Brightly fluorescent purple and blue labels for amines and proteins

Novel amino-reactive phenoxazines were obtained by reasonably simple synthetic protocols and characterized in terms of their use as fluorescent labels for amines, amino acids and proteins in general. Purple labels (alternatives to Texas Red) and blue labels (alternatives to Cy-1) were obtained by this strategy. The absorption/emission maxima, in aqueous solution, are at around 589/630 nm and 648/670 nm, respectively, thus indicating larger Stokes' shifts than those of common cyanine-type of labels. The new labels are compatible with commercial diode laser light sources.     

Oligomeric fluorescent labels for DNA

In an effort to find fluorescent labels that have large Stokes shifts and increased emission intensity, a strategy for fluorescence labeling of DNA was explored in which multiple individual fluorophores are incorporated at adjacent positions at the end of a DNA probe. To encourage close interactions, hydrocarbon and heterocycle fluorophores were substituted at C-1 of deoxyribose, replacing the DNA base. The C-glycosides studied contained the well-known fluorophores terphenyl, pyrene, and terthiophene. For comparison, a commercial fluorescein-dU nucleotide was examined. Oligomeric labels containing up to five fluorophores were tested. Interestingly, all four dyes behaved differently on multiple substitution. Fluorescein displayed strong self-quenching properties, with the quantum yield dropping severalfold with each additional substitution and with a constant, small Stokes shift. In contrast, pyrene showed increases in quantum yield on addition of more than one fluorophore and yielded efficient long-wavelength emission on multiple substitution, with Stokes shifts of >130 nm. Oligomeric terphenyl labels gave a small progressive red shift in absorption and a marked red shift in emission wavelength and showed a strong increase in brightness with more monomers. Finally, terthiophene oligomers showed self-quenching combined with increasing Stokes shifts. Overall, the results suggest that some oligomeric fluorescent labels exhibit properties not available in common fluorescein class (or other commercial) labels, such as large Stokes shifts and increasing brightness with increasing substitution.     

Selective acylation of primary amines in peptides and proteins

N-hydroxysuccinimide (NHS) esters are derivatizing agents that target primary amine groups. However, even a small molar excess of NHS may lead to acylation of hydroxyl-containing amino acids as a side reaction. We report a straightforward method for the selective removal of ester-linked acyl groups after NHS ester-mediated acylation of peptides and proteins. It is based on incubation in a boiling water bath and does not require a change in pH or the addition of chemicals. It is therefore particularly suited for proteomics samples that are often small in volume and contain low amounts of peptides. The method was optimized and evaluated with two peptides and one protein that were acetylated at a high excess of NHS-acetate. While the large molar excess resulted in complete acylation of all primary amines, hydroxyl-containing amino acids were shown to react as well. By incubating the peptide or protein solutions in a boiling water bath, acetyl-ester bonds were hydrolyzed, whereas acetyl-amide bonds remained stable. The reaction was also performed in 6 M guanidine-HCl, which prevented protein precipitation. In conclusion, the present method allows the selective acylation of primary amines by NHS esters and constitutes a valuable alternative to the treatment with hydroxylamine under alkaline conditions.     

2-and 4-phenylethynylpyrenes,novel fluorescent labels for DNA

It was shown by the example of 1-, 2-, and 4-phenylethynylpyrene 2′-arabino-carbamate derivatives of uridine that the position of pyrene substitution substantially affects the spectral and photophysical properties of the fluorophore and its ability to interact with the nucleobase.     

2- and 4-phenylethynylpyrenes--new fluorescent labels for DNA

It was shown by the example of 1-, 2-, and 4-phenylethynylpyrene 2'-arabino-carbamate derivatives of uridine that the position of pyrene substitution substantially affects the spectral and photophysical properties of the fluorophore and its ability to interact with the nucleic base.     

Extrinsic signals for monitoring the association reaction of proteins as introduced by fluorescent and non-fluorescent labels.

Two known dansyl labels (I, II) and 5-[2-(iodoacetamido)ethylamino]-1-naphthalene-sulfonic acid (III) and three new azo-dyes (IV - VI) were covalently attached to alpha-chymotrypsin and to basic pancreatic trypsin inhibitor by four different reactive groups. In order to protect the contact region of the proteins the complex of the two proteins was labeled. Advantage was taken of the fact that a group which is buried in the complex reacts about (see article) times slower than a group which is always exposed (K = dissociation equilibrium constant, [C] = concentration of the complex). The complex was dissociated at pH 3 and the labeled proteins were isolated by column chromatography. They were fully active. The dansyl label was immobilized when introduced by dansyl chloride but highly mobile when attached via the longer imidoester group (II). Changes of absorption and of fluorescence which occur when differently labeled reaction partners recombine were studied. Changes in absorption (up to 18%) were mainly due to interactions of the label of one protein with the other protein. Fluorescence changes of up to 480% could be obtained. They were interpreted in terms of a F?rster type energy transfer between donor and acceptor labels and changes of absorption and quantum yield due to interactions of the labels with the proteins. The kinetic constants of complex formation are not seriously altered by the labels (B?sterling, B & Engel, J. (1976) this J. 357, 1297-1307, succeeding). It is concluded that the labeling technique may be of general value for kinetic and equilibrium studies of protein associations.     

