Binding interaction of cationic phenazinium dyes with calf thymus DNA: a comparative study

Absorption, steady-state fluorescence, steady-state fluorescence anisotropy, and intrinsic and induced circular dichroism (CD) have been exploited to explore the binding of calf thymus DNA (ctDNA) with three cationic phenazinium dyes, viz., phenosafranin (PSF), safranin-T (ST), and safranin-O (SO). The absorption and fluorescence spectra of all the three dyes reflect significant modifications upon interaction with the DNA. A comparative study of the dyes with respect to modification of fluorescence and fluorescence anisotropy upon binding, effect of urea, iodide-induced fluorescence quenching, and CD measurements reveal that the dyes bind to the ctDNA principally in an intercalative fashion. The effect of ionic strength indicates that electrostatic attraction between the cationic dyes and ctDNA is also an important component of the dye-DNA interaction. Intrinsic and induced CD studies help to assess the structural effects of dyes binding to DNA and confirm the intercalative mode of binding as suggested by fluorescence and other studies. Finally it is proposed that dyes with bulkier substitutions are intercalated into the DNA to a lesser extent.     

Relationship between tribology and optics in thin films of mechanically oriented nanocrystals

Many crystalline dyes, when rubbed unidirectionally with cotton on glass slides, can be organized as thin films of highly aligned nanocrystals. Commonly, the linear birefringence and linear dichroism of these films resemble the optical properties of single crystals, indicating precisely oriented particles. Of 186 colored compounds, 122 showed sharp extinction and 50 were distinctly linearly dichroic. Of the latter 50 compounds, 88% were more optically dense when linearly polarized light was aligned with the rubbing axis. The mechanical properties of crystals that underlie the nonstatistical correlation between tribological processes and the direction of electron oscillations in absorption bands are discussed. The features that give rise to the orientation of dye crystallites naturally extend to colorless molecular crystals.     

On the angular dependence of the optical polarization anisotropy in ladder-type polymers

Two ladder-type polymers have been examined using polarized optical absorption and fluorescence spectroscopy in solution and solid state. The fluorescence anisotropy excitation spectra of ladder-type methyl-substituted poly(para-phenylene) and poly(naphthylene-phenylene) follow their absorption profiles, contrary to the typical behavior in other conjugated polymers, which show excitation wavelength dependent anisotropy until the onset of the typical red edge effect. Using Raman microscopy and linear dichroism of aligned stretched polyethylene films containing the ladder polymer, it has been found that the orientation of the absorption transition dipole moment is dependent on the conjugation length. The transition dipole of the shorter conjugation lengths of the distribution is localized approximately 7 degrees off axis, and that of the longer conjugation lengths is delocalized along the chain.     

Study of assembly of arachidic acid/LDHs hybrid films containing photoactive dyes

Hybrid monolayers formed with an floating arachidic acid (AA) anions monolayer binding with a densely packed layered double hydroxides (LDHs) monolayer at an air/LDHs suspension interface has been studied by pi-A isotherms and TEM images. An ordered multilayer film of AA/LDHs has been fabricated by Langmuir-Blodgett technique on various substrates. The photoactive dyes (methyl orange, MO, and Congo red, CR) can be incorporated into the galleries of LDHs in the AA/LDHs hybrid LB film by an ion intercalation method. The results of FTIR and UV-vis absorption spectra can approve the formation of AA/LDHs/dyes composite films. In addition, UV-vis absorption spectra and LAXRD analyses also provide evidence for the good vertical uniformity and stable layered periodic structure of AA/LDHs/dyes films. More interestingly, it was found that the dye molecules intercalated can be induced by a positively charged LDHs sheet to align in a special orientation and form different aggregates: MO molecules form sandwich H-type aggregates, while CR molecules form head-to-tail J-type aggregates. On the basis of these data, a possible model of the AA/LDHs/dyes composite films was proposed. Also, the dye molecules incorporated into AA/LDHs films exhibit excellent configuration stability under the irradiation of UV light because the LDHs matrix offers a more rigid and constrained environment for them.     

