Time-resolved fluorescence of nitrobenzoxadiazole-aminohexanoic acid: effect of intermolecular hydrogen-bonding on non-radiative decay

Conformational dynamics of the plug domain of the SecYEG protein-conducting channel

The central pore of the SecYEG preprotein-conducting channel is closed at the periplasmic face of the membrane by a plug domain. To study its conformational dynamics, the plug was labeled site-specifically with an environment-sensitive fluorophore. In the presence of a stable preprotein translocation inter-mediate, the SecY plug showed an enhanced solvent exposure consistent with a displacement from the hydrophobic central pore region. In contrast, binding and insertion of a ribosome-bound nascent membrane protein did not alter the plug conformation. These data indicate different plug dynamics depending on the ligand bound state of the SecYEG channel.

Transbilayer organization of membrane cholesterol at low concentrations: Implications in health and disease

Cholesterol is an essential and representative lipid in higher eukaryotic cellular membranes and is often found distributed nonrandomly in domains in biological membranes. A large body of literature exists on the organization of cholesterol in plasma membranes or membranes with high cholesterol content. However, very little is known about organization of cholesterol in membranes containing low amounts of cholesterol such as the endoplasmic reticulum or inner mitochondrial membranes. In this review, we have traced the discovery and subsequent development of the concept of transbilayer cholesterol dimers (domains) in membranes at low concentrations. We have further discussed the role of membrane curvature and thickness on the transbilayer organization of cholesterol. Interestingly, this type of cholesterol organization could be relevant in cellular sorting and trafficking, and in pathological conditions.

Aggregation-induced emission enhancement in organic ion pairs

We present here a new example of aggregation-induced emission enhancement (AIEE), which involves an original mechanism based on the formation of organic ion pairs. The phenol 4-hydroxy-7-nitrobenzoxadiazole (NBDOH) is dissociated in water at pH 5.0 to give the corresponding phenolate, which is poorly fluorescent in this medium. We bring evidence that fluorescence quenching is due to an interaction with water molecules. In the presence of a relatively bulky ammonium salt, specifically tetrabutylammonium bromide (TBAB), NBDOH forms a hydrophobic salt, TBA(+)NBDO(-). This has no influence on the fluorescence of the anion as long as the salt is dissolved. However, the salt readily crystallizes in the medium and transition to the solid state is accompanied by a strong increase in fluorescence intensity. This effect can be explained by two reasons. The anions are protected from water molecules, and above all, the presence of the bulky cations prevents parallel-stacking of the anions, thus leading to an original molecular arrangement that is favorable to fluorescence. As the nature of the organic cation may be easily changed, the versatility of the system is very interesting for the design of new organic micro- and nanoparticles that must be fluorescent in the solid state, possibly in an aqueous environment.

Monitoring the organization and dynamics of bovine hippocampal membranes utilizing differentially localized fluorescent membrane probes

Previous work from our laboratory has established bovine hippocampal membranes as a convenient natural source for studying neuronal receptors such as the G-protein coupled serotonin1A receptor. In this paper, we have explored the organization and dynamics of bovine hippocampal membranes using environment-sensitive and differentially localized fluorescent probes NBD-PE and NBD-cholesterol, utilizing wavelength-selective and time-resolved fluorescence measurements. The NBD group in NBD-PE is localized at the membrane interface while in NBD-cholesterol it is localized deeper in the membrane. Our results show that native hippocampal membranes offer considerable motional restriction as evidenced from red edge excitation shift of NBD probes. However, this effect progressively decreases with increasing cholesterol depletion in the case of NBD-cholesterol, possibly indicating a reduction in membrane heterogeneity. In contrast, REES of NBD-PE in hippocampal membranes does not show any significant change upon cholesterol depletion indicating relative lack of sensitivity of the membrane interface to cholesterol depletion. These observations are supported by changes in fluorescence polarization with cholesterol depletion. Taken together, these results imply that the deeper hydrocarbon region of the hippocampal membrane is more sensitive to changes in membrane organization and dynamics due to cholesterol depletion than the interfacial region. The motional restriction in native membranes is maintained even in the absence of proteins. The fluorescence lifetimes of both the NBD probes show slight reduction upon cholesterol depletion indicating a change in micro-environmental polarity possibly due to water penetration. These results are relevant in understanding the complex organization of hippocampal membranes and could have possible functional implications.

