 cm2 s–1, whereas the diffusion coefficients are underestimated by at least a factor of 15 if the dynamics are ignored. Fast rearrangement of dye monolayer configuration may explain the high lateral hole diffusion coefficients determined experimentally. Our results indicate that both chemical structure and the availability of different packing configurations must be considered when designing conductive molecular monolayers.

Distribution of Dye and Mesogen Molecules Orientation in Photoaligning Layer vs. Aperture of Polarized Light Beam

Orientation of dyes and liquid crystals molecules in the field of laser radiation is considered taking into account anisotropy of molecular optical polarizability. A dependence of dyes and liquid crystals clusters energy on the strength of laser radiation electrical field, aperture of the light beam, optical polarizability anisotropy, order parameter and the number of molecules in a cluster, is derived. The angular distribution function of clusters is derived depending on the aperture of the light beam.

Fluorescence nanoscopy by polarization modulation and polarization angle narrowing

When excited with rotating linear polarized light, differently oriented fluorescent dyes emit periodic signals peaking at different times. We show that measurement of the average orientation of fluorescent dyes attached to rigid sample structures mapped to regularly defined (50 nm)(2) image nanoareas can provide subdiffraction resolution (super resolution by polarization demodulation, SPoD). Because the polarization angle range for effective excitation of an oriented molecule is rather broad and unspecific, we narrowed this range by simultaneous irradiation with a second, de-excitation, beam possessing a polarization perpendicular to the excitation beam (excitation polarization angle narrowing, ExPAN). This shortened the periodic emission flashes, allowing better discrimination between molecules or nanoareas. Our method requires neither the generation of nanometric interference structures nor the use of switchable or blinking fluorescent probes. We applied the method to standard wide-field microscopy with camera detection and to two-photon scanning microscopy, imaging the fine structural details of neuronal spines.

Accounting for dye diffusion and orientation when relating FRET measurements to distances: three simple computational methods.

Förster resonance energy transfer (FRET) allows in principal for the structural changes of biological systems to be revealed by monitoring distributions and distance fluctuations between parts of individual molecules. However, because flexible probes usually have to be attached to the macromolecule to conduct these experiments, they suffer from uncertainty in probe positions and orientations. One of the way to address this issue is to use molecular dynamics simulations to explicitly model the likely positions of the probes, but, this is still not widely accessible because of the large computational effort required. Here we compare three simpler methods that can potentially replace MD simulations in FRET data interpretation. In the first, the volume accessible for dye movement is calculated using a fast, geometrical algorithm. The next method, adapted from the analysis of electron paramagnetic studies, utilises a library of rotamers describing probe conformations. The last method uses preliminary MD simulations of fluorescent dyes in solution, to identify all conformational states of dyes and overlays this on the macromolecular system. A comparison of these methods in the simple system of dye-labelled polyproline, shows that in the case of lack of interaction between the dye and host, all give results comparable with MD simulations but require much less time. Differences between these three methods and their ability to compete with MD simulations in the analysis of real experiment are demonstrated and discussed using the examples of cold shock protein and leucine transporter systems.

When Freely-Rotating isn't Enough: A Study of Cyanine Dyes on RNA

Cyanine dyes are commonly attached to the 3' or 5' termini of nucleic acids to study folding and binding using FRET. It has been known for some time now that, to some extent, these dyes stack on the ends of duplex DNA, which complicates the interpretation of FRET. We used molecular dynamics (MD) simulations to study the indocarbocyanine dyes Cy3 and Cy5 attached to the 3' or 5' terminal bases of a 16-base-pair RNA duplex. The resulting trajectories for the inter-dye distance and dye orientation factor (κ2) are then used to predict FRET for the various RNA constructs. The results show that the average value of FRET depends on both the terminal base and the linker position. In particular, 3' attached dyes typically explore a wide region of configuration space, and the relative orientation factor, κ2, has a distribution that approaches that of free-rotators. This is in contrast to 5' attached dyes, which spend a significant fraction of their time in one or more configurations that are effectively stacked on the ends of the RNA duplex. However, even for the relatively free 3' attached dyes, the correlation time of κ2 is still too long to justify the use of a free-rotation approximation.

Effect of dye dispersion on the relaxation modes of smectic C* phase

We study how the dye dispersion influences the properties of ferroelectric liquid crystal (FLC). The polarisation measurement shows the decreasing linear behaviour with the increasing concentration of dye, indicating the orientation of dye in a direction opposite to FLC molecules. Accordingly, the response time increases with increasing concentration of dye. Dielectric data clearly show the existence of two relaxation phenomena in FLC and dye–dispersed systems. The relaxation strength of the Goldstone mode, which is observed around 200 Hz, has decreased with the dispersion of dye, and the relaxation frequency of this mode shifts towards the lower frequency side, due to increase in the rotational viscosity. The second relaxation mode, observed at ∼30 KHz, arises due to the formation of domains at the surface interface. This domain mode got suppressed with the dispersion of dye into FLC.

