Principal component and decomposition analysis of multicomponent mixtures of carcinogenic fluorophores

A series of binary and tertiary mixtures of polycyclic aromatic hydrocarbons is analyzed by using principal component and decomposition analysis of molecular fluorescence spectra. The results demonstrate the ability to determine the number and identity of species that are present. Failures caused by high correlation among spectra are considered.     

Hydroxycruciforms: amine-responsive fluorophores

The synthesis of three hydroxy-substituted cruciforms (XF, 1,4-bis(4'-hydroxystyryl)-2,5-bis(4'-methoxyphenylethynyl)benzene, 1,4-bis(4'-methoxystyryl)-2,5-bis(4'-hydroxyphenylethynyl)benzene, and 1,4-bis(4'-hydroxystyryl)-2,5-bis(4'-hydroxyphenylethynyl)benzene) starts with a Horner reaction followed by a Sonogashira coupling and subsequent deprotection. The three herein described XFs contain either two or four free phenolic hydroxyl groups. All three XFs were subjected to photometric UV/Vis titrations in a methanol/water mixture. The respective pK(a) values were obtained by data deconvolution. As the three XFs display a significant change in emission color upon photoinduced deprotonation, the XFs were taken up in different solvents and exposed to twelve amines. The amine-dependent change in emissivity of the tetrahydroxy XF is sufficiently distinct in the eight solvents that all of the inspected amines are discerned by a linear discriminant analysis. The tetrahydroxy XF in different solvents forms a sensor array, the response of which is based on the excited-state proton transfer (ESPT) to amines and mediated by the choice of the battery of solvents that are utilized.     

Oligonucleotide-stabilized Ag nanocluster fluorophores

Single-stranded oligonucleotides stabilize highly fluorescent Ag nanoclusters, with emission colors tunable via DNA sequence. We utilized DNA microarrays to optimize these scaffold sequences for creating nearly spectrally pure Ag nanocluster fluorophores that are highly photostable and exhibit great buffer stability. Five different nanocluster emitters have been created with tunable emission from the blue to the near-IR and excellent photophysical properties. Ensemble and single molecule fluorescence studies show that oligonucleotide encapsulated Ag nanoclusters exhibit significantly greater photostability and higher emission rates than commonly used cyanine dyes.     

Assay amplification-multiple valent fluorophores

The synthesis of a dendrimeric, internally quenched, fluorogenic peptide allowed signal amplification following enzymatic cleavage.     

Synthesis of calixarene-based ketocyanine fluorophores

Cup-shaped calix[4]arenes bearing one or two ketocyanine fluorophore fragments at the wide rim of the macrocycle are synthesized by condensation of formyl calix[4]arenes with arylmethylene(hetarylmethylene)cyclopentanones in the presence of the ionic liquid, dimethylammonium dimethylcarbamate (DIMCARB) and characterized using UV-vis and fluorescence spectroscopy. Strong positive solvatofluorochromism for the calixarene ketocyanines is observed.     

Cavitands bearing four fluorophores

The synthesis of novel cavitands containing four fluorophores [tert-butoxycarbonyl protected 2,2′-bis(furyl)benzidine (t-BOC FurylBz) or 5,5′-bis(4-aminophenyl)-2,2′-bifuryl (t-BOC PFDA)] and ionophoric functional groups on the upper rim is reported. The cavitands bearing the four fluorophores emit blue light photoluminescence. In particular, the cavitand containing PFDA moieties exhibits a high photoluminescence quantum yield.     

Synthesis of functionalized ethynylphenothiazine fluorophores

Alkynylated and butadiynyl-bridged phenothiazines with variable functionalization can be synthesized in good yields by cross-coupling and condensation approaches. In addition, the structure of the diethynylated phenothiazine (7a) has been corroborated by an X-ray structure analysis. These oligofunctional heterocycles are fluorescent with modest quantum yields (Phi(f) = 20-35%) and represent suitable building blocks for novel photoexcitable molecular wires.     