Suspensions of organic microcrystals produced in the presence of polymers: diversity of UV/Vis absorption and fluorescence properties according to the preparation conditions

Free-standing microcrystals of an organic fluorescent dye, specifically, 4-n-octylamino-7-nitrobenz-2-oxa-1,3-diazole, were prepared using a solvent-exchange process at room temperature, in the presence of polymers used as additives. Parameters such as the dye concentration, the nature and concentration of the polymer, and the pH of the solution were varied. Six samples of microcrystals were therefore obtained and characterized by fluorescence microscopy and by electron microscopy (TEM and SEM). They differed by their content in microcrystals, the shape and size of which depends strongly on experimental conditions. Curiously, the UV/vis absorption spectra of the microcrystal suspensions were very different from one sample to another. As a result the emission spectra were also varied. The diversity of the optical response obtained was attributed to the presence of several dye populations in the microcrystal suspensions. A distinction was made between the intrinsic spectral properties of the microcrystals and artifacts due to the presence of the additives.

Lipid headgroups mediate organization and dynamics in bilayers

We report on the fluorescence lifetime and anisotropy decay dynamics of the tethered chromophore NBD in unilamellar vesicles comprised of phosphoglycerol and phosphocholine lipids with C(12) and C(18) saturated acyl chains, with or without cholesterol and/or sphingomyelin. For the phosphocholine vesicles, we use the chromophore 2-(12-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)dodecanoyl-1-hexadecanoyl-sn-glycero-3-phosphocholine (NBD-PC), and for the phosphoglycerol vesicles, we use the chromophore 2-(12-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)dodecanoyl-1-hexadecanoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (NBD-PG). The addition of cholesterol and/or sphingomyelin to the PC vesicles restricts the chromophore environment, in agreement with the known rigidizing effect of cholesterol on PC membranes. The PG systems do not exhibit an analogous effect with the addition of cholesterol and/or sphingomyelin. The motional freedom of the NBD chromophore is, in general, more restricted in the PC bilayers than it is in the PG bilayers, and we understand this behavior in the context of the role of the lipid headgroups in mediating bilayer organization.

Fluorescence mapping of mitochondrial TIM23 complex reveals a water-facing, substrate-interacting helix surface

Protein translocation across the mitochondrial inner membrane is mediated by the TIM23 complex. While its central component, Tim23, is believed to form a protein-conducting channel, the regions of this subunit that face the imported protein are unknown. To examine Tim23 structure and environment in intact membranes at high resolution, various derivatives, each with a single, environment-sensitive fluorescent probe positioned at a specific site, were assembled into functional TIM23 complexes in active mitochondria and analyzed by multiple spectral techniques. Probes placed sequentially throughout a transmembrane region that was identified by crosslinking as part of the protein-conducting channel revealed an alpha helix in an amphipathic environment. Probes on the aqueous-facing helical surface specifically underwent spectral changes during protein import, and their accessibility to hydrophilic quenching agents is considered in terms of channel gating. This approach has therefore provided an unprecedented view of a translocon channel structure in an intact, fully operational, membrane-embedded complex.

Bright ideas for chemical biology

Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular "core" dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds.

Evaluating the role of chromophore side group identity in mediating solution-phase rotational motion

We report on the rotational diffusion dynamics of the chromophore 7-nitrobenz-2-oxa-1,3-diazole (NBD) in a series of protic and polar aprotic solvents, as a function of the identity of the side group appended to the chromophore amine functionality. The central issue we address is whether or not the side groups play a role in mediating the anisotropic reorientation dynamics of the chromophore. To understand the motional properties of the chromophores in detail, we use both one-photon and two-photon excited fluorescence anisotropy decay measurements, and from these complementary excitation methods, we extract two of the Cartesian components of the rotational diffusion constant, D. The experimental data indicate that, regardless of the functionality of the pendant side group, the reorienting moieties exhibit ratios of Dz/Dx in the range 1.8-2.0. There is a small but discernible difference between the substituted chromophores. For all of the substituted NBD chromophores, dielectric friction plays a discernible role in determining their reorientation dynamics.

Monitoring the looping up of acyl chain labeled NBD lipids in membranes as a function of membrane phase state

Lipids that are labeled with the NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl) group are widely used as fluorescent analogues of native lipids in biological and model membranes to monitor a variety of processes. The NBD group of acyl chain labeled NBD lipids is known to loop up to the membrane interface in fluid phase membranes. However, the organization of these lipids in gel phase membranes is not resolved. In this paper, we monitored the influence of the membrane phase state on the looping up behavior of acyl chain labeled NBD lipids utilizing red edge excitation shift (REES) and other sensitive fluorescence approaches. Interestingly, our REES results indicate that NBD group of lipids, which are labeled at the fatty acyl region, resides in the more hydrophobic region in gel phase membranes, and complete looping of the NBD group occurs only in the fluid phase. This is supported by other fluorescence parameters such as polarization and lifetime. Taken together, our results demonstrate that membrane packing, which depends on temperature and the phase state of the membrane, significantly affects the localization of acyl chain labeled NBD lipids. In view of the wide ranging use of NBD-labeled lipids in cell and membrane biology, these results could have potentially important implications in future studies involving these lipids as tracers.

