Patents by Inventor Barnett Rosenblum
Barnett Rosenblum has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20070212709Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 29, 2006Publication date: September 13, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Publication number: 20070207477Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 29, 2006Publication date: September 6, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Publication number: 20070190564Abstract: The invention includes methods and kits for making and analyzing primer extension products incorporating one or more universal bases, including methods and kits for nucleic acid sequencing and microsatellite analysis.Type: ApplicationFiled: January 25, 2007Publication date: August 16, 2007Inventors: Barnett Rosenblum, Geun-Sook Jeon, Shaheer Khan
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Publication number: 20070161026Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 28, 2006Publication date: July 12, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Publication number: 20070161027Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 28, 2006Publication date: July 12, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Publication number: 20070154927Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 29, 2006Publication date: July 5, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Publication number: 20070154925Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 29, 2006Publication date: July 5, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Publication number: 20070154926Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers facilitate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 29, 2006Publication date: July 5, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Publication number: 20070154924Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers facilitate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: December 28, 2006Publication date: July 5, 2007Applicant: Applera CorporationInventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
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Patent number: 7169939Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: GrantFiled: February 26, 2004Date of Patent: January 30, 2007Assignee: Applera CorporationInventors: Linda G. Lee, Sandra L. Spurgeon, Barnett Rosenblum
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Publication number: 20060286561Abstract: Propargylethoxyamino nucleosides are disclosed having the structure wherein R1 and R2 are —H lower alkyl, or label; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; W1 is —H or —H; W2 is —H or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3?-position; and W3 is —PO4, —P2O7, —P3O10, phosphate analog, or —OH. Additionaly, a primer extension method is provided employing the above propargylethoxyamino nucleosides.Type: ApplicationFiled: March 24, 2006Publication date: December 21, 2006Applicant: Applera Corporation; Applied Biosystems GroupInventors: Shaheer Khan, Steven Menchen, Barnett Rosenblum
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Publication number: 20060188915Abstract: Atropisomeric energy-transfer dye compounds are disclosed. A variety of molecular biology applications utilize atropisomeric xanthene fluorescent dyes as labels for substrates such as nucleotides, nucleosides, polynucleotides, polypeptides and carbohydrates. Methods include DNA sequencing, DNA fragment analysis, PCR, SNP analysis, oligonucleotide ligation, amplification, minisequencing, and primer extension.Type: ApplicationFiled: May 2, 2006Publication date: August 24, 2006Applicant: Applera CorporationInventors: Linda LEE, Meng TAING, Barnett ROSENBLUM
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Publication number: 20060141475Abstract: Methods and software for associating mobility probes with target macromolecules are discussed. By encoding the identities of macromolecules of interest with a universal set of tag portions complementary to a universal set of mobility probes, reactions varying in their input starting material may be identified using the same universal set of mobility probes. This allows the universal collection of mobility probes to be used in a target macromolecule-independent manner. Software is used to decode the associations between the mobility probes and a given target macromolecular identity.Type: ApplicationFiled: November 19, 2003Publication date: June 29, 2006Applicant: Applera CorporationInventors: Barnett Rosenblum, David Holden, Yuandan Lou, Ryan Koehler, Srinivasa Ramachandra
