Quantum yields and fluorescence lifetimes of acridine derivatives interacting with DNA

Interactions of several acridine dyes with DNA from different species were studied by measuring fluorescence lifetimes in the 2–30-nsec range, using the single-photon counting technique, and by measuring fluorescence quantum yields in the steady state. The results confirm the existence of two principal site classes, one in which the dye fluorescence is quenched by interaction with guanine and another in which fluorescence results from the hydrophobic environment of the A·T base pairs. The emitting sites are found, in some cases, to exhibit fluorescent decay curves which can be resolved into two exponential components corresponding to a short and to a long lifetime. The deviation from one exponential component is particularly clear with rivanol, 9-aminoacridine, and quinacrine, with which one component is two or three times longer than the other. The relative proportion of these two components depends only slightly on the DNA base composition and does not depend on the nature of the acridine derivatives. We postulate that this lifetime heterogeneity corresponds to the two discrete steps in the complex formation elucidated by kinetic studies: the first step corresponds to a semi-intercalated, or “external,” dye with a short fluorescence lifetime and the second step corresponds to a totally intercalated dye with a long lifetime. In this model, we assumed that a transient opening of the site near a semi-intercalated dye induces solvent diffusion which in turn is responsible for its short-lived fluorescence.     

Spectral Properties of Single Gold Nanoparticles in Close Proximity to Biological Fluorophores Excited by 2-Photon Excitation

Metallic nanoparticles (NPs) are able to modify the excitation and emission rates (plasmonic enhancement) of fluorescent molecules in their close proximity. In this work, we measured the emission spectra of 20 nm Gold Nanoparticles (AuNPs) fixed on a glass surface submerged in a solution of different fluorophores using a spectral camera and 2-photon excitation. While on the glass surface, we observed the presence in the emission at least 3 components: i) second harmonic signal (SHG), ii) a broad emission from AuNPS and iii) fluorescence arising from fluorophores nearby. When on the glass surface, we found that the 3 spectral components have different relative intensities when the incident direction of linear polarization was changed indicating different physical origins for these components. Then we measured by fluctuation correlation spectroscopy (FCS) the scattering and fluorescence signal of the particles alone and in a solution of 100 nM EGFP using the spectral camera or measuring the scattering and fluorescence from the particles. We observed occasional fluorescence bursts when in the suspension we added fluorescent proteins. The spectrum of these burst was devoid of the SHG and of the broad emission in contrast to the signal collected from the gold nanoparticles on the glass surface. Instead we found that the spectrum during the burst corresponded closely to the spectrum of the fluorescent protein. An additional control was obtained by measuring the cross-correlation between the reflection from the particles and the fluorescence arising from EGFP both excited at 488 nm. We found a very weak cross-correlation between the AuNPs and the fluorescence confirming that the burst originate from a few particles with a fluorescence signal.     

Analysis of diffusion and relaxation behavior of water in apple parenchymal cells

It has been demonstrated by an example of apple parenchymal cells that NMR spectroscopy can be used to analyze the relaxation and diffusion of water molecules in plant cells. With small diffusion times, three relaxation components have been distinguished, which correspond to water in a vacuole, in the cytoplasm, and in intercellular liquid. The coefficient of self-diffusion corresponding to these components have been determined. With large diffusion times, it is possible to distinguish two components. For the slowly relaxing component (which corresponds to water in a vacuole), the regime of restricted diffusion was observed. For a quickly relaxing component, an anomalous increase in the coefficient of self-diffusion with the time of diffusion took place.     

Combined analysis of diffusion and relaxation behavior of water in apple parenchyma cells

With apple parenchymal cells as an example, we demonstrate the expedience of combined analysis of the relaxation and diffusion of water molecules in plant cells by NMR spectroscopy. At small diffusion times, our approach discerns three relaxation components pertaining to water in the vacuole, cytoplasm, and intercellular space. The corresponding self-diffusion coefficients are determined. At long diffusion times, it is possible to distinguish two components. For the slow-relaxing component (vacuolar water) we observe the mode of restricted diffusion. For the fast-relaxing components, the diffusion coefficient anomalously increases with time.     

Qualitative measurements of the mitochondrial membrane potential in situ in Ehrlich ascites tumour cells using the safranine method.