Parallel factor analysis combined with PLS regression applied to the on-line monitoring of Pichia pastoris cultures

Various key variables (biomass, substrate and product) of bioprocesses should be monitored in order to retrieve useful information on the system, with the biomass (the cell density) the principal target. Although several analytical methods have been adapted and used to monitor the evolution of cell density evolution in cultures, a general method for performing this determination has not yet been established, as each technique has its own advantages and drawbacks. In the present work, noninduced glycerol batch cultures (for which biomass and substrate are the key variables) were monitored using multiwavelength fluorescence spectroscopy. The data gathered were modelled via PARAFAC-PLS chemometric methodologies, resulting in important qualitative and quantitative information about the behaviours of different biogenic fluorophors in batch cultures of the yeast Pichia pastoris. This information was used to predict the target process variables in such cultures; this permitted the applicability of this combined technique to bioprocess monitoring to be assessed.     

Novel fluorophores for single-molecule imaging

Nonlinear optical chromophores based on dicyanodihydrofuran acceptors paired with amine donors have been found to exhibit sufficiently large fluorescence quantum yields and stability to enable single-molecule detection in polymeric hosts. To illustrate the breadth of this class, six fluorophores are presented, spanning the emission range from 505 to 646 nm. In contrast to conventional single-molecule fluorophores, the new molecules feature sensitivity to local rigidity, large ground-state dipole moments, and large polarizability anisotropies, properties that can be used to design new reporter experiments at the single-molecule level.     

Push-pull aminobithiophenes--highly fluorescent stable fluorophores

Stable 2-aminobithiophenes were prepared using the Gewald reaction. The resulting push-pull bithiophenes exhibited both unprecedented high fluorescence yields and stability in addition to demonstrating fluorescence on-off properties.     

Quantitative analysis of infrared absorption coefficient of spider silk fibers

Spider silk has a high degree of crystallinity comprising nanocrystals which are interlinked by amorphous regions containing pre-strained spidroin chains. Both, crystal volume fraction and crystal size were shown to be critical for the macroscopic mechanical properties of silk. In this study, for the first time, quantitative results were obtained from absorption IR spectra. Two main difficulties must be overcome: the cylindrical sample geometry and the absence of suitable reference spectra. We show that it is possible to get reproducible absorption coefficient spectra from dense parallel fiber grids immersed in a refractive index matching liquid. Comparison with model polypeptides yields the nanocrystal volume fraction that is close to the crystallinity values given by solid-state NMR or X-ray scattering.     

“Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”

Protein secondary structural analysis is important for understanding the relationship between protein structure and function, or more importantly how changes in structure relate to loss of function. The structurally sensitive protein vibrational modes (amide I, II, III and S) in deep-ultraviolet resonance Raman (DUVRR) spectra resulting from the backbone C–O and N–H vibrations make DUVRR a potentially powerful tool for studying secondary structure changes. Experimental studies reveal that the position and intensity of the four amide modes in DUVRR spectra of proteins are largely correlated with the varying fractions of α-helix, β-sheet and disordered structural content of proteins. Employing multivariate calibration methods and DUVRR spectra of globular proteins with varying structural compositions, the secondary structure of a protein with unknown structure can be predicted. A disadvantage of multivariate calibration methods is the requirement of known concentration or spectral profiles. Second-order curve resolution methods, such as parallel factor analysis (PARAFAC), do not have such a requirement due to the “second-order advantage.” An exceptional feature of DUVRR spectroscopy is that DUVRR spectra are linearly dependent on both excitation wavelength and secondary structure composition. Thus, higher order data can be created by combining protein DUVRR spectra of several proteins collected at multiple excitation wavelengths to give multi-excitation ultraviolet resonance Raman data (ME-UVRR). PARAFAC has been used to analyze ME-UVRR data of nine proteins to resolve the pure spectral, excitation and compositional profiles. A three factor model with non-negativity constraints produced three unique factors that were correlated with the relative abundance of helical, β-sheet and poly-proline II dihedral angles. This is the first empirical evidence that the typically resolved “disordered” spectrum represents the better defined poly-proline II type structure.     

