Free Dye In Solution Research Articles

Synthesis of novel tetracationic asymmetric monomeric monomethine cyanine dyes – highly fluorescent dsDNA probes

Quaternisation of monomethine cyanine dyes bearing haloalkyl chains, with the appropriate monoquaternised 1,4‐diazabicyclo[2.2.2]octane derivatives, yielded novel tetracationic asymmetric monomeric monomethine cyanine dyes belonging to the thiazole orange family. The optimal conditions for this reaction were investigated. The longest wavelength absorption maxima of the studied dyes are in the region 504–507 nm. The molar absorptivities of the target dyes are high, with values between 70 500 and 99 500 l mol−1 cm−1. The fluorescence intensity and the fluorescence quantum yields of the free dyes in solution or in the presence of double‐stranded DNA were determined using thiazole orange for comparison. The dyes are suitable for nucleic acid detection and have a high binding affinity, attributable to their four positive charges.

Characterization of PicoGreen Interaction with dsDNA and the Origin of Its Fluorescence Enhancement upon Binding

PicoGreen is a fluorescent probe that binds dsDNA and forms a highly luminescent complex when compared to the free dye in solution. This unique probe is widely used in DNA quantitation assays but has limited application in biophysical analysis of DNA and DNA-protein systems due to limited knowledge pertaining to its physical properties and characteristics of DNA binding. Here we have investigated PicoGreen binding to DNA to reveal the origin and mode of PicoGreen/DNA interactions, in particular the role of electrostatic and nonelectrostatic interactions in formation of the complex, as well as demonstrating minor groove binding specificity. Analysis of the fluorescence properties of free PicoGreen, the diffusion properties of PG/DNA complexes, and the excited-state lifetime changes upon DNA binding and change in solvent polarity, as well as the viscosity, reveal that quenching of PicoGreen in the free state results from its intramolecular dynamic fluctuations. On binding to DNA, intercalation and electrostatic interactions immobilize the dye molecule, resulting in a >1000-fold enhancement in its fluorescence. Based on the results of this study, a model of PicoGreen/DNA complex formation is proposed.

Cucurbituril complexes cross the cell membrane

Cucurbiturils (CBs) of the appropriate size (CB[7] and CB[8]) form strong guest-host complexes in phosphate buffer solution (PBS) with acridine orange (AO) and pyronine Y (PYY) with 1 : 1 and 2 : 1 stoichiometries for CB[7] and CB[8] complexes, respectively. Binding constants in the range 0.87-1.60 x 10(6) M(-1) and 5.2-6.3 x 10(13) M(-2) were determined by titration with fluorescence spectroscopy for 1 : 1 and 2 : 1 complexes, respectively. These binding constants in PBS and the eight-fold excess of CBs minimize the presence of free dye in solution and also stabilize the host-guest complex in the culture medium. Images showing that the CB complexes can cross the cell membrane of 3T3 cells have been acquired using fluorescence microscopy. Given the current importance of supramolecular CB complexes and the search for new drug delivery systems, the present findings open avenues for the use of CBs as nanocapsules to transport drugs into the cells.

Metal-enhanced PicoGreen fluorescence: Application for double-stranded DNA quantification

PicoGreen (PG) is a fluorescent probe for both double-stranded DNA (dsDNA) detection and quantification based on its ability to form a luminescent complex with dsDNA as compared with the free dye in solution. To expand the sensitivity of PG detection, we have studied the spectral properties of PG, both free and in complex with DNA in solution, when the fluorophore is in proximity to silver nanoparticles. We show that for a broad range of PG concentrations (20 pM–3.5 μM), it does not form dimers/oligomers and it exists in a monomeric state. On binding to DNA in the absence of silver, PG fluorescence increases approximately 1100-fold. Deposition of PG/DNA complex onto silver island films (SiFs) increases fluorescence approximately 7-fold due to the metal-enhanced fluorescence (MEF) effect, yielding fluorescence enhancement of 7700-fold as compared with the free dye on glass. In contrast to PG in complex with DNA, the free dye on SiFs demonstrates a decrease in brightness approximately 5-fold. Therefore, the total enhancement of PG on binding to DNA on silver reaches a value of approximately 38,000 as compared with free PG on SiFs. Consequently, the metal-enhanced detection of PG fluorescence is likely to find important utility for amplified dsDNA quantification.

Metal-enhanced ethidium bromide emission: Application to dsDNA detection

Ethidium bromide (EB) is a commonly used probe for fluorescence detection and quantification of nucleic acids, since EB forms a highly luminescent complex with dsDNA. Typical detection sensitivity of EB-based assays to dsDNA in solution is about 0.1 μg. With the aim to increase the sensitivity of EB assays we have employed the Metal-Enhanced Fluorescence technology. We show that deposition of the EB/DNA complex solutions onto the silver nanoparticle surface additionally increases the far-field observable fluorescence ≈5-fold, yielding a net fluorescence enhancement factor of ≈180-fold, as compared to the free dye in solution. Subsequently, our approach enables the more sensitive detection of dsDNA.