Radiative and nonradiative processes were investigated in subchloroplast particles highly enriched in P-700 (1 P-700 to 10 chlorophyll molecules) according to the method of classical fluorescence and of photoacoustical spectroscopy. The envelope of fluorescence spectrum divided into three Gaussian bands and their quantum yields of fluorescence were calculated. Indpendently the quantum yield of fluorescence was determined from the spectral course of the photoacoustical signal. Finally, the estimate of the photochemical activity of P-700, based upon the measured fluorescence quantum yield and upon the measured nonradiative losses of excitation energy, was done.     

Characterizing diffusion dynamics of a membrane protein associated with nanolipoproteins using fluorescence correlation spectroscopy

Nanolipoprotein particles (NLPs) represent a unique nanometer-sized scaffold for supporting membrane proteins (MP). Characterization of their dynamic shape and association with MP in solution remains a challenge. Here, we present a rapid method of analysis by fluorescence correlation spectroscopy (FCS) to characterize bacteriorhodopsin (bR), a membrane protein capable of forming a NLP complex. By selectively labeling individual components of NLPs during cell-free synthesis, FCS enabled us to measure specific NLP diffusion times and infer size information for different NLP species. The resulting bR-loaded NLPs were shown to be dynamically discoidal in solution with a mean diameter of 7.8 nm. The insertion rate of bR in the complex was ～55% based on a fit model incorporating two separate diffusion properties to best approximate the FCS data. More importantly, based on these data, we infer that membrane protein associated NLPs are thermodynamically constrained as discs in solution, while empty NLPs appear to be less constrained and dynamically spherical.     

Fluorescence imaging of single molecules in polymer microspheres.

We report on far-field fluorescence imaging of single molecules in spherical polymer microparticles produced from solution by using microdroplet techniques. The fluorescence photobleaching quantum yields of rhodamine 6G in a common water-soluble polymer (polyvinyl alcohol) are at least five times smaller, corresponding to proportionally larger average fluorescence signals, than those in ethanolic solvents. This allows for acquisition of multiple images from a single molecule on a time scale of several minutes. We also show that fluorescent images of single molecules in microspheres can be calculated from semiclassic electrodynamics, which may ultimately be useful in retrieving dynamical information from experimental images.     

Diffusion in Pseudomonas aeruginosa biofilms: a pulsed field gradient NMR study

A Pseudomonas aeruginosa biofilm is studied with pulsed field gradient echo nuclear magnetic resonance. Although not all spectral components are assigned yet, the experimental results show that a biofilm consists of components with very different diffusion coefficients. The various biofilm components that give motionally narrowed 1H NMR signals, can be grouped into five classes with diffusion coefficients, ranging from 2 x 10(-9) to 1 x 10(-13) m2 s-1. Investigation of the diffusion behavior of water in the biofilm shows three fractions with different diffusion coefficients. Besides the highly mobile bulk water at least two other fractions with much lower diffusion coefficients are detected. It is shown that one of the fractions with the low diffusion coefficient probably arises from intracellular water. Also for another component of the biofilm, glycerol, three fractions with diffusion coefficients that differ more than a factor ten are detected. Also a group of signals exists which result from practically immobile components.     

Tracking single quantum dot and its spectrum in free solution with controllable thermal diffusion suppression

Thermal motions of semiconductor quantum dots (QDs) are suppressed on a dehydrated agarose-modified surface. The diffusion coefficients (D) of particles can be controlled by modifying the surface with an appropriate agarose concentration. The value of D is more than 100 times lower than the theoretical value when the dried agarose surface is made with an 8% agarose solution. This makes it possible to real-time record the diffusion process of single particles and single molecules in low-viscosity solution. A transmission grating installed in front of the charge-coupled device separates the QD fluorescence into the zeroth-order and first-order spectrum. Therefore, the spectrum of dynamic QDs is tracked on the modified surface. Tracking the dynamic QD spectral image is a promising method to explore the process of the molecular interactions in the physiological buffer.     