Orientation and dynamics of melittin in membranes of varying composition utilizing NBD fluorescence

Melittin is a cationic hemolytic peptide isolated from the European honey bee, Apis mellifera. The organization of membrane-bound melittin has earlier been shown to be dependent on the physical state and composition of membranes. In this study, we covalently labeled the N-terminal (Gly-1) and Lys-7 of melittin with an environment-sensitive fluorescent probe, the NBD group, to monitor the influence of negatively charged lipids and cholesterol on the organization and dynamics of membrane-bound melittin. Our results show that the NBD group of melittin labeled at its N-terminal end does not exhibit red edge excitation shift in DOPC and DOPC/DOPG membranes, whereas the NBD group of melittin labeled at Lys-7 exhibits REES of approximately 8 nm. This could be attributed to difference in membrane microenvironment experienced by the NBD groups in these analogs. Interestingly, the membrane environment of the NBD groups is sensitive to the presence of cholesterol, which is supported by time-resolved fluorescence measurements. Importantly, the orientation of melittin is found to be parallel to the membrane surface as determined by membrane penetration depth analysis using the parallax method in all cases. Our results constitute the first report to our knowledge describing the orientation of melittin in cholesterol-containing membranes. These results assume significance in the overall context of the role of membrane lipids in the orientation and function of membrane proteins and peptides.

Probing organization and communication at layered interfaces

We have investigated the local organization intrinsic to a variety of interfacial structures, by both electrochemical and spectroscopic means. Our focus has been on the design and construction of biomimetic interfaces, where a lipid bilayer or a hybrid bilayer membrane can be bound to an interface. The goal of this work is ultimately to create an interface on a transducer surface that can support an enzyme in its active form. To this point, we have examined the extent of organization that is achievable in monolayers that will be used to bind bilayer structures to a transducer surface. Our electrochemical data point to the important role of the substrate surface in determining adlayer organization. We have also investigated the fluidity and structural heterogeneity of lipid bilayers using time-resolved and steady state fluorescence spectroscopy. Our data point to the highly interactive nature of lipid bilayer constituents, where perturbations introduced to one region have significant consequences on other regions of the bilayer. Such information is directly relevant to the existence and properties of lipid raft structures in both model and biological bilayers.

Raft-like domain formation in large unilamellar vesicles probed by the fluorescent phospholipid analogue, C12NBD-PC

The liquid-ordered/disordered-phase domain co-existence in large unilamellar vesicle membranes consisting of phosphatidylcholine:sphingomyelin (2:1) with different amounts of cholesterol has been examined using a concentration-dependent self-quenching of a single reporter molecule, C12NBD-PC. A temperature-dependent decrease of fluorescence intensity was associated with the expected formation and increase of l(o)-phase membrane fraction in the vesicles. The result is consistent with exclusion of the fluorescent probe from the liquid-ordered phase which partitions preferentially into the liquid-disordered phase membrane domains. This leads to an increase of the local concentration of fluorophore in the liquid-disordered phase and a decrease of the quantum yield. This effect was used to obtain a quantitative estimation of the fraction of the vesicle membrane occupied by the liquid-ordered phase, Phi(o), as a function of temperature and cholesterol content between 0 and 45 mol%. The value of Phi(o) was related to the assumed partition coefficient k(p) of probe between liquid-ordered/disordered phases. For large unilamellar vesicles containing 20 and 4 mol% cholesterol and probe, respectively, with k(p) = 0 (probe completely excluded from liquid-ordered phase), Phi(o) = 0.16 and with k(p) = 0.2, Phi(o) = 0.2. The results are relevant to the action of detergent in the fractionation of detergent-resistant membrane from living cells.

Dynamics of 4-benzylamino-7-nitrobenzofurazan in the 1-propanol/water binary solvent system. Evidence for composition-dependent solvent organization

We report on the fluorescence lifetime and rotational diffusion dynamics of 4-benzylamino-7-nitrobenzofurazan (BBD) in a series of 1-propanol/water binary solvent systems. The fluorescence lifetime of BBD increases monotonically with increasing 1-propanol concentration. The rotational diffusion dynamics of BBD also vary with solution 1-propanol content, but this variation is not monotonic. Comparison of the BBD rotational diffusion time constant to solution viscosity and 1-propanol composition reveals the presence of a solution composition dependence of solvent-solute interactions, with a relative decrease in solvent-solute interaction strength for solvent system compositions where the 1-propanol/water azeotrope is known to exist. These data point collectively to the existence of microscopic heterogeneity in these binary solvent systems.

