Compartmental analysis in photophysics: kinetics and identifiability of models for quenching of fluorescent probes in micelles

The parameters describing the kinetics of excited-state processes can possibly be recovered by analysis of the fluorescence decay surface measured as a function of the experimental variables. The identifiability analysis of a photophysical model assuming errorless time-resolved fluorescence data can verify whether the model parameters can be determined. In this work, we have used the methods of similarity transformation and Taylor series to investigate the identifiability of two models utilized to describe the time-resolved fluorescence quenching of stationary probes in micelles. The first model assumes that exchange of the quencher between micelles is much slower than the fluorescence decay of the unquenched probe (the 'immobile' quencher model). The second model assumes that quenchers exchange between the aqueous and micellar phases (the 'mobile' quencher model). For the 'immobile' quencher model, the rate constants for deactivation (k(0)) and quenching (k(q)) of the excited probe are uniquely identified together with the average number of quencher molecules per micelle. For the 'mobile' quencher model, the rate constants k(0) and k(q) are uniquely identified, as are the rate constants for entry (k(+)) and exit (k(-)) of one quencher molecule into and from a micelle, and the micellar aggregation number. The concomitant rate equations describing the time-resolved fluorescence are solved using z-transforms.     

On the mechanism of the PMS-effected quenching of chloroplast fluorescence

Evidence is presented which suggests that N-methylphenazonium methosulfate suppresses the fluorescence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea-poisoned chloroplasts by two mechanisms: (i) indirectly, by catalyzing the buildup of the phosphorylating potential X_E across the thylaknid membrane; (ii) directly, by interacting with excited chlorophyll molecules.Arguments in support of direct quenching are as follows: (i) N-methylphenazonium methosulfate is an efficient quencher of the fluorescence of chlorophyll a in methanol; (ii) the dark-irreversible portion of the light-induced fluorescence lowering in the presence of N-methylphenazonium-methosulfate increases with the concentration of the cofactor, (iii) N-methylphenazonium methosulfate lowers the fluorescence of chloroplasts at an excitation that is too weak to allow formation of X_E.Ascorbate-reduced N-methylphenazonium methosulfate (PMS-SQ) is a more efficient direct quencher of chloroplast fluorescence than oxidized PMS because the thylakoid membrane is more permeable to the reduced species. The permeability to these quenchers is enhanced by the light-induced protonation of the membrane, and suppressed by added Mg²⁺. Different permeability barriers appear to exist for the direct and for the X_E-mediated quenching by N-methylphenazonium methosulfate, since the latter is known to be insensitive to the presence of Mg²⁺.     

Membrane phosphorylation leads to the partial detachment of the chlorophyll a/b protein from Photosystem II

The hypothesis that the chlorophyll fluorescence decline due to membrane phosphorylation is caused principally by the detachment and removal of LHCP from the LHCP-PS II matrix is examined. It is demonstrated that when membranes are phosphorylated in the dark (a) the fluorescence decline is greater when excited by light enriched in wavelengths absorbed mainly by LHCP (475 nm) than when excited by light absorbed to a large extent also by the PS II complex (435 nm), (b) titration with different artificial quenchers of chlorophyll fluorescence is unchanged after the phosphorylation-induced fluorescence decline, and (c) the F_v/F_m ratio does not change after the phosphorylation-induced fluorescence decline. These data indicate that it is indeed principally LHCP that interacts with the quencher (PS I presumably). This interaction involves a small fraction of the total PS II-coupled LHCP, which becomes functionally detached from the LHCP-PS II matrix.     

Investigation of the mechanism for rapid heating of nitrogen and air in gas discharges

A rapid heating of nitrogen-oxygen mixtures excited by gas discharges is investigated numerically with allowance for the following main processes: the reactions of predissociation of highly excited electronic states of oxygen molecules (which are populated via electron impact or via the quenching of the excited states of N₂ molecules), the reactions of quenching of the excited atoms O(¹ D) by nitrogen molecules, the VT relaxation reactions, etc. The calculated results adequately describe available experimental data on the dynamics of air heating in gas-discharge plasmas. It is shown that, over a broad range of values of the reduced electric field E/N, gas heating is maintained by a fixed fraction of the discharge power that is expended on the excitation of the electronic degrees of freedom of molecules (for discharges in air, η_E?28%). The lower the oxygen content of the mixture, the smaller the quantity η_E. The question of a rapid heating of nitrogen with a small admixture of oxygen is discussed.     