Selective placement of electron spin resonance spin labels: new structural methods for peptides and proteins.

Electron spin resonance (ESR) is more powerful than ever as a technique for solving biochemical and biophysical problems. Part of the great utility of ESR arises from the use of modern biochemical methods to place spin labels at important positions along the primary sequence of a peptide or protein.     

PEP and CADY-mediated delivery of fluorescent peptides and proteins into living cells

Cell-penetrating peptides (CPPs) constitute a family of peptides with the characteristic ability to cross biological membranes and deliver cargo into the intracellular milieu. Several CPPs have been proposed for delivery of polypeptides and proteins into cells through either of two strategies: covalent or complexed in a non-covalent fashion. Members of the PEP family are primary amphipathic peptides which have been shown to deliver peptides and proteins into a wide variety of cells through formation of non-covalent complexes. CADY is a secondary amphipathic peptide which has been demonstrated to deliver short nucleic acids, in particular siRNA with high efficiency. Here we review the characteristics of the PEP and CADY carriers and describe a novel derivative of CADY termed CADY2, which also presents sequence similarities to Pep1. We have compared Pep1, CADY and CADY2 in their efficiency to interact with and internalize short fluorogenic peptides and proteins into cultured cells, and provide evidence that CADY2 can interact with proteins and peptides and deliver them efficiently into living cells, similar to Pep1, but in contrast to CADY which is unable to deliver any peptide, even short negatively charged peptides. This is the first study to investigate the influence of the cargo on the interactions between PEP and CADY carriers, thereby providing novel insights into the physicochemical parameters underlying interactions and cellular uptake of peptides and proteins by these non-covalent CPPs.     

Long-wavelength iodide-sensitive fluorescent indicators for measurement of functional CFTR expression in cells

Limitations of available indicators [such as6-methoxy-N-(3-sulfopropyl)quinolinium(SPQ)] for measurement of intracellular Cl are their relatively dimfluorescence and need for ultraviolet excitation. A series oflong-wavelength polar fluorophores was screened to identify compoundswith Cl and/orI sensitivity, brightfluorescence, low toxicity, uniform loading of cytoplasm with minimalleakage, and chemical stability in cells. The best compound found was7-(-D-ribofuranosylamino)-pyrido[2,1-h]-pteridin-11-ium-5-olate (LZQ). LZQ is brightly fluorescent with excitation andemission maxima at 400-470 and 490-560 nm, molar extinction11,100 M¹ · cm¹(424 nm), and quantum yield 0.53. LZQ fluorescence is quenched byI by a collisionalmechanism (Stern-Volmer constant 60 M¹) and is not affectedby other halides, nitrate, cations, or pH changes (pH 5-8). AfterLZQ loading into cytoplasm by hypotonic shock or overnight incubation,LZQ remained trapped in cells (leakage <3%/h). LZQ stained cytoplasmuniformly, remained chemically inert, did not bind to cytoplasmiccomponents, and was photobleached by <1% during 1 h of continuousillumination. Cytoplasmic LZQ fluorescence was quenched selectively byI (50% quenching at 38 mMI). LZQ was used tomeasure forskolin-stimulatedI/ClandI/NO₃exchange in cystic fibrosis transmembrane conductance regulator(CFTR)-expressing cell lines by fluorescence microscopy and microplatereader instrumentation using 96-well plates. The substantially improvedoptical and cellular properties of LZQ over existing indicators shouldpermit the quantitative analysis of CFTR function in gene deliverytrials and high-throughput screening of compounds for correction of thecystic fibrosis phenotype.

     

Long-wavelength absorbing antenna pigments and heterogeneous absorption bands concentrate excitons and increase absorption cross section

The light-harvesting apparatus of photosynthetic organisms is highly optimized with respect to efficient collection of excitation energy from photons of different wavelengths and with respect to a high quantum yield of the primary photochemistry. In many cases the primary donor is not an energetic trap as it absorbs hypsochromically compared to the most red-shifted antenna pigment present (long-wavelength antenna). The possible reasons for this as well as for the spectral heterogeneity which is generally found in antenna systems is examined on a theoretical basis using the approach of thermal equilibration of the excitation energy. The calculations show that long-wavelength antenna pigments and heterogeneous absorption bands lead to a concentration of excitons and an increased effective absorption cross section. The theoretically predicted trapping times agree remarkably well with experimental data from several organisms. It is shown that the kinetics of the energy transfer from a long-wavelength antenna pigment to a hypsochromically absorbing primary donor does not represent a major kinetic limitation. The development of long-wavelength antenna and spectrally heterogeneous absorption bands means an evolutionary advantage based on the chromatic adaptation of photosynthetic organelles to spectrally filtered light caused by self-absorption.Abbreviations LHC light-harvesting complex - P primary donor - PSI Photosystem I of green plants - PS II Photosystem II of green plants - RC reaction center - X primary acceptor     

