Compositions, methods, and systems are provided for fluorescent polymerase enzyme substrates comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Fluorescent polymerase enzyme substrates of the invention have a protein shield between the fluorescent dye moieties and nucleotide moieties of the polymerase enzyme substrate. The polymerase enzyme substrates have a nucleotide component and a dye component, each attached to a protein. The attachments can be covalent. The protein can, for example, prevent the direct interaction of the fluorescent dye moiety with the enzyme when carrying out nucleotide synthesis, preventing photodamage to the enzyme. The polymerase enzyme substrates of the invention can have multiple dyes and multiple nucleotide moieties.

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.

The present disclosure relates to polymers which contain a hydrophobic and hydrophilic segment which is sensitive to pH. In some aspects, the polymers form a micelle which is sensitive to pH and results in a change in fluorescence based upon the particular pH. In some aspects, the disclosure also provides methods of using the polymers for the imaging of cellular or extracellular environment or delivering a drug.

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.

A polymer dye includes at least one repeating unit represented by the following structural formula 1 and at least one selected from the group consisting of repeating units represented by the following structural formulas 2 and 3.

##STR00001##

Hydrogen peroxide present in or generated through enzymatic reaction in a biological sample can be detected by using the polymer dye.

The present invention relates to a fluorescent polymer cast on the surface of wells of a plate and a plate comprising the fluorescent polymer. The plate is used in a method for calibrating read-out values of plate readers. The method for calibrating the plate readers can effectively reduce the deviation of read-out values among different plate readers.

A copolymer useful as an ingredient of a colored resin composition, comprising a structural unit derived from an aromatic carboxylic acid having an ethylenically unsaturated bond, a structural unit (Ab) represented by formula (Z), and a structural unit (Ac) derived from an unsaturated compound having a cyclic ether structure having 2 to 4 carbon atoms, wherein L represents a single bond or a divalent linking group, A represents a phenyl group optionally having a substituent other than a carboxy group or a naphthyl group optionally having a substituent other than a carboxy group, R.sup.a represents a hydrogen atom, or an alkyl group having 1 to 4 carbon atoms, and a hydrogen atom contained in the alkyl group is optionally replaced by a hydroxy group.

##STR00001##

Provided is an aqueous dispersion of colored particles suitable for colorants for writing instrument inks, inkjet inks, painting materials, aqueous coatings, and the like. The aqueous dispersion of colored particles includes a polymer having at least a unit of a monomer derived from a dye having a polymerizable unsaturated group. The monomer derived from the dye is preferably derived from the compound represented by General Formula (1) below:

##STR00001##

where Dye represents a dye residue, R.sub.1 represents a hydrogen atom or a methyl group,
Y.sub.2 represents O or NR.sub.10, where R.sub.10 represents a hydrogen atom or an alkyl group,
A.sub.1 represents an alkylene group which is unsubstituted or substituted by at least one group selected from OCO, COO, NHCONH, and the like in the chain thereof and/or at the terminal thereof, and/or a hydroxy group.

Compounds useful as fluorescent or colored dyes are disclosed. The compounds have the following structure (I), 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.sup.2, L.sup.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.

Provided herein are compounds that are able to bind metal ions (e.g., free metal ions or metal ions bound to low affinity ligands) in a sample or subject. Also provided herein are methods of using the compounds for chelating metal ions and for the treatment of diseases associated with abnormal levels of metal ions. Methods of preparing the compounds and pharmaceutical compositions are also provided.