On the photo-physical behavior and electro-optical effect of oxazine dyes in anisotropic host

The optical characterization and polarized spectroscopy of oxazine 720, oxazine 750, and Nile blue were obtained in a nematic matrix. The interaction of these ionic dyes with the anisotropic surrounding and with that of the isotropic organic solvents was investigated and compared. The influence of the host nature on the molecular interaction of the guest molecules was also investigated. Dichroic ratios R and degree of anisotropy S of these ionic dyes in the liquid crystalline host were investigated by measuring the intensity of the absorption bands in the visible region of parallel aligned samples. The electro-optical effects of the guest-host systems were also investigated in an electro-optical system using polarized spectroscopic method based on homogeneous-homeotropic alignment.     

Crystal structure of friction-transferred poly(2,5-dioctyloxy-1,4-phenylenevinylene)

Poly(2,5-dioctyloxy-1,4-phenylenevinylene) (DOPPV) was found to form a highly oriented film by a friction-transfer technique. Structural investigation of friction-transferred DOPPV was studied by means of polarized ultraviolet-visible (UV-vis) absorption spectroscopy, polarized photoluminescence (PL) spectroscopy, and synchrotron-sourced grazing incident X-ray diffraction (GIXD) analysis. The polarized UV-vis absorption and PL spectra indicate clear axial alignment. DOPPV backbones in friction-transferred film are highly aligned along the drawing direction of the friction-transfer. Further information of the molecular arrangement in friction-transferred DOPPV film was investigated by both the out-of-plane and the in-plane GIXD analyses with synchrotron source. The DOPPV molecules in friction-transferred films were perfectly arranged three-dimensionally: the backbones aligned along the drawing direction of friction-transfer, the alkyl side chains lay in the film plane, and the planar backbones were arranged parallel to the film surface. Additionally, two neighboring DOPPV molecules along the direction of inter-backbones separation by alkyl side chains were found to be shifted with respect to one another by the mean distance of half of a monomeric repeat.     

Rapid on-chip postcolumn labeling and high-resolution separations of DNA

When performing genetic analysis on microfluidic systems, labeling the sample DNA for detection is a critical preparation step. Labeling procedures often involve fluorescently tagged primers and PCRs, which lengthen experimental run times and introduce higher levels of complexity, increasing the overall cost per analysis. Alternatively, on-chip labeling techniques based on intercalating dyes permit rapid labeling of DNA fragments. However, as noted in the literature, the stochastic nature of dye-DNA complex formation hinders the native electrophoretic migration of DNA fragments, degrading the separation resolution. In this study, we present a novel method of controllably labeling DNA fragments at the end of the electrophoretic separation channel in a glass microfluidic chip. Permitting the DNA to separate and labeling just before detection, achieves the rapid labeling associated with intercalators while maintaining the high resolution of native DNA separations. Our analyses are completed in minutes, rather than the hours typical of sample prelabeling. We demonstrate an electrophoretic microchip-based intercalator labeling technique that achieves higher resolution performance than reported in the literature to date.     

Molecular orientation of rigid‐rod polyimide films characterized by polarized attenuated total reflection/fourier transform infrared spectroscopy

The variations in the molecular orientation of uniaxially drawn rigid‐rod polyimide films were systematically characterized in all three dimensions with polarized attenuated total reflection/Fourier transform infrared spectroscopy. The second‐order orientation coefficients were directly deduced from the anisotropy in IR absorptions of particular bands. With the draw ratio increasing, the state of the molecular orientation changed from being nearly planar to completely uniaxial via biaxial orientation, and the degree of orientation was much larger than that of a semirigid polyimide having an ether linkage at the same draw ratio, which originated from the rigid‐rod structure. In addition, the imide planes were rotationally oriented to the out‐of‐plane direction of the film geometry. Furthermore, the relationship between the molecular chain orientation and the in‐plane birefringence in the biaxial orientation state was examined. The intrinsic birefringence was estimated from biaxial orientation films to be 0.33 at a wavelength of 1307 nm. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 418–428, 2003     

