Applied Biosystems, LLC

The Perkin-elmer Corporation

Applera Corporation

Dh Technologies Development Pte. Ltd.

Pe Corporation

Life Technologies Corporation

Krishna G Upadhya

Scott C Benson

Ruiming N Zou

Steven Menchen

Ronald J Graham

Paul M Kenney

Jonathan M Cassel

Weiguo Zhen

Joe Y Lam

Subhasish Purkayastha

Subhakar Dey

Darryl J C Pappin

Sasi K Pillai

Xiongwei Yan

Peter D Theisen

Joan D Hauser

Pau-Miau Yuan

Peggy A Radel

Kuo-Liang Hsi

Sylvia W Yuen

Helena Huang

Ruiming Zou

The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.

Reagents useful for synthesizing rhodamine-labeled oligonucleotides

The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof.

Fluorescent dye compounds, conjugates and uses thereof

Dark quencher constructs, termed 'multi-chromophoric quenchers' are described herein that comprise at least two dark quenching moieties, which can be the same or different, linked together by at least one multivalent linking moiety. The structure of the multi-chromophoric quenchers can be varied to selectively enhance quenching within a specific range of reporter emission wavelengths. This can be accomplished by linking together, into a single molecule, two or more identical quenchers, by reacting the quenchers with a multivalent linker. The structure of the multi-chromophoric quencher can also be varied to quench a broader range of reporter emission wavelengths than previously possible. This can be accomplished by linking together, into a single molecule, two or more different quenchers, by reacting the quenchers with a multivalent linker. The structure of the multi-chromophoric quencher can also be varied to simultaneously broaden the absorption range and increase the total absorption within the absorption range. This can be done by combining the two concepts described above. In other words, multiple types of quenching moieties can be employed to increase the absorption range and a multiple number of each type of quenching moiety can be used to increase the total absorptivity within the absorption range. The multi-chromophoric quenchers can be tethered to probes for biomolecules, insoluble supports and/or fluorescent dyes for use in a wide variety of biomolecular assays.

Multi-chromophoric quencher constructs for use in high sensitivity energy transfer probes

This invention pertains to methods, mixtures, kits and/or compositions for the determination of analytes by mass analysis using unique labeling reagents or sets of unique labeling reagents. The labeling reagents can be isomeric or isobaric and can be used to produce mixtures suitable for multiplex analysis of the labeled analytes.

Mass tags for quantitative analyses

The invention provides compositions electron-deficient nitrogen heterocycle-substituted fluorescein dyes and methods in which the dyes are conjugated to substrates and used as detection labels in molecular biology experiments. The electron-deficient nitrogen heterocycles include pyridine, quinoline, pyrazine, and the like. Substrates include polynucleotides, nucleosides, nucleotides, peptides, proteins, carbohydrates, and ligands.

Electron-deficient nitrogen heterocycle-substituted fluorescein dyes

Dibenzorhodamine compounds having the structure ##STR1## are disclosed, including nitogen- and aryl-substituted forms thereof. In addition, intermediates useful for synthesizing such compounds are disclosed, such intermediates having the structure ##STR2## In Formula I, R.sub.1 is H or ##STR3## wherein Y is H, lower alkyl, lower alkene, lower alkyne, aromatic, phenyl, polycyclic aromatic, heterocycle, water-solubilizing group, or linking group, including substituted forms thereof. When R.sub.1 is H, the C-12-bonded nitrogen and the C-12 and C-13 carbons form a first ring structure having from 4 to 7 members, and/or the C-12-bonded nitrogen and the C-11 and C-12 carbons form a second ring structure having from 5 to 7 members. The compounds of Formula I further include aryl- and nitrogen-substituted forms thereof. The invention further includes energy transfer dyes comprising the dibenzorhodamine compounds, nucleosides labeled with the dibenzorhodamine compounds, and nucleic acid analysis methods employing the dibenzorhodamine compounds.

Dibenzorhodamine dyes

A class of aromatic-substituted xanthene compounds useful as fluorescent dyes is disclosed, the compounds having the general structure where Y.sub.1 and Y.sub.2 taken separately are selected from the group consisting of hydroxyl, oxygen, imminium, linking group and amine, or Y.sub.1 taken together with R.sub.2 is cyclic imine, or Y.sub.2 taken together with R.sub.3 is cyclic amine; R.sub.2, R.sub.3, R.sub.5, and R.sub.7 taken separately are selected from the group consisting of hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, imminium, amido, nitrile, lower alkoxy, phenyl, and linking group; R.sub.1 taken separately is selected from the group consisting of phenyl, substituted phenyl, polycyclic aromatic, substituted polycyclic aromatic, linking group and electron-rich heterocycle, or when taken together with R.sub.7 is selected from the group consisting of electron-rich heterocycle and indene; R.sub.4 taken separately is selected from the group consisting of amino, amido, phenyl, substituted phenyl, polycyclic aromatic, substituted polycyclic aromatic, indene, linking group and electron-rich heterocycle, or when taken together with R.sub.5 is selected from the group consisting of phenyl, substituted phenyl, polycyclic aromatic, substituted polycyclic aromatic, indene, and electron-rich heterocycle; and R.sub.6 is selected from the group consisting of acetylene, lower alkyl, lower alkene, cyano, phenyl, substituted phenyl, and heterocyclic aromatic. In another aspect, the invention includes methods for synthesizing the above dye compounds and intermediates. In yet another aspect, the present invention includes reagents labeled with the asymmetric benzoxanthene dye compounds, including deoxynucleotides, dideoxynucleotides, phosphoramidites, and polynucleotides. In an additional aspect, the invention includes methods utilizing such dye compounds and reagents including dideoxy polynucleotide sequencing and fragment analysis methods.

Aromatic-substituted xanthene dyes

Growing community of inventors

Union City, CA, United States of America

Krishna G Upadhya