Functionalized fluorescent core-shell nanoparticles used as a fluorescent labels in fluoroimmunoassay for IL-6

Nanoparticle labels conjugated with biomolecules are used in a variety of different assay applications. In this paper, a sensitive fluoroimmunoassay for recombinant human interleukin-6 (IL-6) with the functionalized Rubpy-encapsulated fluorescent core-shell silica nanoparticles labeling technique has been proposed. IL-6 was measured based on the specific interaction between captured IL-6 antigen and functionalized fluorescent core-shell nanoparticles-labeled anti-IL-6 monoclonal antibody. The calibration graph for IL-6 was linear over the range 20-1250 pg ml(-1) with a detection limit of 7 pg ml(-1) (3 sigma). The regression equation of the working curve is I(F)=7.665+32.499[IL-6] (ng ml(-1)) (r=0.9980). The relative standard deviation (R.S.D.) for 11 parallel measurements of 78 pg ml(-1) IL-6 was 3.2%. Furthermore, the application of fluorescence microscopy imaging in the study of the antibody labeling and sandwich fluoroimmunoassay with the functionalized fluorescent core-shell silica nanoparticles was also explored. This proposed method has the advantage of showing the specificity of immunoassay and sensitivity of fluorescent nanoparticle labels technology. The results demonstrate that the method offers potential advantages of sensitivity, simplicity and reproducibility for the determination of IL-6, and is applicable to the determination of IL-6 in serum samples and enabling fluorescence microscopy imaging for the determination of IL-6.     

Aminoquinolines as fluorescent labels for hydrophilic interaction liquid chromatography of oligosaccharides

Abstract In this study, we investigated the potential of four different aminoquinoline (AQ) compounds as fluorescent labels for glycan analysis using hydrophilic interaction liquid chromatography (HILIC) and fluorescence detection (FLD). We confirmed the optimal excitation and emission wavelengths of 3-AQ and 6-AQ conjugated to glycan standards using three-dimensional fluorescent spectral scanning. The optimal excitation and emission wavelengths for 6-AQ were confirmed at λex=355 nm and λem=440 nm. We concluded that the optimal wavelengths for 3-AQ were λex=355 nm and λem=420 nm, which differed considerably from the wavelengths applied in previous reports. HILIC-FLD chromatograms using experimentally determined wavelengths were similar to 2-aminobenzamide controls, but the peak capacity and resolution differed significantly when published 3-AQ λex/em values were applied. Furthermore, we found that 5-AQ and 8-AQ labeled maltohexaose did not display any fluorescent pro\xadperties when used as a carbohydrate tag for HPLC analysis. Finally, we applied experimentally determined wavelengths to 3-AQ labeled N-glycans released from human IgG to illustrate changes in retention time as well as to demonstrate that AQ labeling is applicable to complex sample analysis via exoglycosidase sequencing.     

Models for rotating spin labels and probes in proteins and membranes

A method of comparative analysis of ESR spectra has been proposed. It allows to distinguish between two models, slow reorientation of spin labels, and rapid rotation of the cone. Comparison of experimental data for a number of biological objects the theoretical predictions has shown that the rotation of nitroxyl fragment of spin labels can be described by the model of slow anisotropic rotation with correlation time 10(-6) less than or equal to tau less than or equal to 10(-8) s in conditions where the rotation of macromolecules is "frozen".     

Element-coded affinity tags for peptides and proteins

Isotope-coded affinity tags (ICAT) represent an important new tool for the analysis of complex mixtures of proteins in living systems [Aebersold, R., and Mann, M. (2003) Nature, 422, 198-207]. We envisage an alternative protein-labeling technique based on tagging with different element-coded metal chelates, which affords affinity chromatography, quantification, and identification of a tagged peptide from a complex mixture. As proof of concept, a synthetic peptide was modified at a cysteine side chain with either a carboxymethyl group or acetamidobenzyl-1,4,7,10-tetraazacyclododecane-N,N',N' ',N' "-tetraacetic acid (AcBD) chelates of terbium or yttrium. A mixture of the three modified peptides in a mole ratio of 100:1.0:0.83 carboxymethyl:AcBD-Tb:AcBD-Y was trypsinized, purified on a new affinity column that binds rare-earth DOTA chelates, and analyzed by LC-MS/MS. Chelate-tagged tryptic peptides eluted cleanly from the affinity column; the tagged peptides chromatographically coeluted during LC-MS analysis, were present in the expected ratio as indicated by MS ion intensity, and were sequence-identified by tandem mass spectrometry. DOTA-rare earth chelates have exceptional properties for use as affinity tags. They are highly polar and water-soluble. Many of the rare earth elements are naturally monoisotopic, providing a variety of simple choices for preparing mass tags. Further, the rare earths are heavy elements, whose mass defects give the masses of tagged peptides exact values not normally shared by molecules that contain only light elements.