Spectral properties of TMPyP intercalated in thin films of layered silicates

The objective of this study was to investigate the spectral characteristics of tetracationic porphyrin dye (TMPyP), intercalated into films of three smectites. The smectites represented the specimens of high (Fluorohectorite; FHT), medium (Kunipia F montmorillonite; KF), and low layer charge (Laponite; LAP). Intercalation of TMPyP molecules was proven by XRD measurements. The molecular orientations of the dye cations were studied by means of linearly polarized ultraviolet-visible (UV-vis) and infrared (IR) spectroscopies. Both the UV-vis and the IR spectroscopy proved the anisotropic character of the films. The spectral analysis of the polarized UV-vis spectra and consequent calculations of tilting angles of the transition moments in the region of Soret band transitions were in the range of 25-35 degrees . The determined angles indicated that the molecular orientation of the dye cations was almost parallel to the surface of the silicates. Slightly higher values, determined for a FHT film, indicated either a slightly more tilted orientation of the dye cations or the change of molecular conformation after the intercalation of the dye. Quenching of TMPyP fluorescence was observed, resulting from the formation of bimolecular layer arrangements with sandwich-type assemblies of the dye molecules.     

Polarized surface enhanced Raman and absorbance spectra of aligned silver nanorod arrays

Polarized surface-enhanced Raman scattering (SERS) and UV-vis absorbance spectra were measured for a nonplanar Ag nanorod array substrate prepared by oblique angle vapor deposition. The anisotropy of the SERS polarization was shown to differ from that of the polarized UV-vis absorbance. The maximum SERS intensity was observed in the polarization direction perpendicular to the long axis of the Ag nanorods, while the UV-vis absorbance was strongly polarized along the direction of the long axis of the nanorod array. Analysis of the polarization data showed that molecular orientation was not the cause of the anisotropic SERS scattering. Rather, the SERS anisotropy was primarily attributed to the lateral arrangement of the three-dimensional tilted nanorod lattice in which highly localized plasmon modes are created by strong electromagnetic coupling between adjacent metallic nanorods.     

Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution.

The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye-DNA complexes; the result is a comprehensive study providing a vast amount of information for users of DNA strains. The dyes examined were the bisbenzimide or indole-derived stains (Hoechst 33342, Hoechst 33258 and 4',6-diamidino-2-phenylindole), phenanthridinium stains (ethidium bromide and propidium iodide) and cyanine dyes (PicoGreen, YOYO-1 iodide, SYBR Green I and SYBR Gold). All were evaluated under the same experimental conditions in terms of ionic strength, pH and dye-DNA ratio. Among the photophysical properties evaluated only fluorescence lifetimes for the cyanine stilbene dyes allowed a convenient differentiation between ssDNA and dsDNA. The bisbenzimide dyes showed multiexponential decays when bound to either form of DNA, making lifetime-based analysis cumbersome with inherent errors. These dyes also presented biexponential decay when free in aqueous buffered solutions at different pH. A mechanism for their deactivation is proposed based on two different conformers decaying with different kinetics. The phenanthridinium dyes showed monoexponential decays with ssDNA and dsDNA, but there was no discrimination between them. High dye-DNA ratios (e.g. 1:1) resulted in multiexponential decays for cyanine dyes, resulting from energy transfer or self-quenching deactivation. Shifts in both absorption and fluorescence maxima for both ssDNA and dsDNA DNA-cyanine dye complexes were small. Broadening of dye-ssDNA absorption and fluorescence bands for the cyanine dyes relative to dye-dsDNA bands was detected and attributed to higher degrees of rotational freedom in the former.     

Influence of molecular mass on the liquid crystal alignment of photosensitive fluorinated polyester films

Photosensitive fluorinated polyesters (polymer-n) of varying molecular mass M _n (number-average molecular mass) were synthesized. The thin films formed from polymer-n samples could induce liquid crystal (LC) alignment after irradiation by linearly polarized ultraviolet light. The LC alignment direction on the irradiated films was investigated in detail by linearly polarized infrared spectroscopy and polarizing optical microscopy. It was found that LC alignment behaviour changed with change in the molecular mass of polymer-n: irradiated films with lower or higher M _n induced homeotropic or homogenous alignment, respectively. There was no clear morphological anisotropy in these aligned films, as observed by atomic force microscopy. The surface energies of the irradiated films were also measured using the indirect contact angle method, where both surface energy and its polar component increased with increasing M _n. The variation in M _n could be considered as a main reason for varying alignment behaviour.     