Supercritical Angle Fluorescence Correlation Spectroscopy

We explore the potential of a supercritical angle (SA) objective for fluorescence correlation spectroscopy (FCS). This novel microscope objective combines tight focusing by an aspheric lens with strong axial confinement of supercritical angle fluorescence collection by a parabolic mirror lens, resulting in a small detection volume. The tiny axial extent of the detection volume features an excellent surface sensitivity, as is demonstrated by diffusion measurements in model membranes with an excess of free dye in solution. All SA-FCS measurements are directly compared to standard confocal FCS, demonstrating a clear advantage of SA-FCS, especially for diffusion measurements in membranes. We present an extensive theoretical framework that allows for accurate and quantitative evaluation of the SA-FCS correlation curves.

Fluorescence Properties and Photophysics of the Sulfoindocyanine Cy3 Linked Covalently to DNA

The sulfoindocyanine Cy3 is one of the most commonly used fluorescent dyes in the investigation of the structure and dynamics of nucleic acids by means of fluorescence methods. In this work, we report the fluorescence and photophysical properties of Cy3 attached covalently to single-stranded and duplex DNA. Steady-state and time-resolved fluorescence techniques were used to determine fluorescence quantum yields, emission lifetimes, and fluorescence anisotropy decays. The existence of a transient photoisomer was investigated by means of transient absorption techniques. The fluorescence quantum yield of Cy3 is highest when attached to the 5' terminus of single-stranded DNA (Cy3-5' ssDNA), and decreases by a factor of 2.4 when the complementary strand is annealed to form duplex DNA (Cy3-5' dsDNA). Substantial differences were also observed between the 5'-modified strands and strands modified through an internal amino-modified deoxy uridine. The fluorescence decay of Cy3 became multiexponential upon conjugation to DNA. The longest lifetime was observed for Cy3-5' ssDNA, where about 50% of the decay is dominated by a 2.0-ns lifetime. This value is more than 10 times larger than the fluorescence lifetime of the free dye in solution. These observations are interpreted in terms of a model where the molecule undergoes a trans-cis isomerization reaction from the first excited state. We observed that the activation energy for photoisomerization depends strongly on the microenvironment in which the dye is located. The unusually high activation energy measured for Cy3-5' ssDNA is an indication of dye-ssDNA interactions. In fact, the time-resolved fluorescence anisotropy decay of this sample is dominated by a 2.5-ns rotational correlation time, which evidences the lack of rotational freedom of the dye around the linker that separates it from the terminal 5' phosphate. The remarkable variations in the photophysical properties of Cy3-DNA constructs demonstrate that caution should be used when Cy3 is used in studies employing DNA conjugates.

Electron multiplying CCD based detection for spatially resolved fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is carried out with an electron multiplying CCD (EMCCD). This new strategy is compared to standard detection by an avalanche photo diode showing good agreement with respect to the resulting autocorrelation curves. Applying different readout modes, a time resolution of 20 micros can be achieved, which is sufficient to resolve the diffusion of free dye in solution. The advantages of implementing EMCCD cameras in wide-field ultra low light imaging, as well as in multi-spot confocal laser scanning microscopy, can consequently also be exploited for spatially resolved FCS. First proof-of-principle FCS measurements with two excitation volumes demonstrate the advantage of the flexible CCD area detection.

Excited-state metal-to-ligand charge transfer dynamics of a ruthenium(II) dye in solution and adsorbed on TiO2 nanoparticles from resonance Raman spectroscopy.

The dynamics of metal-to-ligand charge transfer (MLCT) in a cis-bis(4,4'-dicarboxy-2,2'-bipyridine)-bis(isothiocyanato)ruthenium(II) dye (N3) are compared for the free dye in solution and the dye adsorbed on the surface of the TiO(2) nanoparticles from resonance Raman spectroscopy. The 544-nm MLCT absorption band of N3 adsorbed on TiO(2) is slightly blue-shifted from that of the free N3, indicating a weak electronic coupling between N3 and TiO(2). The resonance Raman spectra of N3 and the N3|TiO(2) complex obtained upon excitation within the lowest-lying MLCT singlet state of the dye are similar except for slight shifts in band positions. Resonance Raman cross sections have been obtained for the vibrational modes of both N3 and N3|TiO(2) with excitation frequencies spanning the 544-nm MLCT band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism over two electronic states yields mode-specific vibrational and solvent reorganization energies. Despite the weak electronic coupling between N3 and TiO(2) in N3|TiO(2), adsorption strongly affects the reorganization energies of N3 in the intramolecular MLCT state. Adsorption of N3 onto TiO(2) increases the absolute Raman cross section of each mode by a factor of ca. 1.6 and decreases the vibrational and solvent reorganization energies by factors of 2 and 6, respectively. The excited-state dynamics of N3 adsorbed on the surface of TiO(2) nanoparticles were observed to be independent of the number of N3 molecules adsorbed per TiO(2) nanoparticle. The effect of TiO(2) on the dynamics of the adsorbed N3 is primarily due to both mode-specific vibrational and electronic pure dephasing, with the dominant contribution from the latter process.

