The present invention relates to a chemical compound comprising (i) a polycationic polymer, coupled to (ii) a dye. The present invention further relates to a method for visualizing a glycosamine-containing structure in a biological sample comprising a) contacting an inner lumen of said biological sample with a dye-conjugated polycationic polymer, preferably with the chemical compound according to the present invention; b) tissue-clearing said biological sample; and, thereby, c) visualizing an internal glycosamine-containing structure in said biological sample. The present invention also relates to a method for determining the number and/or size of glomeruli in a kidney or a sample thereof making use of the method for visualizing a glycosamine-containing structure; and also relates to kits and uses related to said chemical compounds and said methods.

Described herein are polymeric compounds including an acceptor dye and donor luminophore, a polymer, and optionally a bioconjugate group. A polymeric compound of the present invention may have a structure represented by: A-B-C or C-A-B, wherein A is an acceptor dye; B is a polymer comprising one or more hydrophobic unit(s) and one or more hydrophilic unit(s); and optionally C, wherein C, when present, comprises a bioconjugate group, wherein one or more donor luminophore(s) are each separately attached to a portion of the polymer and/or to a portion of the acceptor dye. Also described herein are compositions comprising the polymeric compounds and methods of preparing and using the same.

Water-soluble dipyrromethene-based dyes are provided herein. In certain cases, the water-soluble dye is a dipyrromethene-boron dye. Embodiments of the subject water-soluble dipyrromethene-based dyes have a narrow absorption maxima in the yellow green range close to or at the 561 nm laser line, and are suitable for use in tandem dye systems. Embodiments of the subject dyes efficiently transfer energy to an acceptor chromophore while a second dipyrromethene-based dye of the same or different chemical structure is within energy-receiving proximity therewith. Also provided herein are tandem dyes that include the subject water-soluble dipyrromethene-based dyes, e.g., as donor chromophores. Methods of evaluating a sample for the presence of a target analyte and methods of labelling a target molecule in which the subject dyes find use are also provided. Systems and kits for practicing the subject methods are also provided.

Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.

Provided are multi-chromophore dyes. Embodiments of the multi-chromophore dyes include two or more dyes each comprising a water solubilizing group, two or more polymeric spacer domains and a linking moiety. Such multi-chromophore dyes can have advantageously high brightness by including multiple dyes while also reducing the rate of self-quenching. Also provided are methods of using such dyes, as well as kits that includes such dyes.

Water-soluble dipyrromethene-based dyes are provided herein. In certain cases, the water-soluble dye is a dipyrromethene-boron dye. Embodiments of the subject water-soluble dipyrromethene-based dyes have a narrow absorption maxima in the yellow green range close to or at the 561 nm laser line, and are suitable for use in tandem dye systems. Embodiments of the subject dyes efficiently transfer energy to an acceptor chromophore while a second dipyrromethene-based dye of the same or different chemical structure is within energy-receiving proximity therewith. Also provided herein are tandem dyes that include the subject water-soluble dipyrromethene-based dyes, e.g., as donor chromophores. Methods of evaluating a sample for the presence of a target analyte and methods of labelling a target molecule in which the subject dyes find use are also provided. Systems and kits for practicing the subject methods are also provided.

Water solvated polymeric dyes and polymeric tandem dyes are provided. The polymeric dyes include a water solvated light harvesting multichromophore having a conjugated segment of aryl or heteroaryl co-monomers linked via covalent bonds, vinylene groups or ethynylene groups. The polymeric tandem dyes further include a signaling chromophore covalently linked to the multichromophore in energy-receiving proximity therewith. Also provided are labeled specific binding members that include the subject polymeric dyes. Methods of evaluating a sample for the presence of a target analyte and methods of labeling a target molecule in which the subject polymeric dyes find use are also provided. Systems and kits for practicing the subject methods are also provided.

Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.

Water-soluble photoactive polymers, included polymer tandem dyes, as described as well as methods for their preparation and use. The photoactive polymers can be prepared by direct modification of core polymers (e.g., violet excitable polymers) with dyes or other functional groups. Methods of detecting analytes using the polymers are also described.

Compounds useful as fluorescent or colored dyes are disclosed. In some embodiments, the compounds have the following structure (I):

##STR00001##

or a stereoisomer, tautomer or salt thereof, wherein R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, L.sup.1, L.sub.2, L.sub.3, L.sup.4, M.sup.1, M.sup.2, m, and n are as defined herein. Methods associated with preparation and use of such compounds is also provided.