Abstract: The invention describes reactive dyes having an alkyl spacer attached via a sulfonamide bond to a sulforhodamine 101 fluorophore, and a variety of useful conjugates prepared therefrom. The increased length of the covalent linkage due to the alkyl spacer results in dye-conjugates having a number of surprisingly advantageous properties relative to previous sulforhodamine 101-labeled conjugates, including enhanced solubility and increased fluorescence. The reactive dyes of the present invention are more stable than the known compound sulforhodamine 101 sulfonyl chloride. Novel reactive dyes are described for selective modification of groups other than amines, including thiols and photoreactive derivatives.

Abstract: The invention describes novel fluorescently labeled microspheres, where the microspheres possess at least one internal fluorescent spherical zone. The invention also describes the method of preparing the novel microspheres, the method of calibrating microscopy instrumentation using the novel microspheres, the method of using the novel microspheres as distinct labels for combinatorial analysis and the use of the labeled microspheres as tagging agents and tracers.

Abstract: This invention describes bifunctional polysaccharides conjugated to both a chelating group suitable for the selective complexation of metal cations, and a targeting peptide specific for a cellular substructure. These bifunctional polysaccharides are primarily useful for the regulation, detection and quantification of metal ion levels, such as Ca.sup.2+, Mg.sup.2+, Na.sup.+, K.sup.+, or Li.sup.+, in specific cellular structures. Localization within the cellular structure is accomplished by the targeting peptide, whereupon the large, water-soluble polysaccharide prevents diffusion of the chelating group from the targeted site. When the target cell structure is the nucleus of a fertilized egg cell, the polysaccharide-chelator conjugate remains sequestered within the nucleus until the breakdown of the nuclear envelope, whereupon the reagent becomes sequestered into both daughter nuclei. This means of tracking daughter cells is practical even through several cell divisions.

Abstract: The invention is a novel fluorescently labeled microparticle, where the microparticle internally incorporates at least one dipyrrometheneboron difluoride dye. Appropriate selection of substituents results in dipyrrometheneboron difluoride derivatives that, when incorporated into polymer microparticles, give the desired excitation and emission wavelengths. The spectral characteristics of the labeling dyes in liquid are not greatly changed when the dye is incorporated into the particles, and the spectral excitation and emission wavelengths are compatible with commonly used filter sets. Other embodiments of the fluorescent microparticles include additional dyes and/or bioreactive substances.

Abstract: This invention relates to polymers labeled with fluorescent dye to the point that significant fluorescence quenching occurs, such that degradation of the polymer results in fluorescence enhancement. The resulting fluorescence enhancement is useful for measuring the degradation of such polymers, for example as a result of enzymatic hydrolyis of a protein, carbohydrate, nucleic acid, or other natural or synthetic polymer.

Abstract: The present invention describes 7-aminocoumarin dyes that are substituted one or more times at the 3-, 6- and/or 8-positions by a sulfonic acid or a salt of a sulfonic acid, said dyes being useful as fluorescent probes or in the preparation of enzyme substrates, caged probes, or adducts with reducing sugars. The dyes of the invention optionally possess a reactive group useful for preparing fluorescent conjugates, which conjugates and methods for their preparation are described herein.

Abstract: The present invention describes a method of staining mitochondria, and analyzing mitochondrial function, using a class of fluorescent substituted 3',6'-diaminoxanthenes and their reduced analogs 3',6'-diaminodihydroxanthenes, which are oxidized to the fluorescent form of the dye in situ. In their oxidized form, the dyes selectively localize within mitochondria. The dyes of the invention are substituted by an alkylating group that allows their retention in mitochondria even after cell death, fixation, and permeabilization.

Abstract: The invention describes the preparation and use of fluorescent stains for nucleic acids derived from unsymmetrical cyanine dyes comprising a substituted benzazolium ring system linked by a methine bridge to a pyridinium or quinolinium ring system having at least one substituent on the pyridinium or quinolinium ring that contains a heteroatom. The presence of the heteroatom-containing substituent results in higher sensitivity to oligonucleotides and larger nucleic acid polymers in a wide range of cells and gels, and for use in analysis of cell structure, membrane integrity or function.