Fluorescent probe and NMR studies of the aggregation of bile salts in aqueous solution

The binding of the fluorescent probes 1-anilino-8-naphthalene sulfonate and dansyl cadaverine to the sodium salts of cholic, deoxycholic and dehydrocholic acids has been investigated. Enhanced probe solubilisation accompanies aggregation. Monitoring of fluorescence intensities as a function of bile salt concentration permits the detection of primary micelle formation, as well as secondary association. The transition concentrations obtained by fluorescence are in good agreement with values determined for the critical micelle concentrations, by other methods. Differences in the behaviour of cholate and deoxycholate have been noted. Fluorescence polarisation studies of 1,6-diphenyl-1,3,5-hexatriene solubilised in bile salt micelles suggest a higher microviscosity for the interior of the deoxycholate micelle as compared to cholate. ¹H NMR studies of deoxycholate over the range 1–100 mg/ml suggest that micelle formation leads to a greater immobilisation of the C₁₈ and C₁₉ methyl groups as compared to the C₂₁ methyl group. Well resolved ¹³C resonances are observed for all three steroids even at high concentration. Both fluorescence and NMR studies confirm that dehydrocholate does not aggregate.     

Determination of the aggregation number of detergent micelles using steady-state fluorescence quenching.

The development of a simple, reliable method for determination of detergent micelle aggregation number that relies solely on measurement of steady-state fluorescence quenching is presented. The degree of steady-state fluorescence quenching of a micelle-solubilized fluorophore (pyrene) by a quencher that partitions greatly into the micelles (coumarin 153) is dependent on the micelle concentration, which can therefore be determined. The aggregation number is calculated as the micelle concentration/detergent monomer concentration (the total detergent concentration above the critical micelle concentration). For the determination to be accurate, the partition coefficient of the quencher into the micelle phase is determined and used to calculate the micellar concentration of quencher. Also, the quenching of pyrene by a coumarin 153 molecule within the same micelle must be complete, and this was confirmed by time-resolved fluorescence measurements. Aggregation numbers were determined for one cationic and several nonionic detergents and were found to be consistent with literature values. The approach presented is an improvement on a previous luminescence quenching technique (Turro, N.J., and A. Yekta. 1978. J. Am. Chem. Soc. 100:5951-5952) and can be used on cationic, anionic, and nonionic detergents with micelles ranging greatly in size and under varying conditions, such as detergent concentration, ionic strength, or temperature.     

Ab initio study of singlet excited states of bicyclo[2.2.0]hexasilane and tricyclo[4.2.0.02,5]octasilane

The singlet excited states in the optimized geometries of bicyclo[2.2.0]hexasilane and tricyclo[4.2.0.0^2,5]octasilane are studied theoretically using the ab initio molecular orbital method at the RHF/3-21G^* level with the all-singles CI approximation. These molecules are found to have zigzag structures in both the ground states and the singlet excited states corresponding to the lowest absorptions, and the estimated Stokes shifts between the lowest absorption and fluorescence are similar to the experimental values.     

Heterogeneity of the two tryptophanyl residues in the lac repressor of Escherichia coli.

The wild-type lac repressor of Escherichia coli is a tetrameric protein which contains two tryptophanyl residues per subunit at positions 190 and 209. Solute perturbation studies of the tryptophan fluorescence of the repressor were performed using a polar but uncharged quencher, acrylamide, to prevent possible bias caused by ionic quenchers. The results indicate that the two tryptophan residues have different accessibilities to the quencher. In addition, contrary to a previous report, the accessibility of these tryptophan residues is not altered by isopropyl-β-d-thiogalactoside (IPTG) binding to the repressor. Similar studies with mutant lac repressor containing only a single tryptophan either at positions 190 or 209 suggest that tryptophan 209 is located in a region which is perturbed by inducer binding. That the two tryptophanyl residues have heterogeneous environments was further confirmed by nanosecond fluorescence spectroscopy which showed the wild-type lac repressor exhibiting two excited-state lifetimes, τ₁ = 5.3 ns and τ₂ = 10 ns. In the presence of 10^?3m IPTG, only a single lifetime of 6 ns was observed for the wild-type repressor suggesting that the inducer perturbs the tryptophan residue with the longer lifetime but not the one with the shorter lifetime. This is in accord with the observation that the mutant repressor containing only tryptophan 190 (the Tyr-209 repressor) has a single lifetime of 4.5 ns which is not altered by IPTG binding. The surprising finding that the mutant repressor which contains only tryptophan 209 (the Tyr-190 repressor) shows two excited-state lifetimes has been interpreted to indicate that the repressor either does not exhibit fourfold symmetry in its subunit arrangement or is present in two different conformational states.     