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Publication number: 20050250119Abstract: Provided are nucleotide-dye conjugates and related compounds in which a dye is linked to a nucleobase directly or indirectly by an anionic linker. The anionic character of the linker is provided by one or more anionic moieties which are present in the linker, such as phosphate, phosphonate, sulfonate, and carboxylate groups. When the dye is a provided as a donor/acceptor dye pair, the anionic linker can be located between the donor and the acceptor, or between the nucleobase and either the donor or acceptor, or both. In one embodiment, conjugates of the invention provide enhanced electrophoretic mobility characteristics to sequencing fragments, e.g., for dideoxy sequencing using labeled terminators.Type: ApplicationFiled: October 28, 2004Publication date: November 10, 2005Applicant: Applera CorporationInventors: Meng Taing, Shaheer Khan, Steven Menchen, Barnett Rosenblum
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Publication number: 20050214843Abstract: The present teachings relate to nucleobase, nucleoside and nucleotide compounds, methods of synthesis, and uses thereof. The present teachings provide compounds, such as nucleobase, nucleoside and/or nucleotide compounds including a propargyl linker, and methods for making or using such compounds.Type: ApplicationFiled: April 12, 2005Publication date: September 29, 2005Applicant: Applera CorporationInventors: Barnett Rosenblum, Geun-sook Jeon, Shaheer Khan
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Publication number: 20050191660Abstract: Methods and compositions to label oligonucleotides and analogs directly on a solid-support having the structure where S is a solid-support, A is a cleavable linker, X is a moiety with three or more attachment sites, L is a label, Y is a nucleophile, i.e. O, NH, NR or S, and P1 is an acid cleavable protecting group are provided. The labelled solid-support is reacted in a cyclical fashion to synthesize a labelled oligonucleotide on a solid-support in the 5? to 3? direction, having the structure: Labelled oligonucleotides are also synthesized by reacting: (i) a label reagent bearing functionality consisting of carboxylic acid, sulfonic acid, phosphonic acid, or phosphoric acid, (ii) an oligonucleotide on solid support with nucleophilic functionality, and (iii) a coupling reagent, whereby an ester, amide, thioester, sulfonamide, sulfonate, phosphonate, phosphoramidate, phosphorothioate, or phosphate bond is formed.Type: ApplicationFiled: December 6, 2004Publication date: September 1, 2005Applicant: Applera CorporationInventors: Ravi Vinayak, Linda Lee, Khairuzzaman Mullah, Barnett Rosenblum
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Publication number: 20050170388Abstract: The present teachings relate to nucleobase, nucleoside and nucleotide compounds, methods of synthesis, and uses thereof. The present teachings provide compounds, such as nucleobase, nucleoside and/or nucleotide compounds including a propargyl linker, and methods for making or using such compounds.Type: ApplicationFiled: December 17, 2004Publication date: August 4, 2005Applicant: Applera CorporationInventors: Barnett Rosenblum, Geun-sook Jeon, Shaheer Khan
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Publication number: 20050112781Abstract: A set of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structures wherein R1-R6 are hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group, or, when taken together, R1 and R6 is benzo, or, when taken together, R4 and R5 is benzo; R7-R10, R12-R16 and R18 may be hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group; R11 and R17 may be hydrogen, lower alkyl, lower alkene, lower alkyne, phenyl, aryl, linking group; Y1-Y4 are hydrogen, lower alkyl, or cycloalkyl, or, when taken together, Y1 and R2, Y2 and R1 Y3 and R3, and/or Y4 and R4 is propano, ethano, or substituted forms thereof, and X1-X3 taken separately are hydrogen, chlorine, fluorine, lower alkyl, carboxylate, sulfonate, hydroxymethyl, and linking group, or any combinations thereof.Type: ApplicationFiled: February 26, 2004Publication date: May 26, 2005Inventors: Linda Lee, Scott Benson, Barnett Rosenblum, Sandra Spurgeon, Ronald Graham
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Publication number: 20050107617Abstract: The present invention provides a novel class of fluorescent cyanine dye compounds that are modified at one of the hetercyclic ring nitrogen atoms with a mobility-modifying moiety that permits the electrophoretic mobilities of polynucleotides labeled with the mobility-modifying cyanine dyes to be adjusted or tuned in a predictable fashion while retaining enzymatic activity. The ability to predictably tune the relative electrophoretic mobilities of the dyes permits the creation of sets of mobility-matched fluorescent dyes of a variety of structures for a variety of applications, including fluorescence-based 4-color nucleic acid sequencing reactions.Type: ApplicationFiled: March 15, 2004Publication date: May 19, 2005Applicant: Applera CorporationInventors: Steven Menchen, Scott Benson, Barnett Rosenblum, Shaheer Khan
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Publication number: 20050069912Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.Type: ApplicationFiled: February 26, 2004Publication date: March 31, 2005Inventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum