Parameters Influencing the On- and Off-Times in the Fluorescence Intensity Traces of Single Cyanine Dye Molecules

Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways

Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented by steady-state and time-resolved fluorescence and phosphorescence measurements. The relaxation processes of the dyes in dichloromethane are resolved with sub-100 fs temporal resolution using SWIR, near-IR, and visible photoexcitation. Different population members of the ground-state inhomogeneous ensemble are found to equilibrate via skeletal deformation changes with time constants of 90 fs and either 230 fs (Chrom7) and 350 fs (Flav7) followed by slower evolution matching the 1-ps timescale of diffusive solvation dynamics. Molecules excited into high-lying singlet electronic states (Sn) by visible excitation repopulate with time constants of 400 fs (Chrom7) and 450 fs (Flav7) the corresponding first excited singlet S1 states, which decay within several hundreds of picoseconds in dichloromethane and chloroform solvents. Vibrational relaxation in S1 for both Chrom7 and Flav7 in dichloromethane occurs with time constants of 350 and 800 fs for excess of vibrational energy of ∼1000 and 10 000 cm-1 deposited by near-IR and visible excitation, respectively. Two competing non-radiative processes are present in S1: temperature-independent internal conversion, and thermally-activated twisting about a carbon-carbon bond of the conjugated chain, which is substantial at room temperature but essentially nonreactive, producing traces of isomer product. Intersystem crossing in S1, and thus the triplet quantum yield, is minor. The importance of absorption bands from the excited S1 state in applications requiring high-intensity excitation conditions is discussed.

Photonic Crystal Enhanced Fluorescence: A Review on Design Strategies and Applications

Nanoscale fluorescence emitters are efficient for measuring biomolecular interactions, but their utility for applications requiring single-unit observations is constrained by the need for large numerical aperture objectives, fluorescence intermittency, and poor photon collection efficiency resulting from omnidirectional emission. Photonic crystal (PC) structures hold promise to address the aforementioned challenges in fluorescence enhancement. In this review, we provide a broad overview of PCs by explaining their structures, design strategies, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-enhanced fluorescence-based biosensors incorporated with emerging technologies, including nucleic acids sensing, protein detection, and steroid monitoring. Finally, we discuss current challenges associated with PC-enhanced fluorescence and provide an outlook for fluorescence enhancement with photonic-plasmonics coupling and their promise for point-of-care biosensing as well monitoring analytes of biological and environmental relevance. The review presents the transdisciplinary applications of PCs in the broad arena of fluorescence spectroscopy with broad applications in photo-plasmonics, life science research, materials chemistry, cancer diagnostics, and internet of things.

A Novel Six-Gene Signature for Prognosis Prediction in Ovarian Cancer

Ovarian cancer (OC) is the most malignant tumor in the female reproductive tract. Although abundant molecular biomarkers have been identified, a robust and accurate gene expression signature is still essential to assist oncologists in evaluating the prognosis of OC patients. In this study, samples from 367 patients in The Cancer Genome Atlas (TCGA) database were subjected to mRNA expression profiling. Then, we used a gene set enrichment analysis (GSEA) to screen genes correlated with epithelial–mesenchymal transition (EMT) and assess their prognostic power with a Cox proportional regression model. Six genes (TGFBI, SFRP1, COL16A1, THY1, PPIB, BGN) associated with overall survival (OS) were used to construct a risk assessment model, after which the patients were divided into high-risk and low-risk groups. The six-gene signature was an independent prognostic biomarker of OS for OC patients based on the multivariate Cox regression analysis. In addition, the six-gene model was validated with samples from the Gene Expression Omnibus (GEO) database. In summary, we established a six-gene signature relevant to the prognosis of OC, which might become a therapeutic tool with clinical applications in the future.

Identification of Nonradiative Decay Pathways in Cy3

Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing nonradiative decay pathways. Small-molecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the nonradiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing nonradiative decay pathways in fluorescent markers such as Cy3.