Quantitating the Dynamics of NBD Hexanoic Acid in Homogeneous Solution and in Solutions Containing Unilamellar Vesicles

We report here on the motional and fluorescence lifetime dynamics of the chromophore NBDHA (6-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoic acid) in neat solvents and in aqueous solutions containing unilamellar vesicles of varying composition. We measure the transient response of this chromophore by time-correlated single-photon counting, using one- and two-photon excitation to resolve the Cartesian components of the rotational diffusion constant, D. Our experimental data for NBDHA in selected solvents of varying viscosity demonstrate that one- and two-photon excitation probe different components of the rotational diffusion constant and that this chromophore reorients as a prolate rotor with an aspect ratio of approximately 2. For NBDHA in aqueous solutions containing unilamellar vesicles of varying composition, we recover the same reorientation behavior regardless of vesicle composition. Fluorescence lifetime and steady-state fluorescence data show the chromophore to reside in a polar environment that is different from neat water. We understand these data in the context of the chromophore residing in close proximity to the unilamellar vesicle polar headgroups in all cases.

Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor

We previously reported the construction of a family of reagentless fluorescent biosensor proteins by the structure-based design of conjugation sites for a single, environmentally sensitive small molecule dye, thus providing a mechanism for the transduction of ligand-induced conformational changes into a macroscopic fluorescence observable. Here we investigate the microscopic mechanisms that may be responsible for the macroscopic fluorescent changes in such Fluorescent Allosteric Signal Transduction (FAST) proteins. As case studies, we selected three individual cysteine mutations (F92C, D95C, and S233C) of Escherichia coli maltose binding protein (MBP) covalently labeled with a single small molecule fluorescent probe, N-((2-iodoacetoxy)ethyl)-N-methyl)amino-7-nitrobenz-2-oxa-1,3-diazole (NBD), each giving rise to a robust FAST protein with a distinct maltose-dependent fluorescence response. The fluorescence emission intensity, anisotropy, lifetime, and iodide-dependent fluorescence quenching were determined for each conjugate in the presence and absence of maltose. Structure-derived solvent accessible surface areas of the three FAST proteins are consistent with experimentally observed quenching data. The D95C protein exhibits the largest fluorescence change upon maltose binding. This mutant was selected for further characterization, and residues surrounding the fluorophore coupling site were mutagenized. Analysis of the resulting mutant FAST proteins suggests that specific hydrogen-bonding interactions between the fluorophore molecule and two tyrosine side-chains, Tyr171 and Tyr176, in the open state but not the closed, are responsible for the dramatic fluorescence response of this construct. Taken together these results provide insights that can be used in future design cycles to construct fluorescent biosensors that optimize signaling by engineering specific hydrogen bonds between a fluorophore and protein.

Fluorescent ligands for the histamine H2 receptor: synthesis and preliminary characterization

3-[3-(Piperidinomethyl)phenoxy]alkyl, N-cyano-N'-[omega-[3-(1-piperidinylmethyl)phenoxy]alkyl]guanidine and 2-(5-methyl-4-imidazolyl)methyl thioethyl derivatives containing fluorescent functionalities were synthesized and the histamine H2 receptor affinity was evaluated using the H2 antagonist [125I]-aminopotentidine. The compounds exhibited weak to potent H2 receptor affinity with pKi values ranging from <4 to 8.85. The highest H2 receptor affinity was observed for N-cyano-N'-[omega-[3-(1-piperidinylmethyl)phenoxy]alkyl]guanidines substituted with methylanthranilate (13), cyanoindolizine (6) and cyanoisoindole (11) moieties via an ethyl or propyl linker.

Singlet Excited-State Interactions in Naphthalene-Thymine Dyads

Two thymidine-derived nucleosides 1 and 2 were prepared by attaching a chiral naphthalene to the positions 5' and 3' of the sugar. The resulting dyads, which contain key substructures present in drugs and nucleic acids, exhibit different spatial arrangements (transoid or cisoid) of the fluorophore relative to the thymine unit. Emission measurements on these compounds in the presence of ROH molecules revealed a remarkable intramolecular prescence quenching for dyad 1. The obtained results are consistent with quenching of the singlet excited state of 1 by hydrogen-bond donor solvents. Thus, a physical deactivation process (vibronically induced internal conversion) would be the pathway responsible for the accelerated decay of 1*, favorably competing with fluorescence and intersystem crossing to the triplet. This effect appears to be strongly dependent on the relative spatial arrangement between the naphthalene and thymine units, together with the hydrogen-bonding ability of the employed ROH.