Fluorescence quantum yield of thioflavin T in rigid isotropic solution and incorporated into the amyloid fibrils

In this work, the fluorescence of thioflavin T (ThT) was studied in a wide range of viscosity and temperature. It was shown that ThT fluorescence quantum yield varies from 0.0001 in water at room temperature to 0.28 in rigid isotropic solution (T/η→0). The deviation of the fluorescence quantum yield from unity in rigid isotropic solution suggests that fluorescence quantum yield depends not only on the ultra-fast oscillation of ThT fragments relative to each other in an excited state as was suggested earlier, but also depends on the molecular configuration in the ground state. This means that the fluorescence quantum yield of the dye incorporated into amyloid fibrils must depend on its conformation, which, in turn, depends on the ThT environment. Therefore, the fluorescence quantum yield of ThT incorporated into amyloid fibrils can differ from that in the rigid isotropic solution. In particular, the fluorescence quantum yield of ThT incorporated into insulin fibrils was determined to be 0.43. Consequently, the ThT fluorescence quantum yield could be used to characterize the peculiarities of the fibrillar structure, which opens some new possibilities in the ThT use for structural characterization of the amyloid fibrils.     

A revised energy partitioning approach to assess the yields of non-photochemical quenching components

Non-photochemical quenching (NPQ) is a complex and still unclear mechanism essential for higher plants. The intensive research on this subject has highlighted three main components of NPQ: energy-dependent process (qE); state transitions to balance the excitation of PSII and PSI (qT); and photoinhibitory processes (qI). Recently, these components have been resolved as quantum yields according to the energy partitioning approach that takes into account the rate constants of every process involved in the quenching mechanisms of excited chlorophylls. In this study a fully extended quantum yield approach and the introduction of novel equations to assess the yields of each NPQ component are presented. Furthermore, a complete analysis of the yield of NPQ in Beta vulgaris exposed to different irradiances has been carried out. In agreement with experimental results here it is shown that the previous approach may amplify the yield of qE component and flatten the quantitative results of fluorescence analysis. Moreover, the significance of taking into account the physiological variability of NPQ for a correct assessment of energy partitioning is demonstrated.     

Light-induced quenching of chlorophyll fluorescence at 77 K in leaves,chloroplasts and Photosystem II particles

The light-induced chlorophyll (Chl) fluorescence decline at 77 K was investigated in segments of leaves, isolated thylakoids or Photosystem (PS) II particles. The intensity of chlorophyll fluorescence declines by about 40% upon 16 min of irradiation with 1000 μmol m⁻² s⁻¹ of white light. The decline follows biphasic kinetics, which can be fitted by two exponentials with amplitudes of approximately 20 and 22% and decay times of 0.42 and 4.6 min, respectively. The decline is stable at 77 K, however, it is reversed by warming of samples up to 270 K. This proves that the decline is caused by quenching of fluorescence and not by pigment photodegradation. The quantum yield for the induction of the fluorescence decline is by four to five orders lower than the quantum yield of Q_A reduction. Fluorescence quenching is only slightly affected by addition of ferricyanide or dithionite which are known to prevent or stimulate the light-induced accumulation of reduced pheophytin (Pheo). The normalised spectrum of the fluorescence quenching has two maxima at 685 and 695 nm for PS II emission and a plateau for PS I emission showing that the major quenching occurs within PS II. ‘Light-minus-dark’ difference absorbance spectra in the blue spectral region show an electrochromic shift for all samples. No absorbance change indicating Chl oxidation or Pheo reduction is observed in the blue (410–600 nm) and near infrared (730–900 nm) spectral regions. Absorbance change in the red spectral region shows a broad-band decrease at approximately 680 nm for thylakoids or two narrow bands at 677 and 670–672 nm for PS II particles, likely resulting also from electrochromism. These absorbance changes follow the slow component of the fluorescence decline. No absorbance changes corresponding to the fast component are found between 410 and 900 nm. This proves that the two components of the fluorescence decline reflect the formation of two different quenchers. The slow component of the light-induced fluorescence decline at 77 K is related to charge accumulation on a non-pigment molecule of the PS II complex. This revised version was published online in June 2006 with corrections to the Cover Date.     

Correlation spectroscopy of minor fluorescent species: signal purification and distribution analysis

We are performing experiments that use fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) to monitor the movement of an individual donor-labeled sliding clamp protein molecule along acceptor-labeled DNA. In addition to the FRET signal sought from the sliding clamp-DNA complexes, the detection channel for FRET contains undesirable signal from free sliding clamp and free DNA. When multiple fluorescent species contribute to a correlation signal, it is difficult or impossible to distinguish between contributions from individual species. As a remedy, we introduce "purified FCS", which uses single molecule burst analysis to select a species of interest and extract the correlation signal for further analysis. We show that by expanding the correlation region around a burst, the correlated signal is retained and the functional forms of FCS fitting equations remain valid. We demonstrate the use of purified FCS in experiments with DNA sliding clamps. We also introduce "single-molecule FCS", which obtains diffusion time estimates for each burst using expanded correlation regions. By monitoring the detachment of weakly-bound 30-mer DNA oligomers from a single-stranded DNA plasmid, we show that single-molecule FCS can distinguish between bursts from species that differ by a factor of 5 in diffusion constant.     