Modulation and study of photoblinking behavior in dye doped silver-silica core-shell nanoparticles for localization super-resolution microscopy

Blinking of fluorescent nanoparticles is a compelling phenomenon with widely debated mechanisms. The ability to inhibit or control blinking is important for applications in the field of optical, semiconductor and fluorescent imaging. Self-blinking nanomaterials are also attractive labels for localization-based super-resolution microscopy. In this work, we have synthesized silver core silica nanoparticles (Ag@SiO2) doped with Rhodamine 110 and studied the parameters that affect blinking. We found that under nitrogen rich conditions the nanoparticles shifted towards higher duty cycles. Also, it was found that hydrated nanoparticles showed a less drastic response to nitrogen rich conditions as compared to dried nanoparticles, indicating that surrounding matrix played a role in the response of nanoparticles to molecular oxygen. Further, the blinking is not a multi-body phenomena, super-resolution localization combined with intensity histogram analysis confirmed that single particles are emitting.

Towards white-light generation through upconversion of low-power near-infrared photons

A broadband upconverted emission combined with a broadband infrared absorption takes place in films composed of the same infrared dye molecules.

Field-Controlled Charge Separation in a Conductive Matrix at the Single-Molecule Level: Toward Controlling Single-Molecule Fluorescence Intermittency

The fluorescence intermittency or "blinking" of single molecules of ATTO647N (ATTO) in the conductive matrix polyvinylcarbazole (PVK) is described in the presence of an external applied electric field. It is shown that due to the energy distribution of the highest occupied molecular orbital (HOMO) level of PVK, which is energetically close to the HOMO of ATTO, sporadic electron transfer occurs. As a result, the on/off dynamics of blinking can be influenced by the electric field. This field will, depending on the respective position and orientation of the dye/polymer system with respect to those of the electrodes, either enhance or suppress electron transfer from PVK to ATTO as well as the back electron transfer from reduced ATTO to PVK. After the charge-transfer step, the applied field will pull the hole in PVK away from the dye, increasing the overall time the dye resides in a dark state.

Lanthanide Ion Doped Upconverting Nanoparticles: Synthesis, Structure and Properties

Lanthanide doped upconverting nanoparticles (UCNPs) have emerged as a new class of luminescent materials, with major discoveries and overall significant progress during the last decade. Unlike multiphoton absorption in organic dyes or semiconductor quantum dots, lanthanide doped UCNPs involve real intermediate quantum states and convert infrared (IR) into visible light via sequential electronic excitation. The relatively high efficiency of this process even at low radiation flux makes UCNPs particularly attractive for many current and emerging areas of technology. The aim of this article is to highlight several recent advances in this rapidly growing field, emphasizing the relationships between structure and properties of UCNPs. Additionally, various strategies developed for the synthesis of UCNPs with a focus on the various synthetic approaches that yield high-quality monodisperse samples with controlled size, shape and crystalline phase are reviewed. Emerging synthetic approaches towards designed structure to improve the optical and electronic properties of UCNPs are discussed. Finally, recent examples of applications of UCNPs in biomedical and optoelectronics research, giving our own perspectives on future directions and emerging possibilities of the field are described.

Subsurface Super-resolution Imaging of Unstained Polymer Nanostructures

Optical imaging has offered unique advantages in material researches, such as spectroscopy and lifetime measurements of deeply embedded materials, which cannot be matched using electron or scanning-probe microscopy. Unfortunately, conventional optical imaging cannot provide the spatial resolutions necessary for many nanoscopic studies. Despite recent rapid progress, super-resolution optical imaging has yet to be widely applied to non-biological materials. Herein we describe a method for nanoscopic optical imaging of buried polymer nanostructures without the need for extrinsic staining. We observed intrinsic stochastic fluorescence emission or blinking from unstained polymers and performed spatial-temporal spectral analysis to investigate its origin. We further applied photon localization super-resolution imaging reconstruction to the detected stochastic blinking, and achieved a spatial resolution of at least 100 nm, which corresponds to a six-fold increase over the optical diffraction limit. This work demonstrates the potential for studying the static heterogeneities of intrinsic polymer molecular-specific properties at sub-diffraction-limited optical resolutions.

Diffusion behavior of the fluorescent proteins eGFP and Dreiklang in solvents of different viscosity monitored by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy relies on temporal autocorrelation analysis of fluorescence intensity fluctuations that spontaneously arise in systems at equilibrium due to molecular motion and changes of state that cause changes in fluorescence, such as triplet state transition, photoisomerization and other photophysical transformations, to determine the rates of these processes. The stability of a fluorescent molecule against dark state conversion is of particular concern for chromophores intended to be used as reference tags for comparing diffusion processes on multiple time scales. In this work, we analyzed properties of two fluorescent proteins, the photoswitchable Dreiklang and its parental eGFP, in solvents of different viscosity to vary the diffusion time through the observation volume element by several orders of magnitude. In contrast to eGFP, Dreiklang undergoes a dark-state conversion on the time scale of tens to hundreds of microseconds under conditions of intense fluorescence excitation, which results in artificially shortened diffusion times if the diffusional motion through the observation volume is sufficiently slowed down. Such photophysical quenching processes have also been observed in FCS studies on other photoswitchable fluorescent proteins including Citrine, from which Dreiklang was derived by genetic engineering. This property readily explains the discrepancies observed previously between the diffusion times of eGFP- and Dreiklang-labeled plasma membrane protein complexes.