Evolution of peptides that modulate the spectral qualities of bound, small-molecule fluorophores.

Fluorophore dyes are used extensively in biomedical research to sensitively assay cellular constituents and physiology. We have created, as proof of principle, fluorophore dye binding peptides that could have applications in fluorescent dye-based approaches in vitro and in vivo. A panel of Texas red, Rhodamine red, Oregon green 514 and fluorescein binding peptides, termed here 'fluorettes', was selected via biopanning of a combinatorial library of 12-mer peptides fused to a minor coat pIII protein of the filamentous bacteriophage M13. The 'best' fluorette sequences from each of the groups were subjected to further mutagenesis, followed by a second biopanning to select a new generation of improved fluorettes. Phage were selected that had higher avidity for each fluorophore except Rhodamine red. Of these, peptides were characterized that could specifically and with high affinity bind at least one dye, Texas red, in solution. In addition, the binding of certain peptides to Texas red shifted the peak excitation and/or the emission spectra of the bound dye. Peptides in the context of phage display could readily be selected that could bind to small-molecule fluorophores. The affinities of selected mutant fluorettes could be increased by mutation and further selection. Only a subset of the free peptides could bind free dyes in solution, suggesting that phage context contributed to the selection and ability of certain peptidic regions to independently bind the dyes. Future screens might lead to the creation of other dye-binding peptides with novel characteristics or Texas red derivatives with cross-linking substituents might be designed to increase the utility of the system.

Ultrafast study of interfacial electron transfer between 9-anthracene-carboxylate and TiO2 semiconductor particles

The excited state dynamics of 9-anthracene-carboxylic acid adsorbed onto the surface of TiO2 semiconductor particles were examined with ca. 250 fs time resolution. A combination of transient absorption and time-resolved anisotropy measurements show that approximately 76% of the photo-excited dye molecules transfer an electron to the TiO2 particles. The time scale for the forward electron transfer reaction was determined to be ⩽1 ps. The 9-anthracene-carboxylate radical cations produced by this reaction undergo back electron transfer on a 54 ps time scale. A more accurate estimate of the forward electron transfer reaction time is not possible, due to the contribution to the transient absorption signal from adsorbed dye molecules that do not transfer electrons to TiO2. These nonreactive species are deactivated by either nonradiative decay or fluorescence emission. The fluorescence spectrum from the dye molecules bound to the TiO2 particles is very different to that of the free dye in solution. The free dye has a broad red-shifted spectrum, whereas, the adsorbed molecules have a structured spectrum that displays a small Stokes shift. The red shift in the free dye fluorescence spectrum is due to stabilization of the excited electronic state through torsional motion of the carboxylate group. This motion cannot occur when the dye is bound to the particle surface. Thus, the excited molecules emit from a nuclear configuration that is similar to the ground-state geometry, producing a structured fluorescence spectrum. The dual behavior of the adsorbed dye molecules (electron transfer versus nonradiative decay/fluorescence) is attributed to the existence of two different sites for adsorption at the surface of the TiO2 particles: electron transfer can occur from one site but not the other.

Fluorescence spectra of DNA dyes measured in a flow cytometer.

The spectral properties of fluorescent dyes often vary with experimental conditions. Spectral changes contain information about the particles to which the dye is bound and can have practical consequences for the design of flow cytometry experiments. It is therefore desirable to have spectral information obtained under conditions that approach those under which the measurements in a flow cytometer are performed. This report describes the measurement of fluorescence spectra in a flow cytometer. We have attached a monochromator to one of the detector ports of our flow cytometer. The monochromator scans continuously over a range of wavelengths. For each measured particle, the monochromator wavelength is recorded along with the fluorescence intensity at that wavelength. Other fluorescence and scatter signals can also be recorded to distinguish different particle populations within the sample. This method for measurement of fluorescence spectra has advantages over conventional fluorimetry in that it distinguishes between bound and unbound dye and that spectral properties of different particle populations within a single sample can be separately reconstructed. Fluorescence spectra of common DNA dyes bound to chromatin are presented. A shift to the red in Hoechst 33258 fluorescence with increasing dye concentration is demonstrated. The spectra of DNA-bound Hoechst and ethidium bromide are compared with those of the free dyes in solution. Energy transfer between several pairs of DNA dyes is demonstrated using spectral measurements. We also find slight spectral variations between the different human chromosomes dualstained with Hoechst and chromomycin.