A study of the relationship between the chemical structures and the fluorescence quantum yields of coumarins, quinoxalinones and benzoxazinones for the development of sensitive fluorescent derivatization reagents

To develop new fluorescent derivatization reagents, we investigated the relationship between the chemical structures and the fluorescence quantum yields (phi(f)) of coumarins, quinoxalinones and benzoxadinones. Forty-six compounds were synthesized and their fluorescence spectra were measured in n-hexane, ethyl acetate, methanol and water. The energy levels of these compounds were calculated by combination of the semi-empirical AM1 and INDO/S (CI = all) methods. The deltaE(Tn(n,pi*), S1(pi,pi*)) (the energy gap between the Tn(n,pi*) and S1(pi,pi*) states) values were well correlated with the phi(f) values, which enables us to predict the phi(f) values from their chemical structures. Based on this relationship, 3-phenyl-7-N-piperazinoquinoxalin-2(1H)-one (PQ-Pz) and 7-(3-(S)-aminopyrrolidin-1-yl)-3-phenylquinoxalin-2-(1H)-one (PQ-APy) were developed as fluorescent derivatization reagents for carboxylic acids. The derivatives of the carboxylic acids with PQ-Pz and PQ-APy showed large phi(f) values even in polar solvents, suggesting that these reagents are suitable for the microanalysis of biologically important carboxylic acids by reversed phase HPLC.

Exploring membrane organization and dynamics by the wavelength-selective fluorescence approach

Wavelength-selective fluorescence comprises a set of approaches based on the red edge effect in fluorescence spectroscopy which can be used to directly monitor the environment and dynamics around a fluorophore in a complex biological system. A shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of absorption band, is termed red edge excitation shift (REES). This effect is mostly observed with polar fluorophores in motionally restricted media such as very viscous solutions or condensed phases where the dipolar relaxation time for the solvent shell around a fluorophore is comparable to or longer than its fluorescence lifetime. REES arises from slow rates of solvent relaxation (reorientation) around an excited state fluorophore which is a function of the motional restriction imposed on the solvent molecules in the immediate vicinity of the fluorophore. Utilizing this approach, it becomes possible to probe the mobility parameters of the environment itself (which is represented by the relaxing solvent molecules) using the fluorophore merely as a reporter group. Further, since the ubiquitous solvent for biological systems is water, the information obtained in such cases will come from the otherwise 'optically silent' water molecules. This makes REES and related techniques extremely useful since hydration plays a crucial modulatory role in a large number of important cellular events, including lipid-protein interactions and ion transport. The interfacial region in membranes, characterized by unique motional and dielectric characteristics, represents an appropriate environment for displaying wavelength-selective fluorescence effects. The application of REES and related techniques (wavelength-selective fluorescence approach) as a powerful tool to monitor the organization and dynamics of probes and peptides bound to membranes, micelles, and reverse micelles is discussed.

Determination of fluoxetine and norfluoxetine in rat plasma by HPLC with pre-column derivatization and fluorescence detection

Both fluoxetine (FLX) and its N-demethylated metabolite, norfluoxetine (NFLX), have been reported to be potent serotonin-reuptake inhibitors. A sensitive and reliable method that allows simultaneous quantification of their plasma levels would be valuable and was developed in this work. The procedure included extraction of FLX and NFLX from plasma, fluorescence derivatization with 4-(N-chloroformylmethyl-N-methyl) amino-7-nitro-2,1,3-benzoxadiazole (NBD-COCl), separation of the derivatives on an octadecylsilica column with acetonitrile-water (55:45,v/v) as mobile phase and fluorescence detection with emission at 537 nm and excitation at 478 nm. The calibration curves were linear for FLX and NFLX concentration over the range of 10-1000 nM (r = 0.9992 and r = 0.9997) and the limits of quantitation were 10 nM in 100 micro L of plasma. Precision of intra- and inter-day RSD of less than 12% and accuracy of intra- and inter-day RE within -6.0-13% were achieved. The method described was applied to analysis of the plasma samples from rats treated with FLX hydrochloride and to the pharmacokinetic study.