Magnetic-field-enabled resolution enhancement in super-resolution imaging

A novel strategy for modulating the photophysics of organic dyes in super-resolution fluorescence imaging using an external magnetic field was reported. The magnetic field induced increase in fluorescence intensity, localization number of probe molecules, and the number of photons emitted per molecule as compared to those acquired without a magnetic field were experimentally confirmed. Improved dSTORM localization precision and imaging resolution were consequently achieved.

A multi-property fluorescent probe for the investigation of polymer dynamics near the glass transition

In addition to the commonly observed single molecule fluorescence intensity fluctuations due to molecular reorientation dynamics, a perylene bisimide-calixarene compound (1) shows additional on-off fluctuations due to its ability to undergo intramolecular excited state electron transfer (PET). This quenching process is turned on rather sharply when a film of poly(vinylacetate) containing 1 is heated above its glass transition temperature (T g), which indicates that the electron transfer process depends on the availability of sufficient free volume. Spatial heterogeneities cause different individual molecules to reach the electron transfer regime at different temperatures, but these heterogeneities also fluctuate in time: in the matrix above T g molecules that are mostly nonfluorescent due to PET can become fluorescent again on timescales of seconds to minutes.

The two different mechanisms for intensity fluctuation, rotation and PET, thus far only observed in compound 1, make it a unique probe for the dynamics of supercooled liquids.

Preparation of non-aggregated fluorescent nanodiamonds (FNDs) by non-covalent coating with a block copolymer and proteins for enhancement of intracellular uptake

Fluorescent nanodiamonds (FNDs) are very promising fluorophores for use in biosystems due to their high biocompatibility and photostability. To overcome their tendency to aggregate in physiological solutions, which severely limits the biological applications of FNDs, we developed a new non-covalent coating method using a block copolymer, PEG-b-P(DMAEMA-co-BMA), or proteins such as BSA and HSA. By simple mixing of the block copolymer with FNDs, the cationic DMAEMA and hydrophobic BMA moieties can strongly interact with the anionic and hydrophobic moieties on the FND surface, while the PEG block can form a shell to prevent the direct contact between FNDs. The polymer-coated FNDs, along with BSA- and HSA-coated FNDs, showed non-aggregation characteristics and maintained their size at the physiological salt concentration. The well-dispersed, polymer- or protein-coated FNDs in physiological solutions showed enhanced intracellular uptake, which was confirmed by CLSM. In addition, the biocompatibility of the coated FNDs was expressly supported by a cytotoxicity assay. Our simple non-covalent coating with the block copolymer, which can be easily modified by various chemical methods, projects a very promising outlook for future biomedical applications, especially in comparison with covalent coating or protein-based coating.

A novel method for automatic single molecule tracking of blinking molecules at low intensities

Single molecule tracking provides unprecedented insights into diffusional processes of systems in life and material sciences. Determination of molecule positions with high accuracy and correct connection of the determined positions to tracks is a challenging task with, so far, no universal solution for single fluorescing molecules tackling the challenge of low signal-to-noise ratios, frequent blinking and photo bleaching. Thus, the development of novel algorithms for automatic single molecule fluorescence tracking is essential to analyse the huge amount of diffusional data obtained with single molecule widefield fluorescence microscopy. Here, we present a novel tracking model using a top-down polyhedral approach which can be implemented effectively using standard linear programming solvers. The results of our tracking approach are compared to the ground truth of simulated data with different diffusion coefficients, signal-to-noise ratios and particle densities. We also determine the dependency of blinking on the analysed distribution of diffusion coefficients. To confirm the functionality of our tracking method, the results of automatic tracking and manual tracking by a human expert are compared and discussed.