Period four oscillations in chlorophyll a fluorescence

The discovery of period four oscillations of the fluorescence yield under flashing light demonstrated that not only the redox state of the Photosystem II (PS II) electron acceptor Q_A, but also the oxygen evolving cycle (described by the S states) modulates the fluorescence yield of chlorophyll (Chl). The positive charges accumulated on the donor side of PS II act on the fluorescence yield (measured in the Q_A ⁻ state during a strong flash) through the concentration of the quencher P₆₈₀ ⁺, the oxidized form of PS II reaction center Chl a. However, the period four oscillations of the fluorescence yield detected 1 s after a strong flash (in the P₆₈₀Q_A state) have not yet been fully explained. This revised version was published online in June 2006 with corrections to the Cover Date.     

Rotovibrational states of the water molecule on the sun

The infrared spectrum of water observed in sunspots is complex and dense, with bands separated by approximately 0.01 cm^?1. For top asymmetrical molecules, there is no theoretical approach that allows for the calculation of rotovibrational energy with such precision. Experimentally derived rotovibracional energy levels of water at high temperatures combined with variational calculations have been used for the band assignments. These energy levels are employed to refine the analysis of a small portion of the infrared absorption spectrum. Such procedure has allowed for the identification of additional 55 bands to the 70 already identified as rotovibrational transitions of the water molecule. Our new assignments, which include pure and cross transitions, offer additional evidence of the existence of water on the sun, but above all they illustrate the complexity of the solar spectrum that involves states with higher levels of rotational excitation. Given the conditions on the sun, more molecules of water would occur in excited electronic states, which include apolar and paramagnetic states, generating intense bands in the spectrum. Since there is an analytical solution for the rotovibrational transitions of linear molecules, we were able to identify 16 bands relative to the excited electronic states ¹B₂ and ³A₁ in the sunspot spectrum. Density functional B3LYP/AUG-cc-pVTZ calculations of the electric and magnetic dipole are employed to discuss some consequences of the presence of excited states of water in the dynamics of sunspots and solar magnetic field.     

Spectroscopic investigation of the interaction of water-soluble azocalix[4]arenes with bovine serum albumin

In this work, three hydrosoluble azocalix[4]arene derivatives, 5-(o-methylphenylazo)-25,26,27-tris(carboxymethoxy)-28-hydroxycalix[4]arene (o-MAC-Calix), 5-(m-methylphenylazo)-25,26,27-tris(carboxymethoxy)-28-hydroxycalix[4]arene (m-MAC-Calix) and 5-(p-methylphenylazo)-25,26,27-tris(carboxymethoxy)-28-hydroxycalix[4]arene (p-MAC-Calix) were synthesized. Their structures were characterized by infrared spectrum (IR), nuclear magnetic resonance spectrum (¹H NMR and ¹³C NMR) and mass spectrum (MS). The interactions between these compounds and bovine serum albumin (BSA) were studied by fluorescence spectroscopy, UV–vis spectrophotometry and circular dichroic spectroscopy. According to experimental results, three azocalix[4]arene derivatives can efficiently bind to BSA molecules and the o-MAC-Calix displays more efficient interactions with BSA molecules than m-MAC-Calix and p-MAC-Calix. Molecular docking showed that the o-MAC-Calix was embedded in the hydrophobic cavity of helical structure of BSA molecular and the tryptophan (Trp) residue of BSA molecular had strong interaction with o-MAC-Calix. The fluorescence quenching of BSA caused by azocalix[4]arene derivatives is attributed to the static quenching process. In addition, the synchronous fluorescence spectroscopy indicates that these azocalix[4]arene derivatives are more accessible to Trp residues of BSA molecules than the tyrosine (Tyr) residues. The circular dichroic spectroscopy further verified the binding of azocalix[4]arene derivatives and BSA.     

Characterization of the Quenching of Chlorophyll a Fluorescence by β-Carotene Using the Non-Linear Analysis

Carotenoids (Car) regulate energy flow in photosynthesis by a specific Car-chlorophyll (Chl) interaction in the singlet-excited states, leading to a reduction in Chl fluorescence. We studied quenching of Chl a-fluorescence in benzene by trans--carotene. Non-linear analysis of the quenching process enables to explain the possible molecular mechanism leading to the de-excitation of Chl a. The fluorescence intensity was measured at 670 nm for excitation wavelengths of 380, 430, 640, and 650 nm. The -carotene concentrations ranged from 4×10^–5 M to 5×10^–3 M. When the samples were excited at 640 and 650 nm, the Stern-Volmer plots showed that the quenching process has high rate constants, hence -carotene is a very efficient quencher. Two different types of quenching process could take place.     