Cholesterol organization in membranes at low concentrations: effects of curvature stress and membrane thickness

Cholesterol is often found distributed nonrandomly in domains in biological and model membranes and has been reported to be distributed heterogeneously among various intracellular membranes. Although a large body of literature exists on the organization of cholesterol in plasma membranes or membranes with high cholesterol content, very little is known about organization of cholesterol in membranes containing low amounts of cholesterol. Using a fluorescent cholesterol analog (25-[N-[(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-methyl]amino]-27-norcholesterol, or NBD-cholesterol), we have previously shown that cholesterol may exhibit local organization even at very low concentrations in membranes, which could possibly be attributable to transbilayer tail-to-tail dimers. This is supported by similar observations reported by other groups using cholesterol or dehydroergosterol, a naturally occurring fluorescent cholesterol analog which closely mimics cholesterol. In this paper, we have tested the basic features of cholesterol organization in membranes at low concentrations using spectral features of dehydroergosterol. More importantly, we have investigated the role of membrane surface curvature and thickness on transbilayer dimer arrangement of cholesterol using NBD-cholesterol. We find that dimerization is not favored in membranes with high curvature. However, cholesterol dimers are observed again if the curvature stress is relieved. Further, we have monitored the effect of membrane thickness on the dimerization process. Our results show that the dimerization process is stringently controlled by a narrow window of membrane thickness. Interestingly, this type of local organization of NBD-cholesterol at low concentrations is also observed in sphingomyelin-containing membranes. These results could be significant in membranes that have very low cholesterol content, such as the endoplasmic reticulum and the inner mitochondrial membrane, and in trafficking and sorting of cellular cholesterol.

Fluorogenic and fluorescent labeling reagents with a benzofurazan skeleton

Fluorogenic and fluorescent labeling reagents having a benzofurazan (2,1,3-benzoxadiazole) skeleton such as 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), 4-N,N-dimethylaminosulfonyl-7-fluoro-2,1,3-benzoxadiazole (DBD-F), 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole (ABD-F), ammonium 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate (SBD-F), 4-hydrazino-7-nitro-2,1,3-benzoxadiazole (NBD-H), 4-N,N-dimethylaminosulfonyl-7-hydrazino-2,1,3-benzoxadiazole (DBD-H), 4-nitro-7-N-piperazino-2,1,3-benzoxadiazole (NBD-PZ), 4-N,N-dimethylaminosulfonyl-7-N-piperazino-2,1,3-benzoxadiazole (DBD-PZ), 4-(N-chloroformylmethyl-N-methyl)amino-7-N,N-dimethylaminosulfonyl-2,1,3-benzoxadiazole (DBD-COCl) and 7-N,N-dimethylaminosulfonyl-4-(2,1,3-benzoxadiazolyl) isothiocyanate (DBD-NCS) are reviewed in terms of synthetic method, reactivity, fluorescence characteristics, sensitivity and application to analytes.

Control of a redox reaction on lipid bilayer surfaces by membrane dipole potential

Nitro-2,1,3-benzoxadiazol-4-yl (NBD) group is a widely used, environment-sensitive fluorescent probe. The negatively charged dithionite rapidly reduces the accessible NBD-labeled lipids in liposomes to their corresponding nonfluorescent derivatives. In this study both the phospholipid headgroup and acyl chain NBD-labeled L-alpha-1,2-dipalmitoyl-sn-glycero-3-phospho-[N-(4-nitrobenz-2-oxa-1,3-diazole)-ethanolamine] (DPPN) and 1-acyl-2-[12-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]dodecanoyl]-sn-glycero-3-phosphocholine (NBD-PC), respectively, were employed. The correlation of both the rate coefficient k(1) of the redox reaction and the fluorescence properties of the two probes with the membrane dipole potential Psi in fluid dipalmitoylglycerophosphocholine (DPPC) liposomes is demonstrated. When Psi of the bilayer was varied (decreased by phloretin or increased by 6-ketocholestanol), the value for k1 decreased for both DPPN and NBD-PC with increasing Psi. For both fluorophores a positive correlation to Psi was evident for the relative fluorescence emission intensity (RFI, normalized to the emission of the fluorophore in a DPPC matrix). The relative changes in emission intensity as a function of Psi were approximately equal for both NBD derivatives. Changes similar to those caused by phloretin were seen when dihexadecylglycerophosphocholine (DHPC) was added to DPPC liposomes, in keeping with the lower dipole potential for the former lipid compound compared with DPPC. These effects of Psi on NBD fluorescence should be taken into account when interpreting data acquired using NBD-labeled lipids as fluorescent probes.