Two-step resonance energy transfer between dyes in layered silicate films

Single- and two-step fluorescence resonance energy transfer (FRET) was investigated between laser dyes rhodamine 123 (R123), rhodamine 610 (R610), and oxazine 4 (Ox4). The dye molecules played the role of molecular antennas and energy donors (ED, R123), energy acceptors (EA, Ox4), or both (R610). The dye cations were embedded in the films based on layered silicate laponite (Lap) with the thickness of several μm. Optically homogeneous films were prepared directly from dye/Lap colloids. Dye concentration in the films was high enough for FRET to occur but sufficiently low to prevent the formation of large amounts of molecular aggregates. The films were characterized by absorption and fluorescence spectroscopies, and their optical properties were compared with colloid precursors and dye aqueous solutions. The phenomenon of FRET was confirmed by means of steady-state and time-resolved fluorescence spectroscopies. Significant quenching of ED emission in favor of the luminescence from EA molecules was observed. FRET led to the decrease in the lifetimes of excited states of ED molecules. Molecular orientation of dye molecules was determined by polarized absorption and fluorescence spectroscopies. Almost parallel orientation with respect to silicate surface (～30°) was determined for all fluorescent species of the dyes. Theoretical model on relationship between anisotropy and molecular orientation of the fluorophores fits well with measured data. The analysis of anisotropy measurements confirmed the significant role of FRET in the phenomenon of light depolarization.     

Studies on the Interaction of Novel Organogermanium Sesquioxides with DNA

The affinity and mode of interaction of four novel organogermanium sesquioxides with calf thymus DNA(CT-DNA) and two synthetic oligonucleotides, d(AT)₂₂d(AT)₂₂ and d(GC)₂₂d(GC)₂₂, were investigated by a combination of absorption spectroscopy, DNA thermal denaturalization method, viscosity method, fluorometric technique, and competitive binding study with ethidium bromide(EB). The results show that the organogermanium compounds can interact with DNA by intercalation, the binding ability of the compounds to CT-DNA and the synthetic oligonucleotides was found to be modest(in comparison to the proven intercalators), with binding constants on the order of 10³―10⁵ L/mol, respectively. Generally, the binding of the organogermanium sesquioxides with naphthalene moiety to DNA is stronger than that of the compounds with anthraquinone moiety. And the compounds with anthraquinone moiety have preference for binding to AT-rich duplexes, whereas the compounds with naphthalene moiety have a little preference for binding to GC-rich duplexes. DNA may be the primary effect target.     

Optical Properties of M(II) Schiff-base Complexes Dispersed in Ethylene based Polymers

Summary: Several salicylaldiminate M(II) complexes of Nickel, Copper and Cobalt have been prepared and mixed with ethylene based polymers in order to prepare new composite materials with interesting morphological and optical properties by profiting of the presence of alkyl chains and push-pull substituents connected to the ligand structure. The phase dispersion behaviour of the binary films has been studied by scanning electron microscopy (SEM) and x-ray microanalysis, whereas the optical properties of the composite samples have been evaluated by UV-vis and fluorescence spectroscopy. The results in absorption have been analysed in terms of the anisotropy induced by the mechanical orientation of the polymer matrix and by the role of the metal centre according to the different strength of the complexes transition dipole moment. The luminescence behaviour have been discussed in terms of potential developments aimed at preparing polymeric supported Schiff base ligands for metal ions sensor applications.     

Spectroscopic and In Silico Evaluation of Interaction of DNA with Six Anthraquinone Derivatives