Location and orientation relative to the micelle surface for glucagon in mixed micelles with dodecylphosphocholine EPR and NMR studies

The spin labels, 5-doxylstearate, 12-doxylstearate, 16-doxylstearate and 1-oxyl-2,2,6,6-tetramethyl-4-dodecylphospiperidine, have been incorporated into dodecylphospocholine micelles and mixed dodecylphosphocholine/ glucagon micelles. The EPR spectral parameters for the different spin labels and the ¹H- and ¹³C-NMR relaxation rates for nuclei of the detergent molecules indicated that inclusion of up to one spin label molecule per micelle had little influence on the spatial organization of the micelles. Furthermore, the location and environment of the spin labels in the dodecylphosphocholine micelles were not noticeably affected by the addition of glucagon and the ¹H-NMR spectra observed for glucagon in mixed spin label/deuterated dodecylphosphocholine/glucagon micelles showed that the different spin labels had essentially no effect on the conformation of glucagon. Approximate spatial locations within the micelle for the nitroxide moieties of the different spin labels were determined from the NMR relaxation rates observed for different nuclei of dodecylphosphocholine. On this basis, the line broadening of individually assigned glucagon ¹H-NMR lines by the different spin labels was used to determine the approximate orientation of the polypeptide chain with respect to the micelle surface. Overall, the data indicate that the glucagon backbone runs roughly parallel to the micelle surface, with the depth of immersion adjusted so that polar and apolar side chains can be oriented towards the surface or interior of the micelle, respectively.     

Effects of Quenching Mechanism and Type of Quencher Association on Stern-Volmer Plots in Compartmentalized Systems

Fluorescence quenching techniques have been used extensively in recent years to examine reaction rates and the compartmentalization of components in lipid micelles and membranes. Steady-state fluorescence methods are frequently employed in such studies but the interpretation of the resulting Stern-Volmer plots is often hampered by uncertainties regarding the mode of association of the quencher with the lipid structure and the nature of the quenching mechanism. This paper presents a method for simulating steady-state Stern-Volmer plots in two phase systems, and shows how the forms of such plots are influenced by the type of association of the quencher with the membrane or micelle (partition and/or binding) and by the type of quenching mechanism (dynamic and/or static). Comparisons of simulated plots with experimental data must take into account the possible combinations of quencher association(s) and quenching mechanism(s). The methods presented are applicable to synthetic and natural membranes and provide a basis for comparing the quenching of fluorescent molecules in biological membranes of differing composition.     

Quenching of fluorescence of pyrene-substituted lecithin by tetracyanoquinodimethane in liposomes.

In this work we have applied a kinetic scheme derived from fluorescence kinetics of pyrene-labeled phosphatidylcholine in phosphatidylcholine membrane to explain the fluorescence quenching of 1-palmitoyl-2-(10-[pyrenl-yl]-sn-glycerol-3-phosphatidylchol ine (PPDPC) liposomes by tetracyanoquinodimethane (TCNQ). The scheme was also found to be applicable to neat PPDPC and the effect of the quencher could be attributed to certain steps of the proposed mechanism. The TCNQ molecules influence the fluorescence of pyrene moieties in PPDPC liposome in two ways. Firstly, an interaction between the quencher molecule and the pyrene monomer in the excited state quenches monomer fluorescence and effectively prevents the diffusional formation of the excimer. Secondly, an interaction between the quencher molecule and the excited dimer quenches the excimer fluorescence. The TCNQ molecule does not prevent the formation of the excimer in pyrene moieties aggregated in such a way that they require only a small rotational motion to attain excimer configuration. The diffusional quenching rate constant is calculated to be 1.0 x 10(8) M-1 s-1 for the pyrene monomer quenching and 1.3 x 10(7) M-1 s-1 for the pyrene excimer quenching. The diffusion constant of TCNQ is 1.5 x 10(-7) cm2 s-1 for the interaction radii of 0.8-0.9 nm. The TCNQ molecules are practically totally partitioned in the membrane phase.     

