セキ－キンセキガイ ソクテイヨウ ブンコウケイコウ コウドケイ ノ コウリョウシケイ シキソ ノ ケントウ

Spectrofluorophotometric quantum counter dye for fluorescent samples under excitation of light 600-700 nm wavelength range was investigated. Five kinds of cyanine, three of methylene blue and three of phthalocyanine dyes respectively, were provided for examination. As the results of characteristic measurements, we found that methylene blue trihydrate has most superior characteristics for absorption-fluorescent spectra and for stabirity. Measuring the fluorescent spectra of fluorescent samples (cyanine dye) under various exciting light intensities, using the methylene blue trihydrate for spectrofluorophotometric quantum counter dye, the practical accuracy of this quantum counter dye was proofed. Adjustment of the compensator of spectrofluorophotometer enabled us to measure corrected fluorescent spectrum until wavelength by 830 nm. Consequently, relative fluorescent quantum yields for samples such as cyanine dyes has become obtainable till nearinfrared wavelength range

Stacking-induced fluorescence increase reveals allosteric interactions through DNA

From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye–DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids

A two-state model of twisted intramolecular chargetransfer in monomethine dyes

A two-state model Hamiltonian is proposed to model the coupling of twisting displacements to charge-transfer behavior in the ground and excited states of a general monomethine dye molecule. This coupling may be relevant to the molecular mechanism of environment-dependent fluorescence yield enhancement. The model is parameterized against quantum chemical calculations on different protonation states of the green fluorescent protein chromophore (GFP), which are chosen to sample different regimes of detuning from the cyanine (resonant) limit. The model provides a simple yet realistic description of the charge transfer character along two possible excited state twisting channels associated with the methine bridge. It describes qualitatively different behavior in three regions that can be classified by their relationship to the resonant (cyanine) limit. The regimes differ by the presence or absence of twist-dependent polarization reversal and the occurrence of conical intersections. We find that selective biasing of one twisting channel over another by an applied diabatic biasing potential can only be achieved in a finite range of parameters near the cyanine limit.Comment: 45 pages, 9 Figures (incl. 2 chemical schemes). Accepted for publication by the Journal of Chemical Physics. Changes include 2 additional figures to and expanded discussion of key points felt to be important, and condensed discussion of some points felt to be less importan

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

Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution.

The ability to directly visualize nanoscopic cellular structures and their spatial relationship in all three dimensions will greatly enhance our understanding of molecular processes in cells. Here we demonstrated multicolor three-dimensional (3D) stochastic optical reconstruction microscopy (STORM) as a tool to quantitatively probe cellular structures and their interactions. To facilitate STORM imaging, we generated photoswitchable probes in several distinct colors by covalently linking a photoswitchable cyanine reporter and an activator molecule to assist bioconjugation. We performed 3D localization in conjunction with focal plane scanning and correction for refractive index mismatch to obtain whole-cell images with a spatial resolution of 20-30 nm and 60-70 nm in the lateral and axial dimensions, respectively. Using this approach, we imaged the entire mitochondrial network in fixed monkey kidney BS-C-1 cells, and studied the spatial relationship between mitochondria and microtubules. The 3D STORM images resolved mitochondrial morphologies as well as mitochondria-microtubule contacts that were obscured in conventional fluorescence images

Molecular imaging of oxidative stress using an LED-based photoacoustic imaging system.

LED-based photoacoustic imaging has practical value in that it is affordable and rugged; however, this technology has largely been confined to anatomic imaging with limited applications into functional or molecular imaging. Here, we report molecular imaging reactive oxygen and nitrogen species (RONS) with a near-infrared (NIR) absorbing small molecule (CyBA) and LED-based photoacoustic imaging equipment. CyBA produces increasing photoacoustic signal in response to peroxynitrite (ONOO-) and hydrogen peroxide (H2O2) with photoacoustic signal increases of 3.54 and 4.23-fold at 50 µM of RONS at 700 nm, respectively. CyBA is insensitive to OCl-, ˙NO, NO2-, NO3-, tBuOOH, O2-, C4H9O˙, HNO, and ˙OH, but can detect ONOO- in whole blood and plasma. CyBA was then used to detect endogenous RONS in macrophage RAW 246.7 cells as well as a rodent model; these results were confirmed with fluorescence microscopy. Importantly, CyB suffers photobleaching under a Nd:YAG laser but the signal decrease is <2% with the low-power LED-based photoacoustic system and the same radiant exposure time. To the best of our knowledge, this is the first report to describe molecular imaging with an LED-based photoacoustic scanner. This study not only reveals the sensitive photoacoustic detection of RONS but also highlights the utility of LED-based photoacoustic imaging