Steering Fluorescence Emission with Metal-Dielectric-Metal Structures of Au, Ag and Al

Directional control over fluorescence emission is important for improving the sensitivity of fluorescence based techniques. In recent years, plasmonic and photonic structures have shown great promise in shaping the spectral and spatial distribution of fluorescence, which otherwise is typically isotropic in nature and independent of the observation direction. In this work we have explored the potential of metal-dielectric-metal (MDM) structures composed of Au, Ag or Al in steering the fluorescence emission from various probes emitting in the NIR, Visible or UV/blue region. We show that depending on the optical properties of the metal and the thickness of the dielectric layer, the emission from randomly oriented fluorophores embedded within the MDM substrate is transformed into beaming emission normal to the substrate. Agreement of the observed angular emission patterns with reflectivity calculations reveals that the directional emission is due to the coupling of the fluorescence with the electromagnetic modes supported by the MDM structure.

Photophysical behaviors of single fluorophores localized on zinc oxide nanostructures

Single-molecule fluorescence spectroscopy has now been widely used to investigate complex dynamic processes which would normally be obscured in an ensemble-averaged measurement. In this report we studied photophysical behaviors of single fluorophores in proximity to zinc oxide nanostructures by single-molecule fluorescence spectroscopy and time-correlated single-photon counting (TCSPC). Single fluorophores on ZnO surfaces showed enhanced fluorescence brightness to various extents compared with those on glass; the single-molecule time trajectories also illustrated pronounced fluctuations of emission intensities, with time periods distributed from milliseconds to seconds. We attribute fluorescence fluctuations to the interfacial electron transfer (ET) events. The fluorescence fluctuation dynamics were found to be inhomogeneous from molecule to molecule and from time to time, showing significant static and dynamic disorders in the interfacial electron transfer reaction processes.

Synthetic pathways to make nanoparticles fluorescent

In biosciences, it is often necessary to follow the pathway of nanoparticles within cells or tissues. The nanoparticles can be used as labeled sensors which may, e.g., address functionalities within a cell, carry other specific agents like drugs or be magnetic for tumor thermotherapy. In the context of nanotoxicology, the fate of a given nanoparticle is of interest. As many methods in cell biology are based on fluorescence detection, there is a strong demand to make nanoparticles fluorescent. Different ways to introduce fluorescence are reviewed and exemplified with typical kinds of nanoparticles, i.e. polymers, silica and calcium phosphate.

Photophysical properties of Zn-substituted cytochrome c investigated by single-molecule and ensemble-averaged spectroscopy

The study of the structural reorganization and photophysical properties of Zn-Cytc using the single-molecule and ensemble-averaged spectroscopy shows that the photoblinking behaviors of single-Zn-Cytc depend on the folded and unfolded structures, whereas the fluorescence dynamics of Zn-Cytc observed in the bulk phase are hardly affected by the conformational change of a protein.

Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments

The breakthroughs in single molecule spectroscopy of the last decade and the recent advances in super resolution microscopy have boosted the popularity of cyanine dyes in biophysical research. These applications have motivated the investigation of the reactions and relaxation processes that cyanines undergo in their electronically excited states. Studies show that the triplet state is a key intermediate in the photochemical reactions that limit the photostability of cyanine dyes. The removal of oxygen greatly reduces photobleaching, but induces rapid intensity fluctuations (blinking). The existence of non-fluorescent states lasting from milliseconds to seconds was early identified as a limitation in single-molecule spectroscopy and a potential source of artifacts. Recent studies demonstrate that a combination of oxidizing and reducing agents is the most efficient way of guaranteeing that the ground state is recovered rapidly and efficiently. Thiol-containing reducing agents have been identified as the source of long-lived dark states in some cyanines that can be photochemically switched back to the emissive state. The mechanism of this process is the reversible addition of the thiol-containing compound to a double bond in the polymethine chain resulting in a non-fluorescent molecule. This process can be reverted by irradiation at shorter wavelengths. Another mechanism that leads to non-fluorescent states in cyanine dyes is cis–trans isomerization from the singlet-excited state. This process, which competes with fluorescence, involves the rotation of one-half of the molecule with respect to the other with an efficiency that depends strongly on steric effects. The efficiency of fluorescence of most cyanine dyes has been shown to depend dramatically on their molecular environment within the biomolecule. For example, the fluorescence quantum yield of Cy3 linked covalently to DNA depends on the type of linkage used for attachment, DNA sequence and secondary structure. Cyanines linked to the DNA termini have been shown to be mostly stacked at the end of the helix, while cyanines linked to the DNA internally are believed to partially bind to the minor or major grooves. These interactions not only affect the photophysical properties of the probes but also create a large uncertainty in their orientation.

