Experimental studies for the detection of protein in trace amounts

Organic cyanine dye for detection of protein in trace amounts - dye reaction mechanism, methods of eliminating inorganic compound reaction with dye, and detection of humic aci

Iodinated Cyanine Dyes: A New Class of Sensitisers for use in NIR Activated Photodynamic Therapy (PDT)

Iodinated cyanine dye 6a has been developed for use as a NIR excited photosensitiser in photodynamic therapy.</p

Investigation of Low-Temperature Effects on DNA Photocleavage Using a Novel Thioether Substituted Cyanine Dye

The implications of temperature effects on photochemical processes when it comes to near-infrared DNA photosensitizing agents are discussed in addition to the unique spectroscopic features of a sulfur meso-substituted heptamethine cyanine dye relative to oxygen and nitrogen analogues. Specifically, reactive oxygen scavenger experiments, preliminary kinetic data, and absorption spectra are considered in this continued investigation. Additionally, binding and stability studies indicate that the general structure of the cyanine dye can be further optimized to potentially improve DNA photocleavage yields at physiological temperatures while employing the exceptional properties of sulfur-incorporated polymethine dyes

Exciton transport in thin-film cyanine dye J-aggregates

We present a theoretical model for the study of exciton dynamics in J-aggregated monolayers of fluorescent dyes. The excitonic evolution is described by a Monte-Carlo wave function approach which allows for a unified description of the quantum (ballistic) and classical (diffusive) propagation of an exciton on a lattice in different parameter regimes. The transition between the ballistic and diffusive regime is controlled by static and dynamic disorder. As an example, the model is applied to three cyanine dye J-aggregates: TC, TDBC, and U3. Each of the molecule-specific structure and excitation parameters are estimated using time-dependent density functional theory. The exciton diffusion coefficients are calculated and analyzed for different degrees of film disorder and are correlated to the physical properties and the structural arrangement of molecules in the aggregates. Further, exciton transport is anisotropic and dependent on the initial exciton energy. The upper-bound estimation of the exciton diffusion length in the TDBC thin-film J-aggregate is of the order of hundreds of nanometers, which is in good qualitative agreement with the diffusion length estimated from experiments.Comment: 16 pages, 14 figure

Study of Cyanine Dye Binding to Amino Acids and Its Analytical Utility

Investigation of the NIR cyanine dye MHI-36 shows binding affinity to charged amino acids. This cyanine dye showed aggregation and dimer formation at higher dye concentration (2.0x10-3 M) induced by lysine. When dye concentration decreased to 1.0x10-4M no strong aggregate formation was viewed. Dye shows strong binding and selectivity properties towards charged amino acids lysine and arginine, compared to neutral leucine. It’s believed the positively charged presence was able to break and disrupt the conjugated π- π bonds at lower dye concentration. Computational work showed intramolecular aggregation of the phenyl groups on the dye. These aggregates are believed to create electron rich environment suitable for lysine interaction

Evidence for Braggoriton Excitations in Opal Photonic Crystals Infiltrated with Highly Polarizable Dyes

We studied angle-dependent reflectivity spectra of opal photonic crystals infiltrated with cyanine dyes, which are highly polarizable media with very large Rabi frequency. We show that when resonance conditions between the exciton-polariton of the infiltrated dye and Bragg frequencies exist, then the Bragg stop band decomposes into two reflectivity bands with a semi-transparent spectral range in between that is due to light propagation inside the gap caused by the existence of braggoriton excitations. These novel excitations result from the interplay interaction between the Bragg gap with spatial modulation origin and the polariton gap due to the excitons, and may lead to optical communication traffic inside the gap of photonic crystals via channel waveguiding.Comment: LaTex, 5 pages, 3 figures include

Temperature dependent polariton emission from strongly coupled organic semiconductor microcavities

We investigated the absorption and photoluminescence (PL) of J-aggregates of a cyanine dye both in a thin film format and when used as the active layer in a strongly-coupled microcavity. We show that as temperature is reduced, the absorption linewidth of the J-aggregates narrows and shifts to higher energy. When the J-aggregate is placed in a microcavity we find that the energy of the polariton modes also shifts to higher energies as temperature is reduced. We compare the intensity of PL emission from the upper and lower branches at resonance as a function of temperature, and find that it can be described by an activation energy of 25 meV. PL emission spectra at resonance also suggest that uncoupled excitons inside the microcavity populate the upper polariton branch states

Structures of an apo and a binary complex of an evolved archeal b family DNA polymerase capable of synthesising highly cy-dye labelled DNA

Thermophilic DNA polymerases of the polB family are of great importance in biotechnological applications including high-fidelity PCR. Of particular interest is the relative promiscuity of engineered versions of the exo- form of polymerases from the Thermo- and Pyrococcales families towards non-canonical substrates, which enables key advances in Next-generation sequencing. Despite this there is a paucity of structural information to guide further engineering of this group of polymerases. Here we report two structures, of the apo form and of a binary complex of a previously described variant (E10) of Pyrococcus furiosus (Pfu) polymerase with an ability to fully replace dCTP with Cyanine dye-labeled dCTP (Cy3-dCTP or Cy5-dCTP) in PCR and synthesise highly fluorescent “CyDNA” densely decorated with cyanine dye heterocycles. The apo form of Pfu-E10 closely matches reported apo form structures of wild-type Pfu. In contrast, the binary complex (in the replicative state with a duplex DNA oligonucleotide) reveals a closing movement of the thumb domain, increasing the contact surface with the nascent DNA duplex strand. Modelling based on the binary complex suggests how bulky fluorophores may be accommodated during processive synthesis and has aided the identification of residues important for the synthesis of unnatural nucleic acid polymers

Nonlinear optical response of wave packets on quantized potential energy surfaces

We calculated the dynamics of nuclear wave packets in coupled electron-vibration systems and their nonlinear optical responses. We found that the quantized nature of the vibrational modes is observed in pump-probe spectra particularly in weakly interacting electron-vibration systems such as cyanine dye molecules. Calculated results based on a harmonic potential model and molecular orbital calculations are compared with experimental results, and we also found that the materials parameters regarding with the geometrical structure of potential energy surfaces are directly determined by accurate measurement of time-resolved spectra.Comment: 19 pages, 6 figures, 1 tabl

Photoinitiated polymerisation of monolithic stationary phases in polyimide coated capillaries using visible region LEDs

The spatially controlled synthesis of poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolithic stationary phases in polyimide coated fused silica capillaries by visible light induced radical polymerisation using a three-component initiator and a 660 nm light emitting diode (LED) as a light source is presented here