Basic Principles of Fluorescence and Energy Transfer Applied to Real-Time PCR

Fluorescence is highly sensitive to environment, and the distance separating fluorophores and quencher molecules can provide the basis for effective homogeneous nucleic acid hybridization assays. Molecular interactions leading to fluorescence quenching include collisions, ground state and excited state complex formation, and long-range dipole-coupled energy transfer. These processes are well understood and equations are provided for estimating the effects of each process on fluorescence intensity. Estimates for the fluorescein-tetramethylrhodamine donor–acceptor pair reveal the relative contributions of dipole-coupled energy transfer, collisional quenching, and static quenching in several common assay formats, and illustrate that the degree of quenching is dependent upon the hybridization complex formed and the manner of label attachment.     

Resolution of initially excited and relaxed states of tryptophan fluorescence by differential-wavelength deconvolution of time-resolved fluorescence decays

We describe a new procedure for the analysis of time-resolved decays of fluorescence intensity. This procedure was used to resolve the emission spectra of the initially excited and solvent relaxed states of a tryptophan derivative in viscous solution. Specifically, we examined N-acetyl-l-tryptophanamide (AcTrpNH₂) in viscous and nonviscous solutions of propylene glycol. Time-resolved decays of fluorescence intensity were collected at wavelengths across the emission spectra. Instead of the usual procedure of deconvolving these data with the time profile of the exciting pulse, we deconvolved these data using the response observed on the short-wavelength side of the emission. If one assumes that this emission results only from the initially excited state (F), then the nonzero decay time calculated using deconvolution is that of the solvent relaxed state (R). For our specific case of AcTrpNH₂ the emission spectra of the F and R states overlap at most wavelengths longer than the short-wavelength side of the emission (310 nm). As a result, differential-wavelength deconvolution yields two lifetimes and amplitudes, one pair representing the relaxed state and the other the initially excited state. The latter appears as a zero-decay-time component whose amplitude can be readily quantified. The wavelength-dependent amplitude of this zero-lifetime component can be used to calculate the emission spectrum of the F state and. by difference, the emission spectrum of the relaxed state. For AcTrpNH₂ in propylene glycol at ?20°C the emission maxima of the F and R states are near 320 and 350 nm, respectively, and the relative proportion of the emission from each state was near 50%. At lower temperatures the emission from the F state becomes dominant and at high temperatures the emission from the R state dominates. We note that this resolution of states is somewhat arbitrary because we assumed a two-state model and the absence of solvent relaxed emission at 310 nm. Nonetheless, differential-wavelength deconvolution simplifies and facilitates the analysis of time-resolved fluorescence data from samples which undergo excited state reactions. Moreover, this deconvolution procedure considerably simplifies the determination of the kinetic constants for reversible excited state reactions. The application of differential-wavelength deconvolution does not increase the time reqaired for data acquisition. This differential analysis procedure should enhance the usefulness and precision of pulse fluorometric methods in studies of nanosecond time scale processes in proteins and membranes.     

Fluorescence excitation profiles of beta-carotene in solution and in lipid/water mixtures

Intrinsic fluorescence from all-trans β-carotene molecules in solution and embedded in lipid/water mixtures has been observed under laser excitation and its excitation profiles measured. The profiles closely correspond to the absorption spectra. The observations can be explained in terms of a low-lying ¹A_g excited state.     

Oxidation-reduction properties of the electron acceptors of Photosystem II I. Redox titration of the flash-induced carotenoid band shift,of C550 and of the variable fluorescence yield in spinach chloroplasts

Redox titration of the electrochromic carotenoid band shift, detected at 50 μs after a saturating actinic flash, in spinach chloroplasts, shows that only one electron acceptor in Photosystem II participates in a transmembrane primary electron transfer. This species, the primary quinone acceptor, Q, shows only one midpoint potential (E_m,7.5) of approx. 0 V and is undoubtedly equivalent to the fluorescence quencher, Q_H. A second titration wave is observed at low potential ($\text{E}{}_{\mathrm{<mtext>m</mtext><mtext>,7.5</mtext>}}\text{? ? 240}\text{mV}$) and at greater than 3 ms after a saturating actinic flash. This wave has an action spectrum different from that of Photosystem II centers containing Q and could arise from a secondary but not primary electron transfer. A low-potential fluorescence quencher is observed in chloroplasts which largely disappears in a single saturating flash at ? 185 mV and which does not participate in a transmembrane electron transfer. This low-potential quencher (probably equivalent to fluorescence quencher, Q_L) and Q are altogether different species. Redox titration of C550 shows that if electron acceptor Q_β is indeed characterized by an E_m,7 of + 120 mV, then this acceptor does not give rise to a C550 signal upon reduction and does not participate in a transmembrane electron transfer. This titration also shows that C550 is not associated with Q_L.