Anthraquinones consist of several hundreds of derivatives that differ in the nature and positions of substituent groups which are known to have several biological activities including antitumor properties. Interaction of molecules with DNA persists to be an extremely vital parameter while endeavouring to formulate therapeutics. In this study, few anthraquinone derivatives such as 1,2-dihydroxyanthraquinone (alizarin), 1,4-dihydroxyanthraquinone (quinizarin), 1,8-dihydroxyanthraquinone (danthron), 1,2,4-trihydroxyanthraquinone (purpurin), 1,4-diaminoanthraquinone, and 1-methylaminoanthraquinone were analyzed for its possible interaction with calf-thymus DNA through spectroscopy and in silico analysis. Our UV spectroscopic results indicate that all selected anthraquinones interact with DNA probably by external binding. Molar extinction coefficient has been calculated for chosen six anthraquinones. FT-IR results suggest that significant shifts of peaks as well as disappearance of certain characteristic peaks were indicators of the plausible interaction going on due to dye-DNA adduct formation. Among the six dyes used, purpurin showed better results and indicates the relatively strong binding affinity with DNA. Our molecular modeling results also show that purpurin has comparatively higher DNA interaction with a score of ?6.18 compared with the ethidium bromide of ?5.02 and intercalate the DNA.     

Synthesis and DNA binding properties of bis-9-acridinyl derivatives containing mono-, di-and tetra-viologen units as a connector of bis-intercalators

Bis-9-acridinyl derivatives 1–3 containing mono-, di-and tetra-viologen units as a rigid connector were synthesized. The binding studies of these intercalators for natural and synthetic DNAs showed that these compounds act as bis-intercalators where viologen moieties lie in the minor groove of the DNA duplex. The DNA binding affinity of the intercalators was enhanced with an increase in the number of the viologen unit.     

Alignment control of liquid crystals on surface relief gratings

Liquid crystal alignment layers of a high T_g polymer containing an azobenzene moiety are prepared by photofabrication of a surface relief grating (SRG). The interference pattern of a circular and linearly polarized Ar⁺ laser beam generated the surface relief grating and the morphology was detected by atomic force microscope. The optical anisotropy of the films was investigated by polarizing optical microscopy. The orientation of the optical axis of the film mainly depends on the direction of the initial polarization plane. Nematic liquid crystals were aligned parallel to the direction of the grating, but the pretilt angles of the liquid crystals were nearly zero. Irradiation with homogeneous linearly polarized light could also align liquid crystals, but this alignment capability was weaker than that of the SRG film.     

Spectroscopic analysis of poly(p-phenylene benzobisthiazole) films

Infrared spectroscopy has been used to determine the relative amount, location, and orientation of residual water and acid molecules in poly(p-phenylene benzobisthiazole) films. By analyzing the relative absorbance of reflected polarized infrared radiation from highly oriented films, the indices of refraction parallel and perpendicular to the chain axis were also obtained.     

Layer-by-layer deposited organic/inorganic hybrid multilayer films containing noncentrosymmetrically orientated azobenzene chromophores

Organic/inorganic hybrid multilayer films with noncentrosymmetrically orientated azobenzene chromophores were fabricated by the sequential deposition of ZrO2 layers by a surface sol-gel process and subsequent layer-by-layer (LbL) adsorption of the nonlinear optical (NLO)-active azobenzene-containing polyanion PAC-azoBNS and poly(diallyldimethylammonium chloride) (PDDA). Noncentrosymmetric orientation of the NLO-active azobenzene chromophores was achieved because of the strong repulsion between the negatively charged ZrO(2) and the sulfonate groups of the azobenzene chromophore in PAC-azoBNS. Regular deposition of ZrO(2)/PAC-azoBNS/PDDA multilayer films was verified by UV-vis absorption spectroscopy and quartz crystal microbalance measurements. Both UV-vis absorption spectroscopy and transmission second harmonic generation (SHG) measurements confirmed the noncentrosymmetric orientation of the azobenzene chromophores in the as-prepared ZrO2/PAC-azoBNS/PDDA multilayer films. The square root of the SHG signal (I(2omega)(1/2)) increases with the increase of the azobenzene graft ratio in PAC-azoBNS as the number of deposition cycles of the ZrO(2)/PAC-azoBNS/PDDA films remains the same, while the second-order susceptibility chi(zzz)(2) of the film decreases with the increase of the azobenzene graft ratio. Furthermore, the present method was successfully extended to realize the noncentrosymmetric orientation of azobenzene chromophores in multilayer films when small organic azobenzene compounds with carboxylic acid and/or hydroxyl groups at one end and sulfonate groups at the other end were used. The present method was characterized by its simplicity and flexibility in film preparation, and it is anticipated to be a facile way to fabricate second-order nonlinear optical film materials.