Ultrafast primary processes in photosystem I of the cyanobacterium Synechocystis sp. PCC 6803

Ultrafast primary processes in the trimeric photosystem I core antenna-reaction center complex of the cyanobacterium Synechocystis sp. PCC 6803 have been examined in pump-probe experiments with approximately 100 fs resolution. A global analysis of two-color profiles, excited at 660 nm and probed at 5 nm intervals from 650 to 730 nm, reveals 430 fs kinetics for spectral equilibration among bulk antenna chlorophylls. At least two lifetime components (2.0 and 6.5 ps in our analysis) are required to describe equilibration of bulk chlorophylls with far red-absorbing chlorophylls (>700 nm). Trapping at P700 occurs with 24-ps kinetics. The multiphasic bulk left arrow over right arrow red equilibration kinetics are intriguing, because prior steady-state spectral studies have suggested that the core antenna in Synechocystis sp. contains only one red-absorbing chlorophyll species (C708). The disperse kinetics may arise from inhomogeneous broadening in C708. The one-color optical anisotropy at 680 nm (near the red edge of the bulk antenna) decays with 590 fs kinetics; the corresponding anisotropy at 710 nm shows approximately 3.1 ps kinetics. The latter may signal equilibration among symmetry-equivalent red chlorophylls, bound to different monomers within trimeric photosystem I.

Effects of gel material on fluorescence lifetime detection of dyes and dye-labeled DNA primers in capillary electrophoresis

Investigations of fluorescence lifetimes of the dye 6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]hexanoic acid (NBD-HA) and of DNA M13 primers labeled with NBD-HA, Cy3, rhodamine green and 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene++ +-3-propionic acid (BODIPY-FL) dyes in polyacrylamide gels of various degrees of crosslinking and different crosslinkers, and in a cellulose sieving buffer with different organic modifiers, are described. The dependence of fluorescence lifetime on gel matrix and on experimental conditions was studied in order to identify which factors may be important for optimization of multiplex fluorescence lifetime detection. Lifetimes were determined in both batch solution and on-the-fly, on-column in CE. Results show that lifetimes of the primer-attached dyes remain constant in gels of different composition. Additionally, multiexponential fluorescence decays are observed for primer-attached dyes in batch solutions of the cellulose sieving buffers but are reduced to monoexponential decays when measured on-the-fly, on-column in CE. Lifetime detectability can be improved by addition of an organic modifier to the gel matrix.

Characterization of visible dyes for four-decay fluorescence detection in DNA sequencing

Dyes of several classes were investigated as candidates for use in a multiplex, four-decay fluorescence detection scheme for DNA sequencing. The dyes include nitrobenzofuran dyes, rhodamine dyes, fluorescein dyes, cyanine dyes, Nile Red, and BODIPY dyes. Based on the results of fluorescence spectral and lifetime studies, an initial set of four dyes was selected for further study: NBD-aminohexanoic acid (NBD-HA, r = 1.1 ns), tetramethyl-rhodamine, methyl ester (r = 2.2 ns), rhodamine green (r = 4.3 ns), and BODIPY 505/515 (r = 5.9 ns). Limits of lifetime detection of the four dyes were investigated, and lifetime resolution was demonstrated for mixtures of the free dyes in batch solution. Lifetime of dye-labeled DNA primers also were determined in batch solution and detected on-the-fly in capillary electrophoresis (CE). Conjugation of the dyes to DNA improved the resolution of their individual lifetimes in mixtures in batch measurements. When attached to the primer, tetramethyl-rhodamine exhibited biexponential decay with a dominant lifetime of 3.8 ns, making it unsuitable for four-decay sequencing. Contact with the CE gel lengthened the lifetime of NBD-HA-labeled primer from 1.3 to 2.1 ns but did not affect the lifetimes of the other dyes. Lifetime detectability of labeled primers at individual points along an electrophoretic peak in the attomole range.

The use of exogenous fluorescent probes for temperature measurements in single living cells

The fluorescent membrane probes 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) and 6-dodecanoyl-2-dimethylamino-naphthalene (laurdan) have been studied for use as optical thermometers in living cells. The thermal sensitivity of NBD is primarily a consequence of rapid, heat-induced electronic changes, which increase the observed fluorescence decay rate. As a result, fluorescence intensity and lifetime variations of membrane-bound NBD-conjugated phospholipids and fatty acids can be directly correlated with cellular temperature. In contrast, laurdan fluorescence undergoes a dramatic temperature-dependent Stokes shift as the membrane undergoes a gel-to-liquid-crystalline phase transition. This facilitates the use of fluorescence spectra to record the indirect effect of microenvironmental changes, which occur during bilayer heating. Microscope and suspension measurements of cells and phospholipid vesicles are compared for both probes using steady-state and fluorescence lifetime (suspension only) data. Our results show that NBD fluorescence lifetime recordings can provide reasonable temperature resolution (approximately 2 degrees C) over a broad temperature range. Laurdan's microenvironmental sensitivity permits better temperature resolution (0.1-1 degree C) at the expense of a more limited dynamic range that is determined solely by bilayer properties. The temperature sensitivity of NBD is based on rapid intramolecular rotations and vibrations, while laurdan relies on a slower, multistep mechanism involving bilayer rearrangement, water penetration and intermolecular processes. Because of these differences in time scale, NBD appears to be more suitable for monitoring ultrafast phenomena, such as the impact of short-pulse microirradiation on single cells.