Abstract: The invention describes the preparation and use of fluorescent stains for nucleic acids derived from neutral unsymmetrical cyanine dyes comprising a substituted benzazolium ring system linked to a methine bridge to a pyridine or quinoline ring system. The fluorescence characteristics of the dyes when complexed with nucleic acids give the dyes utility for the detection of oligonucleotides and nucleic acids in cells, gels and solutions. The dyes have particular utility in the staining of reticulocytes.

Abstract: The present invention describes the use of a family of fluorescent indicators for metal cations. The indicators are fluorophore conjugates of pyridyl-based metal ion chelators. The indicators are very sensitive detection as quantification reagents for a variety of metals, in a variety of oxidation states, even in the presence of high concentrations of Ca.sup.2+, Na.sup.+, or K.sup.+ or other ions, such as is found in seawater, making them highly useful for assaying physiological samples, biological samples, or environmental samples.

Abstract: The invention relates to caged compounds for the study of biological processes, where the caged compound has a photoremoveable .alpha.-carboxy-substituted o-nitrobenzyl group. Covalent attachment of the substituted o-nitrobenzyl to a parent compound yields a caged compound with biological and/or physical properties that are significantly altered from the original properties of the parent compound. Illumination of the caged compounds to cleave the photoremoveable group yields the parent compound with its original properties restored.

Abstract: The present invention describes the use of a variety of merocyanine dyes and substituted merocyanine dyes for detecting and quantifying poly(amino acids), including peptides, polypeptides and proteins. The labeled proteins or peptides are highly colored, but are also detected by their strong fluorescence enhancement. Poly(amino acids) are detected in solution, in electrophoretic gels, and on solid supports, including blots and dipsticks. The present method of staining is highly sensitive, extremely facile, and relatively non-selective.

Abstract: The invention relates to dimers of unsymmetrical cyanine dyes, typically dimers of benzthiazole or benzoxazole derivatives, that exhibit enhanced fluorescence on binding with DNA or RNA, The dimers generally have the formula: ##STR1## where R.sup.1 and R.sup.2, which may be the same or different, are alkyl groups having 1-6 carbons;X is O, S, or N--R.sup.3, where R.sup.3 is H or an alkyl group having 1-6 carbons;Z is O, S, or N--R.sup.4, where R.sup.4 is H or an alkyl group having 1-6 carbons;n and s, which may be the same or different, =0, 1, or 2;Y is HC.dbd.CH; andp, m, q, and r=0 or 1, such that p+m=1 and q+r=1; andwhere -BRIDGE- has the general formula:--(CH.sub.2).sub..alpha. --[A.sup.1 --(CH.sub.2).sub..beta. --].sub.I [A.sup.2 --(CH.sub.2).sub..gamma. --].sub.II A.sup.3 --(CH.sub.2).sub..delta. --where .alpha., .beta., .gamma., and .delta., which may be the same or different, are integers greater than 1 and less than 5;I and II, which may be the same or different, =0 or 1; andA.sup.1, A.sup.2, and A.

Abstract: The subject invention provides substrates useful for analyzing the metabolic activity in cells by improving the retention of a detectable reporter molecule only in intact cells where a particular enzyme is present. In particular, improved retention results from a two part process involving conjugation of haloalkyl-substituted derivatives of a reporter molecule with intracellular cysteine-containing peptides while unblocking the reporter molecule. The substrates have the formXR-SPACER-REPORTER-BLOCKwherein -BLOCK is a group selected to be removable by action of a specific analyte, to give REPORTER spectral properties different from those of the substrate,-REPORTER- is a molecule that, when no longer bound to BLOCK by a BLOCK-REPORTER bond, has spectral properties different from those of the substrate,-SPACER- is a covalent linkage, andXR- is a haloalkyl moiety that can covalently react with an intracellular thiol (Z-S-H) to form a thioether conjugate (Z-S-R-).

Abstract: The invention relates to methods for labeling or detecting one or more target materials using surface coated fluorescent microparticles with unique characteristics. The unique microparticles used to practice the invention have at least two components: an external substance or coating that is selective for each target material and an internal mixture of multiple fluorescent dyes. The mixture of dyes is a series of two or more fluorescent dyes having overlapping excitation and emission spectra allowing efficient energy transfer from the excitation wavelength of the first dye in the series, transfer through the dyes in the series and re-emitted as an optical signal at the emission wavelength of last dye in the series, resulting in a desired effective Stokes shift for the microparticle that is controlled through selection of appropriate dyes. The unique microparticles are combined with a sample thought to contain the target material(s), so that the microparticles label the target materials.