Characterization of skeletal muscle actin labeled with the triplet probe erythrosin-5-iodoacetamide.

We have labeled rabbit skeletal muscle actin with the triplet probe erythrosin-5-iodoacetamide and characterized the labeled protein. Labeling decreased the critical concentration and lowered the intrinsic viscosity of F-actin filaments; labeled filaments were motile in an in vitro motility assay but were less effective than unlabeled F-actin in activating myosin S1 ATPase activity. In unpolymerized globular actin (G-actin), both the prompt and delayed luminescence were red-shifted from the spectra of the free dye in solution and the fluorescence anisotropy of the label was high (0.356); filament formation red shifted all excitation and emission spectra and increased the fluorescence anisotropy to 0.370. The erythrosin phosphorescence decay was at least biexponential in G-actin with an average lifetime of 99 microseconds while in F-actin the decay was approximately monoexponential with a lifetime of 278 microseconds. These results suggest that the erythrosin dye was bound at the interface between two actin monomers along the two-start helix. The steady-state phosphorescence anisotropy of F-actin was 0.087 at 20 degrees C and the anisotropy increased to approximately 0.16 in immobilized filaments. The phosphorescence anisotropy was also sensitive to binding the physiological ligands phalloidin, cytochalasin B and tropomyosin. This study lays a firm foundation for the use of this triplet probe to study the large-scale molecular dynamics of F-actin.

The adsorption of basic dyes by poly(styrene sulphonate)

The adsorption of basic dyes (Safranine, Neutral Red, Acridine Orange and Proflavine) on poly(styrene sulphonate) has been studied by measuring the amount of free dye in solution using a photochemical method. Adsorption free energies are in the range 7.1–5.3 kcal mol . Comparing the values of these energies as a function of the structure of the dyes, three different types of interactions can be postulated to contribute to the binding of the dyes to the polymer, viz., electrostatic (c. 4 kcal mol ), hydrophobic and charge-transfer.

STREAK CAMERA MEASUREMENT OF TRYPTOPHAN AND RHODAMINE MOTIONS WITH PICOSECOND TIME RESOLUTION

Abstract—We have used a signal averaging laser (30 ps pulse)‐streak camera system to measure fluorescence anisotropy decays of dyes in solution and protein tryptophan chromophores with picosecond time resolution. Emission polarization as a function of time can be measured directly and simultaneously for both polarization directions and stored in an optical multichannel analyzer. The corrected anisotropy is computed after background subtraction. Rotations of free dyes in solution (Sulforhodamine 101, tryptophan) and the temperature‐dependent internal motions of human serum albumin (tryptophan emission) are displayed.

Quenching of fluorescence by oxygen. A probe for structural fluctuations in macromolecules.

Quenching of the fluorescence of various fluorophores by molecular oxygen has been studied in aqueous and nonaqueous solutions equilibrated with oxygen pressures up to 100 atm. Temperature dependence of quenching, agreement with the Stern–Volmer equation, and fluorescence lifetime measurements indicate that essentially all the observed quenching is dynamic and close to the diffusion-controlled limits. Studies of charged polyamino acids containing tryptophan show that oxygen quenching, in contrast to I−, is completely insensitive to charge effects. Ethidium bromide, when intercalated into double helical DNA, is quenched with 1/30th of the efficiency of the free dye in solution. Three dyes bound to bovine serum albumin were also found to be relatively protected from the free diffusion of oxygen. Quenching of intrinsic or bound fluorophores by molecular oxygen is therefore an appropriate method to determine the accessibility to oxygen of regions of the macromolecule surrounding the fluorophore and indirectly the structural fluctuations in the macromolecule that permit its diffusion to the fluorophore.

Polyanions and their complexes. Part VII. Mechanism of methylene blue–polyanion interactions

Pulse radiolysis has been employed to study the ion-binding between methylene blue and the anionic sites of a number of polyanions. A comparison between the extent of ion-binding measured by pulse radiolysis, and the apparent amount of free methylene blue indicated by absorption spectra, showed that an equilibrium exists between bound aggregated dye, bound monomeric dye and free dye in solution. The results indicate that dye aggregation rather than ion-binding is mainly responsible for metachromasia. The effect of temperature on the ion-binding was examined. The chemical nature and density of the anionic sites exert a significant influence on the driving force of the interaction, but the reversible aggregation and disaggregation of the dye appears to be the dominant effect.