Femtosecond pump-probe spectroscopy of bacteriochlorophyll a monomers in solution

One- and two-color absorption difference profiles were obtained for BChl a in 1-propanol with approximately 50-fs resolution, using a self-mode-locked Ti:sapphire laser system. Time evolution in the BChl a absorption difference spectrum produces nonexponential photobleaching/stimulated emission (PB/SE) decay kinetics in 800-nm one-color experiments. Nonexponential PB/SE rise behavior occurs for some combinations of pump and probe wavelengths in two-color experiments. Optimized parameters from triexponential fits to the absorption difference profiles depend markedly on the fitting time window; they typically include a minor component with lifetime in the hundreds of fs. Much of the latter component is due to vibrational relaxation and/or intramolecular vibrational redistribution, rather than solvent dielectric relaxation. Measurements of the pump-probe anisotropy indicate that the electronic transition moment for the broad Qy excited state absorption band that overlaps the Qy steady-state absorption spectrum makes an angle of at most 20 degrees from that of the ground-->Qy state transition. No coherent oscillations are observed at early times. Our results bear directly on the interpretation of fs pump-probe experiments on BChl a-containing pigment-protein complexes.

Characterization of the spectroscopic properties of a tetrahydrochrysene system containing a rigidified hydroxynitrostilbene chromophore: an inherently fluorescent ligand designed for the estrogen receptor

A tetrahydrochrysene system that embodies a hydroxy- and nitro-substituted stilbene chromophore held rigidly near planarity by the tetracyclic nature of the compound was prepared as a fluorescent ligand for the estrogen receptor. It shows strong solvent-dependent fluorescence at long wavelengths. The solvent polarity dependence suggests that the fluorescence arises from an excited state with much n pi * character in cyclohexane; stronger emission comes from an intramolecular charge transfer state that has lower energy in more polar solvents, and finally progressive quenching of the charge transfer state occurs in solvents of higher polarity. The quenching effect is particularly evident in protic solvents. In water, however, the compound shows fluorescence of unusually high energy for an intramolecular charge transfer state, which suggests that photochemistry may be occurring. In solutions of gamma-cyclodextrin, emission from the nitrotetrahydrochrysene is red shifted and intensified relative to water. Photobleaching occurs in H2O but not in ethanol or gamma-cyclodextrin solution. The change in dipole moment between the ground and excited states for the nitrochrysene is 12.9 D, similar to our previous measurements for related nitrostilbenes. The compound displays red-shifted emission in triethylamine, perhaps due to an excited state hydrogen-bonded complex. The absorption and emission properties of the corresponding nitrophenolate were also studied. The nitrophenolate exhibits reverse solvatochromism in its absorption spectra. In conclusion, the high sensitivity of the emission energy and quantum yield of the title compound make it of potential utility as a fluorescent probe.

Characterization of dipyridophenazine complexes of ruthenium(II): the light switch effect as a function of nucleic acid sequence and conformation

Spectroscopic parameters for two novel ruthenium complexes on binding to nucleic acids of varying sequences and conformations have been determined. These complexes, Ru(bpy)2dppz2+ and Ru(phen)2dppz2+ (bpy = 2,2'-bipyridine; phen = 1,10-phenanthroline; dppz = dipyrido[3,2:a-2',3':c]-phenazine) serve as "molecular light switches" for DNA, displaying no photoluminescence in aqueous solution but luminescing intensely in the presence of DNA. The luminescent enhancement observed upon binding is attributed to the sensitivity of the excited state to quenching by water; in DNA, the metal complex, upon intercalation into the helix, is protected from the aqueous solvent, thereby preserving the luminescence. Correlations between the extent of protection (depending upon the DNA conformation) and the luminescence parameters are observed. Indeed, the strongest luminescent enhancement is observed for intercalation into DNA conformations which afford the greatest amount of overlap with access from the major groove, such as in triple helices. Differences are observed in the luminescent parameters between the two complexes which also correlate with the level of water protection. In the presence of nucleic acids, both complexes exhibit biexponential decays in emission. Quenching studies are consistent with two intercalative binding modes for the dppz ligand from the major groove: one in which the metal-phenazine axis lies along the DNA dyad axis and another where the metal-phenazine axis lies almost perpendicular to the DNA dyad axis. Ru(bpy)2dppz2+ and Ru(phen)2dppz2+ are shown here to be unique reporters of nucleic acid structures and may become valuable in the design of new diagnostics for DNA.