Design Principles for Two-Dimensional Molecular Aggregates Using Kasha's Model: Tunable Photophysics in Near and Short-Wave Infrared

Technologies which utilize near-infrared (700 – 1000 nm) and short-wave infrared (1000 – 2000 nm) electromagnetic radiation have applications in deep-tissue imaging, telecommunications and satellite telemetry due to low scattering and decreased background signal in this spectral region. It is therefore necessary to develop materials that absorb light efficiently beyond 1000 nm. Transition dipole moment coupling (e.g. J-aggregation) allows for redshifted excitonic states and provides a pathway to highly absorptive electronic states in the infrared. We present aggregates of two cyanine dyes whose absorption peaks redshift dramatically upon aggregation in water from ~800 nm to 1000 nm and 1050 nm respectively with sheet-like morphologies and high molar absorptivities (e ~ 105 M-1cm-1). We use Frenkel exciton theory to extend Kasha’s model for J and H aggregation and describe the excitonic states of 2-dimensional aggregates whose slip is controlled by steric hindrance in the assembled structure. A consequence of the increased dimensionality is the phenomenon of an intermediate “I-aggregate”, one which redshifts yet displays spectral signatures of band-edge dark states akin to an H-aggregate. We distinguish between H-, I- and J-aggregates by showing the relative position of the bright (absorptive) state within the density of states using temperature dependent spectroscopy. I-aggregates hold potential for applications as charge injection moieties for semiconductors and donors for energy transfer in NIR and SWIR. Our results can be used to better design chromophores with predictable and tunable aggregation with new photophysical properties

Ultrafast fluorescent decay induced by metal-mediated dipole-dipole interaction in two-dimensional molecular aggregates

Two-dimensional molecular aggregate (2DMA), a thin sheet of strongly interacting dipole molecules self-assembled at close distance on an ordered lattice, is a fascinating fluorescent material. It is distinctively different from the single or colloidal dye molecules or quantum dots in most previous research. In this paper, we verify for the first time that when a 2DMA is placed at a nanometric distance from a metallic substrate, the strong and coherent interaction between the dipoles inside the 2DMA dominates its fluorescent decay at picosecond timescale. Our streak-camera lifetime measurement and interacting lattice-dipole calculation reveal that the metal-mediated dipole-dipole interaction shortens the fluorescent lifetime to about one half and increases the energy dissipation rate by ten times than expected from the noninteracting single-dipole picture. Our finding can enrich our understanding of nanoscale energy transfer in molecular excitonic systems and may designate a new direction for developing fast and efficient optoelectronic devices.Comment: 9 pages, 6 figure

Fluorescent nanohybrids based on asymmetrical cyanine dyes decorated carbon nanotubes

In this thesis, we focused on imparting new optical properties to carbon nanotubes (CNTs) to allow their optical detection and visualization in biomedical applications. We investigated the interactions of CNTs and DNA wrapped CNTs with asymmetrical cyanine dye molecules to study the applicability of resulting hybrid materials to fluorescent based systems. When CNTs interacted with asymmetrical cyanine dyes, they constructed a light absorbing nanoarray. However, the fluorescence emission of the two component structure was quenched. Alternatively, when single stranded DNA (ssDNA) wrapped CNTs interacted with asymmetrical cyanine dye molecules not only the absorbance intensity was altered but also the fluorescence intensity increased several fold. The assembly of CNT/dye nanohybrids and ssDNA/CNT/dye nanohybrid was also demonstrated by a shift in Raman spectrum indicating noncovalent binding. The thermal stability of ssDNA/CNT/dye nanostructures was investigated by fluorescence-based thermal analysis. Additionally, individually dispersed ssDNA/CNT nanohybrids and ssDNA/CNT/dye nanohybrids were visualized by transmitted electron microscopy (TEM) and scanning electron microscopy (SEM). Moreover the fluorescence of three component nanohybrids was visualized with confocal microscopy. When CNTs were excited with UV light, they became fluorescent. We have demonstrated that ssDNA wrapped CNTs can act as a scaffold on which asymmetrical cyanine dyes can self-assemble with increased quantum yields. Our work demonstrates the first example that a fluorophore lights up when it binds CNTs, thus provides a novel approach for the fluorescent labeling of CNTs