Parallel single-cell analysis microfluidic platform

We report a PDMS microfluidic platform for parallel single-cell analysis (PaSCAl) as a powerful tool to decipher the heterogeneity found in cell populations. Cells are trapped individually in dedicated pockets, and thereafter, a number of invasive or non-invasive analysis schemes are performed. First, we report single-cell trapping in a fast (2-5 min) and reproducible manner with a single-cell capture yield of 85% using two cell lines (P3x63Ag8 and MCF-7), employing a protocol which is scalable and easily amenable to automation. Following this, a mixed population of P3x63Ag8 and MCF-7 cells is stained in situ using the nucleic acid probe (Hoechst) and a phycoerythrin-labeled monoclonal antibody directed at EpCAM present on the surface of the breast cancer cells MCF-7 and absent on the myeloma cells P3x63Ag8 to illustrate the potential of the device to analyze cell population heterogeneity. Next, cells are porated in situ using chemicals in a reversible (digitonin) or irreversible way (lithium dodecyl sulfate). This is visualized by the transportation of fluorescent dyes through the membrane (propidium iodide and calcein). Finally, an electrical protocol is developed for combined cell permeabilization and electroosmotic flow (EOF)-based extraction of the cell content. It is validated here using calcein-loaded cells and visualized through the progressive recovery of calcein in the side channels, indicating successful retrieval of individual cell content.     

Selective complexation of metals with isoxazolidine-containing fluorophores

A series of 1,3-dipolar cycloaddition products of functionalized nitrones with 1,3-propene sultone and maleimide was synthesized through a multi-step scheme. Their fluorescent response to different metal ions was examined. Selective quenching of the fluorescent materials by Cu(II), Fe(III), and Ru(III) in acetonitrile was demonstrated, providing access to new chemosensor design for selected transition metals.     

Phenanthrene-fused boron-dipyrromethenes as bright long-wavelength fluorophores

A new class of boron-dipyrromethene (BDP or BODIPY) dyes was obtained by phenanthrene fusion to the beta-pyrrole positions, absorbing in the wavelength range of important laser sources. Despite a 'propeller-like' distorted structure in the crystalline state, the chromophore absorbs (log epsilon > or = 5) and fluoresces (Phif > or = 0.8) strongly and can be easily turned into a fluorescence light-up probe. Incorporation into latex beads produces bright and photostable single-dye and F?rster Resonance Energy Transfer (FRET) particles for microscopy applications.     

Complexation of metals with piperazine-containing azamacrocyclic fluorophores

Azamacrocyclic fluorophores containing piperazine units were synthesized using sequential rhodium-catalyzed regioselective hydroformylation-reductive amination. A piperazine unit is introduced into the macrocycles to act simultaneously as electron donor and binding site. The macrocycles chelate divalent cations, either Zn2+ or Co2+, which considerably enhanced fluorescence. Complexation with Zn2+ was additionally confirmed by NMR.     

Photon counting histograms for diffusing fluorophores

The theory of photon counting histograms for fluorescent molecules diffusing through a laser spot is presented. Analytic expressions for the factorial cumulants of photon counts are obtained. For an arbitrary counting time window, it is shown how the exact histograms can be obtained by solving an appropriate reaction-diffusion equation. Our formalism reduces correctly when the molecules are immobile. The approximation used in fluorescence intensity multiple distribution analysis (FIMDA) is tested against the exact numerical solution of the problem. FIMDA works very well for a wide range of parameters except for small concentrations and long time windows.     

Parallel factor analysis of HPLC-DAD data for binary mixtures of lidocaine and prilocaine with different levels of chromatographic separation

A set of 17 samples containing a constant amount of lidocaine (667 μM) and a decreasing amount of prilocaine (667-0.3 μM) was analysed by LC-DAD at three different levels of separation, followed by parallel factor analysis (PARAFAC) of the data obtained. In Case 1 no column was connected, the chromatographic resolution (R_s) therefore being zero, while Cases 2 and 3 had partly separated peaks (R_s=0.7 and 1.0). The results showed that in Case 1, analysed without any separation, the PARAFAC decomposition with a model consisting of two components gave a good estimate of the spectral and concentration profiles of the two compounds. In Cases 2 and 3, the use of PARAFAC models with two components resolved the underlying chromatographic, spectral and concentration profiles. The loadings related to the concentration profile of prilocaine were used for regression and prediction of the prilocaine content. The results showed that prediction of prilocaine content was possible with satisfactory prediction (RMSEP<0.01). This study shows that PARAFAC is a powerful technique for resolving partly separated peaks into their pure chromatographic, spectral and concentration profiles, even with completely overlapping spectra and the absence or very low levels of separation.