Host–Guest Interactions and Orientation of Dyes in the One-Dimensional Channels of Zeolite L

A combined experimental and modeling study of methylacridine (MeAcr(+)) dye-zeolite L composites unravels the microscopic origin of their functional properties. The anisotropic orientation of the cationic dye inside the ZL channel is unambiguously determined and understood. The most stable orientation of MeAcr(+), which features both its long and short molecular axes nearly perpendicular to the channel axis, is mainly determined by dye-ZL electrostatic interactions but also depends on the cosolvent water. In ZL, MeAcr(+) is not hydrogen bonded to water or ZL framework oxygens and is hydrophobically solvated by water molecules. These findings further support the hypothesis that the cosolvent can importantly influence properties of dye-zeolite composites. Of relevance for a deeper comprehension of the physical chemistry of these hybrids is the observation that trivial energy transfer processes (self-absorption) are often playing a significant role in the optical properties of the composites.

Photopolymerisation kinetics and electro-optical properties in mixtures of dichroic dye-doped nematic liquid crystal and photocurable polymer

This work reports the effect of dye on the photopolymerisation and electro-optical properties of polymer dispersed liquid crystal (PDLC) composite films. Dichroic PDLC (DPDLC) films based on a photocurable polymer and nematic liquid crystal (LC) with an azo dichroic dye were prepared by photopolymerisation-induced phase separation method. Polarising optical microscopy has been used for monitoring the phase separation kinetics and two-phase morphology evolution in the DPDLC system. LC domains with radial structures during initial period of phase separation adopted a resultant morphology of bipolar configuration over the course of polymerisation. The phase separation and morphology of LC domains was found to be dependent on the amount of dye used. Moreover, the addition of small amount of dye reduced the switching voltage, and enhanced the contrast ratio with improved switching time in the PDLC films. It was shown that, under the application of an electric field, the molecular orientation and absorbance of dichroic dye can be controlled in DPDLC to induce non-linearity and colour contrast without the use of polarisers.

Anisotropic fluorescence materials: Effect of the synthesis conditions over the incorporation, alignment and aggregation of Pyronine Y within MgAPO-5

In order to prepare a highly fluorescent anisotropic material, different hydrothermal synthesis conditions have been studied in an attempt to favor the incorporation of the fluorescing dye Pyronine Y as monomeric species within the large-pore nanoporous aluminophosphate MgAPO-5 (AFI-type structure) during its crystallization (one-pot synthesis). Valuable information regarding the dye orientation, molecular distribution and aggregation behaviour inside the nanochannels of MgAPO-5 as a function of the gel composition has been obtained using the FLIM technique (Fluorescence Lifetime Imaging Microscopy). DFT-based calculations of the different dye species occluded within the nanochannels of MgAPO-5 allowed us to explain the properties of the newly synthesised composite materials. Our results show that although H-aggregates can fit within the MgAPO-5 channels, their presence can be reduced by varying the synthesis parameters, in particular by decreasing the template and PY concentration and increasing Mg content.

Effect of nuclear vibrations, temperature, co-adsorbed water, and dye orientation on light absorption, charge injection and recombination conditions in organic dyes on TiO2

We study the effect of nuclear motions at different temperatures, including the effect of a dye molecule's orientation with respect to the oxide surface, on factors determining the performance of dye sensitized solar cells: light absorption, electron injection, and back-donation. We perform ab initio molecular dynamics simulations of aminophenyl acid dyes NK1 and NK7, differing by the electron donating group, in a vacuum and adsorbed in mono- and bi-dentate modes on a dry and a water-covered anatase (101) surface of TiO(2), at 300 and 350 K. Nuclear vibrations and an increase of temperature cause a red shift in the absorption spectra of free dyes. This effect is preserved in dyes on dry TiO(2) but largely disappears in the presence of water. Averaged over nuclear vibrations, the driving force to injection, ΔG, differs from the static estimate. It depends on the adsorption mode and the presence of H(2)O but is almost the same for 300 and 350 K. Recombination to the dye cation is expected to be much enhanced by the approach of the dye oxidation equivalent hole to the surface during dye wagging around TiO(2). This effect is somewhat mitigated by the co-adsorbed water. The dynamics of ΔG(t) are explained by uncorrelated evolution of the energies of the dye excited state and the conduction band minimum of the oxide due to their respective vibrations, and are almost independent of dye orientation. It may therefore be possible to independently control the conditions of recombination and of injection.