Photoinduced electron transfer of oxazine 1/TiO2 nanoparticles at single molecule level by using confocal fluorescence microscopy

Kinetics of photoinduced electron transfer (ET) from oxazine 1 dye to TiO(2) nanoparticles (NPs) surface is studied at a single molecule level by using confocal fluorescence microscopy. Upon irradiation with a pulsed laser at 630 nm, the fluorescence lifetimes sampled among 100 different dye molecules are determined to yield an average lifetime of 2.9 +/- 0.3 ns, which is close to the value of 3.0 +/- 0.6 ns measured on the bare coverslip. The lifetime proximity suggests that most interfacial electron transfer (IFET) processes for the current system are inefficient, probably caused by physisorption between dye and the TiO(2) film. However, there might exist some molecules which are quenched before fluorescing and fail to be detected. With the aid of autocorrelation analysis under a three-level energy system, the IFET kinetics of single dye molecules in the conduction band of TiO(2) NPs is evaluated to be (1.0 +/- 0.1) x 10(4) s(-1) averaged over 100 single molecules and the back ET rate constant is 4.7 +/- 0.9 s(-1). When a thicker TiO(2) film is substituted, the resultant kinetic data do not make a significant difference. The trend of IFET efficacy agrees with the method of fluorescence lifetime measurements. The obtained forward ET rate constants are about ten times smaller than the photovoltage response measured in an assembled dye-sensitized solar cell. The discrepancy is discussed. The inhomogeneous and fluctuation characters for the IFET process are attributed to microenvironment variation for each single molecule. The obtained ET rates are much slower than the fluorescence relaxation. Such a small ET quantum yield is yet feasibly detectable at a single molecule level.

Enhanced Single-Molecule Detection using Porous Silver Membrane

We evaluated a commercial porous silver membrane as a support substrate for direct localization and visualization of single molecule events. We characterized the fluorescence behaviors of fluorescently labeled DNA oligonucleotides on the silver membranes. The fluorescence from the fluorescent probes that were immobilized on the porous silver is greatly enhanced. Additionally, correlated to reflectance contour image, it appears that enhanced fluorescence came from location close to the "valley" of the pore channels (or in the voids). These results are of great interest to increase the effectiveness of fluorescence-based single molecule DNA analysis.

Proton-transfer mechanism for dispersed decay kinetics of single molecules isolated in potassium hydrogen phthalate

The excited-state decay kinetics of single 2',7'-dichlorofluorescein (DCF) molecules oriented and overgrown within crystals of potassium acid phthalate (KAP) are reported. Time-correlated single-photon counting measurements (TCSPC) of 56 DCF molecules in KAP reveal that single-exponential decay is exhibited by roughly half of the molecules. The remainder demonstrates complex excited-state decay kinetics that are well fit by a stretched exponential function consistent with dispersed kinetics. Histograms of single-molecule luminescence energies revealed environmental fluctuations and distinct chemical species. The TCSPC results are compared to Monte Carlo simulations employing a first-passage model for excited-state decay. Agreement between experiment and theory, on both bulk and single-molecule levels, suggests that a subset of the DCF molecules in KAP experience fluctuations in the surrounding environment that modify the energy barrier to proton transfer leading to dispersed kinetics.

Rapid constructions of microstructures for optical fiber sensors using a commercial CO2 laser system

Exposing an optical fiber core to the measurand surrounding the fiber is often used to enhance the sensitivity of an optical fiber sensor. This paper reports on the rapid fabrication of microstructures in an optical fiber using a CO₂ laser system which help exposing the optical fiber core to the measurand. The direct-write CO₂ laser system used is originally designed for engraving the polymeric material. Fabrications of microstructures such as in-fiber microhole, D-shaped fiber, in-fiber microchannel, side-sliced fiber and tapered fiber were attempted. The microstructures in the fibers were examined using a SEM and an optical microscope. Quality of microstructures shown by the SEM images and promising results from fluorescence sensor tests using in-fiber microchannels of 100μm width, 210μm depth and 10mm length show the prospect of this method for use in optical fiber sensor development. The direct-write CO₂ laser system is a flexible and fast machining tool for fabricating microstructures in an optical fiber, and can possibly be a replacement of the time consuming chemical etching and polishing methods used for microstructure fabrications of optical the fiber sensors reported in other literatures.