Characterization of two quenchers of chlorophyll fluorescence with different midpoint oxidation-reduction potentials in chloroplasts.

The properties of two redox quenchers of chlorophyll fluorescence in chloroplasts at room temperature have been investigated. (1) Redox titration of the fluorescence yield reveals two n = 1 components with Em7.8 at--45 and --247 mV, accounting for approx. 70 and 30% of the total yield, respectively. (2) Neutral red, a redox mediator often used at redox potentials below --300 mV, preferentially quenches the fluorescence controlled by the --247 mV component. Titrations using neutral red artifactually create an n = 2 quenching component with Em7.8 = --375 mV. (3) Analysis of fluorescence induction curves recorded at different redox potentials indicates that both the --45 and --247 mV components can be photochemically reduced. The reduction of the --247 mV component corresponds to a fast phase of the induction curve whilst the slower reduction of the 45 mV component accounts for the tail phase. (4) The excitation spectra for the fluorescence controlled by the two quenchers show small differences in the ratio of chlorophyll a and b. (5) Whereas the --247 mV component readily shows a 60 mV per pH unit dependency on solution pH, the ability of the --45 mV component to respond to pH change is restricted. (6) Triton Photosystem II particles contain both quenchers but the --247 mV component accounts for approx. 70% of the fluorescence and the high component has an Em7.8 of +48 mV. The relative merits of sequential and parallel models in explaining the presence of the two quenchers are considered.     

Single-particle tracking of immunoglobulin E receptors (FcεRI) in micron-sized clusters and receptor patches

When mast cells contact a monovalent antigen-bearing fluid lipid bilayer, IgE-loaded FcεRI receptors aggregate at contact points and trigger degranulation and the release of immune activators. We used two-color total internal reflection fluorescence microscopy and single-particle tracking to show that most fluorescently labeled receptor complexes diffuse freely within these micron-size clusters, with a diffusion coefficient comparable to free receptors in resting cells. At later times, when the small clusters coalesce to form larger patches, receptors diffuse even more rapidly. In all cases, Monte Carlo diffusion simulations ensured that the tracking results were free of bias, and distinguished biological from statistical variation. These results show the diversity in receptor mobility in mast cells, demonstrating at least three distinct states of receptor diffusivity.     

Mechanism of the highly efficient quenching of tryptophan fluorescence in human gammaD-crystallin

Quenching of the fluorescence of buried tryptophans (Trps) is an important reporter of protein conformation. Human gammaD-crystallin (HgammaD-Crys) is a very stable eye lens protein that must remain soluble and folded throughout the human lifetime. Aggregation of non-native or covalently damaged HgammaD-Crys is associated with the prevalent eye disease mature-onset cataract. HgammaD-Crys has two homologous beta-sheet domains, each containing a pair of highly conserved buried tryptophans. The overall fluorescence of the Trps is quenched in the native state despite the absence of the metal ligands or cofactors. We report the results of detailed quantitative measurements of the fluorescence emission spectra and the quantum yields of numerous site-directed mutants of HgammaD-Crys. From fluorescence of triple Trp to Phe mutants, the homologous pair Trp68 and Trp156 were found to be extremely quenched, with quantum yields close to 0.01. The homologous pair Trp42 and Trp130 were moderately fluorescent, with quantum yields of 0.13 and 0.17, respectively. In an attempt to identify quenching and/or electrostatically perturbing residues, a set of 17 candidate amino acids around Trp68 and Trp156 were substituted with neutral or hydrophobic residues. None of these mutants showed significant changes in the fluorescence intensity compared to their own background. Hybrid quantum mechanical-molecular mechanical (QM-MM) simulations with the four different excited Trps as electron donors strongly indicate that electron transfer rates to the amide backbone of Trp68 and Trp156 are extremely fast relative to those for Trp42 and Trp130. This is in agreement with the quantum yields measured experimentally and consistent with the absence of a quenching side chain. Efficient electron transfer to the backbone is possible for Trp68 and Trp156 because of the net favorable location of several charged residues and the orientation of nearby waters, which collectively stabilize electron transfer electrostatically. The fluorescence emission spectra of single and double Trp to Phe mutants provide strong evidence for energy transfer from Trp42 to Trp68 in the N-terminal domain and from Trp130 to Trp156 in the C-terminal domain. The backbone conformation of tryptophans in HgammaD-Crys may have evolved in part to enable the lens to become a very effective UV filter, while the efficient quenching provides an in situ mechanism to protect the tryptophans of the crystallins from photochemical degradation.     

Brownian dynamics simulations of fluorescence fluctuation spectroscopy

We have developed a program for the simulation of the fluorescence fluctuations as detected from highly diluted samples of (bio)molecules. The model is applied to translational diffusion and takes into account the hydrodynamic interactions. The solution concentration is kept constant by assuming periodic boundary conditions and spans here the range 0.5< C < 10 nM. We show that the fluorescence correlation functions can be accurately computed on systems of limited size (a few molecules per simulation box) by simulating for a total time approximately 100-300 times the diffusion relaxation time of the fluorescence autocorrelation function. The model is applied also to the simulation of the scanning fluorescence correlation spectroscopy (FCS) and of the photon counting histograms for the confocal collection configuration. Scanning FCS simulations of highly diluted samples (C approximately equals 0.5 nM) show anticorrelation effects in the autocorrelation functions of the fluorescence signal that are less evident for higher concentrations. We suggest here that this effect may be due to the non-uniform occupancy of the scanning area by the fluorophores.     

Utraviolet adsorption and fluorescence of human thyroalbumin]

Some spectral properties of human thyroalbumin have been studied. Ultra-violet absorption of the aqueous solution of this protein has two maxima: at the wavelengths of 276 and 296--298 nm. Under the excitation by a monochromatic light with the wavelength of 280 nm the thyroalbumin has the fluorescence spectrum with the maximum at 430 nm and the quantum yeild of fluorescence about 5,4%. It has been established that thyroalbumin fluorescence consists of two components with the maxima at 385 and 450 nm. Moreover the "sortwave" component is principally attributed for by the presence do iodoamino acids.     

Imaging Barriers to Diffusion by Pair Correlation Functions

Molecular diffusion and transport are fundamental processes in physical, chemical, biochemical, and biological systems. However, current approaches to measure molecular transport in cells and tissues based on perturbation methods such as fluorescence recovery after photobleaching are invasive, fluctuation correlation methods are local, and single-particle tracking requires the observation of isolated particles for relatively long periods of time. We propose to detect molecular transport by measuring the time cross-correlation of fluctuations at a pair of locations in the sample. When the points are farther apart than two times the size of the point spread function, the maximum of the correlation is proportional to the average time a molecule takes to move from a specific location to another. We demonstrate the method by simulations, using beads in solution, and by measuring the diffusion of molecules in cellular membranes. The spatial pair cross-correlation method detects barriers to diffusion and heterogeneity of diffusion because the time of the correlation maximum is delayed in the presence of diffusion barriers. This noninvasive, sensitive technique follows the same molecule over a large area, thereby producing a map of molecular flow. It does not require isolated molecules, and thus many molecules can be labeled at the same time and within the point spread function.     

几种血卟啉衍生物在中性水溶液中的聚集状态和光敏产生单线态氧量子产额的比较

通过稀释溶液导致吸收谱变化的分析,探讨了三种国产血卟啉衍生物(BHpd、YHpd和DHE)、血卟啉二盐酸(HPdHC)和原卟啉二钠盐(PpdSS)等五种卟啉类化合物在中性水溶液中的聚集状态。结果表明,YHpd和DHE的聚集体与BHpd和HpdHC的聚集体的结合方式可能不同,前两者结合得牢固,后两者结合得较为松懈。PpdSS的聚集形式介於上述两种情况之间。 用色氨酸光降解法测定了相近条件下用628nm光照时,五种卟啉类化合物中性水溶液中的单线态氧相对 量子产额。BHpd产生单线态氧的相对量子产额分别为YHpd和DHE的1.6倍和8.6倍,而HpdHC和PpdSS在表(?)上观察不到单线态氧的产生,它们本身却遭到较多破坏。 研究启示:由于BHpd和YHpd、DHE在聚集体的结合方式上的差异,它们的光动力的作用性更亦有所不同。