Applied Biosystems, LLC

The Perkin-elmer Corporation

Life Technologies Corporation

University of California

Applera Corporation

Other

Pe Corporation

Steven M. Menchen

Vergine C. Furniss

Kevin M. Hennessey

Peter D. Theisen

Scott C. Benson

Joan Hauser

Scott C Benson

Steven Menchen

Joe Y L Lam

Ruiming N Zou

Krishna G Upadhya

Barnett B Rosenblum

Alexander N Glazer

Ronald J Graham

Peter D Theisen

Joan D Hauser

Linda G Lee

Jonathan M Cassel

Vergine C Furniss

Kevin M Hennessey

Alexander J Mastroianni

Sandra L Spurgeon

Joe Y Lam

Sandy M Koepf

Cinna Monighetti

Shaheer Khan

Paul M Kenney

Weiguo Zhen

Wolfgang Hinz

Daqing Sun

Khairuzzaman Bashar Mullah

Shifeng Li

Meng Taing

Christina E Inman

Brian Reed

Jacob K Freudenthal

Brian Lee Evans

Xiongwei Yan

John Scott

Alexander M Glazer

Sandra Spurgeon

Devin Dressman

Chieh-Yuan Li

Srinka Ghosh

Peggy A Radel

Abraham Rosenbaum

Chu-An Chang

David Joun

Craig Obergfell

Andi Broka

Steven M Menchen

Ruiming Zou

Joe YL Lam

Zou Ruiming

The present invention is directed to fluorescent rhodamine dyes having spectral properties suited to the creation of multiplex assay systems for use in molecular biology, cell biology and molecular genetics. The rhodamine dyes have the following structure.

Modified rhodamine dye and use thereof in biological assays

In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.

Multiplex nucleic acid amplification

Disclosed is a probe for use in biological assays. The probe includes a fluorescent dye bound to a quencher compound through an oligonucleotide linker. Also disclosed are methods of using the probe, such as for a polymerase chain reaction (PCR), such as in a quantitative PCR reaction (qPCR), as well as kits including the probe.

Quencher and reporter dye combinations

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

According to the present teachings, methods and compositions are provided that utilize at least one reference dye of formula (I): In some embodiments, a method comprises measuring a detection signal of a reporter dye and at least one reference dye of formula (I). In some embodiments, a composition comprises a reference dye of formula (1), a buffer, a selection of nucleotides and a protein.

DDAO compounds as fluorescent reference standards

A method of preparing a discrete polymer network array include mixing a plurality of nucleic acid polymer networks with a plurality of color-activated polymer networks to form a dispersion, applying the dispersion to an array of wells, the nucleic acid polymer networks selectively depositing into wells of the array of wells, and rinsing the array of wells to selectively remove the plurality of color-activated polymer networks.

Method of distributing discrete polymer networks

A method of manufacturing a sensor, the method including forming an array of chemically-sensitive field effect transistors (chemFETs), depositing a dielectric layer over the chemFETs in the array, depositing a protective layer over the dielectric layer, etching the dielectric layer and the protective layer to form cavities corresponding to sensing surfaces of the chemFETs, and removing the protective layer. The method further includes, etching the dielectric layer and the protective layer together to form cavities corresponding to sensing surfaces of the chemFETs. The protective layer is at least one of a polymer, photoresist material, noble metal, copper oxide, and zinc oxide. The protective protective layer is removed using at least one of sodium hydroxide, organic solvent, aqua regia, ammonium carbonate, hydrochloric acid, acetic acid, and phosphoric acid.

Methods and systems for point of use removal of sacrificial material

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

Extended rhodamine compounds exhibiting favorable fluorescence characteristics having the structure are disclosed. In addition, novel intermediates for synthesis of these dyes are disclosed, such intermediates having the structure  In addition, methods of making and using the dyes as fluorescent labels are disclosed.

Methods and kits using extended rhodamine dyes

Fluorescent phenyl xanthene dyes are described that comprise any fluorescein, rhodamine or rhodol comprising a particular C9 phenyl ring. One or both of the ortho groups on the lower C9 phenyl ring is ortho substituted with a group selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, mercapto, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitroso, nitro, azido, sulfeno, sulfinyl, and sulfino. In one embodiment, halo and/or hydroxy groups are used. Optimal dyes contain a lower C9 phenyl ring in which both ortho groups are the same and the lower ring exhibits some form a symmetry relative to an imaginary axis running from the phenyl rings point of attachment to the remainder of the xanthene dye through a point para to the point of attachment. The phenyl xanthene dyes may be activated. Furthermore, the phenyl xanthene dyes may be conjugated to one or more substances including other dyes. The phenyl xanthene dyes are useful for a number of purposes, including labels for use in automated DNA sequencing as well the formation of fluorescent 'bar codes' for polymeric particles used in the multiplexed analysis of analytes.

Phenyl xanthene dyes

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Alameda, CA, United States of America

Scott C Benson