In silico FRET from simulated dye dynamics

Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(R/R0)6).The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution.To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm.The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity.The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Program summaryProgram title: md2fretCatalogue identifier: AENV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License.No. of lines in distributed program, including test data, etc.: 317880No. of bytes in distributed program, including test data, etc.: 54774217Distribution format: tar.gzProgramming language: Python, Cython, C (ANSI C99).Computer: Any (see memory requirements).Operating system: Any OS with CPython distribution (e.g. Linux, MacOSX, Windows).Has the code been vectorised or parallelized?: Yes, in Ref. [2], 4 CPU cores were used.RAM: About 700MB per process for the simulation setup in Ref. [2].Classification: 16.1, 16.7, 23.External routines: Calculation of Rκ2-trajectories from GROMACS [3] MD trajectories requires the GromPy Python module described in Ref. [4] or a GROMACS 4.6 installation. The md2fret program uses a standard Python interpreter (CPython) v2.6+ and < v3.0 as well as the NumPy module. The analysis examples require the Matplotlib Python module.Nature of problem:Simulation and interpretation of single molecule FRET experiments.Solution method:Combination of force-field based molecular dynamics (MD) simulating the dye dynamics and Monte Carlo sampling to obtain photon statistics of FRET kinetics.Additional comments:!!!!! The distribution file for this program is over 50 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!!Running time:A single run in Ref. [2] takes about 10 min on a Quad Core Intel Xeon CPU W3520 2.67GHz with 6GB physical RAM

Effect of dichroic dye on phase separation kinetics and electro-optical characteristics of polymer dispersed liquid crystals

Dichroic polymer dispersed liquid crystal (PDLC) films were prepared using a nematic liquid crystal, photo-curable polymer and dichroic azo dye by polymerization induced phase separation (PIPS) method. Dynamics of PIPS and morphology development in the mixtures containing dye have been investigated by means of UV–VIS spectroscopy and optical microscopy. The phase separation and segregation of LC droplets was found to be dependent on the amount of dye used. LC droplets predominantly exhibited bipolar configuration that changed to maltese type crosses under the influence of an applied electric field. The extent of interaction and anchoring energy between the LC and polymer were examined by measuring contact angle in consequence of dye addition. Due to less interfacial interaction, PDLC with low dye content (≤0.06wt%) gave a good contrast ratio, relatively low threshold voltage and a value of high transmittance in the ON-state. UV–VIS spectroscopy results show that the molecular orientation of dye in LC droplets can be controlled with an applied field to induce nonlinearity in these materials. In particular, the dye concentration can be optimized to obtain promising electronic materials with minimum threshold and high contrast for display applications.

Dichroic Dye Induced Nonlinearity in Polymer Dispersed Liquid Crystal Materials for Display Devices

The electro-optical characteristics of dye-doped polymer dispersed liquid crystals (PDLCs) have been investigated for display applications. The PDLC samples were obtained by polymerization induced phase separation of the nematic liquid crystal (LC)-dye-prepolymer mixtures under UV illumination with a constant intensity. The optimum conditions for the scattering characteristics of the dye-doped PDLC films as function of the dye concentration have been examined. It was seen that the phase separation and segregation of LC droplets is dependent on the amount of dye used. LC droplets in dye-doped PDLC films exhibit various configurations at lower and higher applied electric field when observed in situ under polarizing optical microscope. The effects of morphology on the electro-optical properties were examined. Experimental results indicate that the driving voltage and contrast ratio were affected considerably by the amount of dye. UV-VIS spectroscopy results showed that the molecular orientation of dye in LC droplets can be controlled to induce nonlinearity in these materials. The results showed that the dye concentration can be optimized to obtain promising electronic materials with minimum threshold and high contrast for display applications.

Orientation and Order of Xanthene Dyes in the One-Dimensional Channels of Zeolite L: Bridging the Gap between Experimental Data and Molecular Behavior

Supramolecular organization in nanochannels is governed by both the nature of the channels and the size, shape, and charge of the guests, and may also depend on the cosolvent in the host. Oxonine (Ox+) and pyronine (Py+) cationic dyes in zeolite L (ZL) could provide important insight on this issue, but their orientation in the composite materials is not understood yet. Theoretical modeling of Ox+/ZL and Py+/ZL composites indicates that the 70–80° orientation, deduced from optical microscopy data but incompatible with host–guest geometry contraints, is not stable and reveals two possible orientations for these dyes in ZL nanochannels: perpendicular or parallel to the channel axis. In the hydrated composite, corresponding to optical microscopy experiments conditions, perpendicular Ox+/Py+ is the favored orientation, suggesting a larger portion of perpendicularly oriented dye molecules and a smaller fraction aligned. Optical microscopy data might therefore be reinterpreted as the vector sum of components ari...