Abstract: The invention relates to a method of analyzing a sample thought to contain bacteria using an aqueous solution comprising one or more fluorescent dyes: a fluorescent dye of formula I, a fluorescent dye of formula II, a fluorescent dye of formula III, and a fluorescent dye of formula IV. Each of the dyes differ each from the other in their affinity for nucleic acids and in their spectral response to different types of bacteria in the sample. The first three dyes are nucleic acid stains and the fourth dye is a fluorescent reagent that binds selectively to cell surface components. The fluorescent dyes of formula I are highly membrane-permeant cyanine dye derivatives and label all bacteria, whether live or dead, whether Gram positive or Gram negative. The dyes of formula II label only live Gram positive bacteria and label all dead bacteria, whether Gram positive or negative. The dyes of formula II bind to nucleic acids preferentially with respect to the dyes of formula I.

Abstract: The invention relates to a method of analyzing the viability of a sample of cells using an aqueous solution comprising two fluorescent dyes. Dye I has the formula: ##STR1## where R.sup.2 is C.sub.1-6 alkyl; Z.sup.- is a biologically compatible counterion;X is O; S; Se; or NR.sup.15, where R.sup.15 is H or C.sub.1-6 alkyl; or CR.sup.16 R.sup.17, where R.sup.16 and R.sup.17, which may be the same or different, are independently H or C.sub.1-6 alkyl, or the carbons of R.sup.16 and R.sup.17 taken in combination complete a five or six membered saturated ring; and the benzazolium is optionally further substituted;n=0, 1, or 2;Y is --CR.sup.3 .dbd.CR.sup.4 --; p and m=0 or 1, such that p+m=1;R.sup.5 is a C.sub.1-6 alkyl, C.sub.1-6 alkenyl, C.sub.1-6 polyalkenyl, C.sub.1-6 alkynyl or C.sub.1-6 polyalkynyl group; or R.sup.5 is an OMEGA;R.sup.3, R.sup.4, R.sup.6 and R.sup.7, which may be the same or different, are independently H; or a C.sub.1-6 alkyl, C.sub.1-6 alkenyl, C.sub.1-6 polyalkenyl, C.sub.1-6 alkynyl or C.

Abstract: This invention describes novel sensors for ions that are based on the combination of xanthylium-based dyes with metal-binding N,N'-diaryldiaza crown ethers. These sensors are primarily useful for detection and quantitation of alkali-metal ions in aqueous solution. Binding of the ion results in a change in the fluorescence properties of the indicating dye that can be correlated with the ion concentration. Methods are provided for attaching reactive groups on these sensors for conjugation to dyes, lipids and polymers and for enhancing entry of the indicators into living cells.

Abstract: The invention describes the synthesis and use of photoactivated (or caged) fluorescent dyes. Upon illumination at less than about 400 nm the caged dyes release highly fluorescent, water soluble hydroxypyrenesulfonic acid dyes according to the following equation: ##STR1## X, Y, and Z are independently sulfonic acid, a sulfonic acid salt, a hydroxyl group, or hydrogen, with at least one of X, Y, and Z being a sulfonic acid or sulfonic acid salt. LINK is either an ether linkage or a carbonate linkage. BLOCK is a caging group whose photolysis results in liberation of a free hydroxypyrenesulfonic acid dye.The caged fluorescent dyes are useful for application in aqueous solutions, including fluids of biological origin. The caged dyes of the present invention are especially useful for flow tagging velocimetry.

Abstract: The indicator compounds of the present invention are substituted or unsubstituted BAPTA-type chelators that contain a benzazolyl-coumarin substructure, and the pharmaceutically acceptable non-toxic salts and esters thereof. These compounds are useful for the detection and quantification of polycationic metal ions, particularly Ca.sup.2+.The compounds of the invention have the core structure ##STR1## or the structure ##STR2## where m=2 or 3 and X can be S, O, or C(CH.sub.3).sub.2. The above core structures are optionally substituted by substituents that alter the binding affinity of the indicator, shift the spectral properties of the indicator, or act as a reactive site for the preparation of a variety of conjugates.