Patents by Inventor Barnett B. Rosenblum
Barnett B. 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: 20090093623Abstract: 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: August 27, 2008Publication date: April 9, 2009Applicant: Applied Biosystems Inc.Inventors: Linda G. Lee, Scott C. Benson, Barnett B. Rosenblum, Sandra L. Spurgeon, Ronald J. Graham
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Publication number: 20090092986Abstract: 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: September 29, 2008Publication date: April 9, 2009Applicant: APPLIED BIOSYSTEMS INC.Inventors: Meng TAING, Shaheer H. KHAN, Steven M. MENCHEN, Barnett B. ROSENBLUM
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Patent number: 7429651Abstract: 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: GrantFiled: October 28, 2004Date of Patent: September 30, 2008Assignee: Applera CorporationInventors: Meng Taing, Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Patent number: 7169557Abstract: 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: GrantFiled: November 7, 2002Date of Patent: January 30, 2007Assignee: Applera CorporationInventors: Barnett B. Rosenblum, Geun-Sook Jeon, Shaheer H. Khan
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Patent number: 7038063Abstract: 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: GrantFiled: November 18, 2003Date of Patent: May 2, 2006Assignee: Applera CorporationInventors: Linda G. Lee, Meng C. Taing, Barnett B. Rosenblum
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Patent number: 7018431Abstract: Sulfonated diarylrhodamine compounds are useful as fluorescent labels of nucleosides, nucleotides, polynucleotides, and polypeptides. The compounds find particular application in the area of fluorescent nucleic acid analysis, e.g., automated DNA sequencing and fragment analysis, detection of probe hybridization in hybridization arrays, detection of nucleic acid amplification products, and the like.Type: GrantFiled: June 24, 2003Date of Patent: March 28, 2006Assignee: Applera CorporationInventors: Steven M. Menchen, Scott C. Benson, Joe Y. L. Lam, Weiguo Zhen, Daqing Sun, Barnett B. Rosenblum, Shaheer H. Khan, Meng Taing
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Patent number: 7019128Abstract: 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 —OH; W2 is —OH 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: GrantFiled: July 9, 2002Date of Patent: March 28, 2006Assignee: Applera CorporationInventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Patent number: 6835827Abstract: 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: GrantFiled: February 20, 2003Date of Patent: December 28, 2004Assignee: Applera CorporationInventors: Ravi S. Vinayak, Linda G. Lee, Khairuzzaman B. Mullah, Barnett B. Rosenblum
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Publication number: 20040229235Abstract: 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: November 18, 2003Publication date: November 18, 2004Applicant: Applera CorporationInventors: Linda G. Lee, Meng C. Taing, Barnett B. Rosenblum
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Patent number: 6811979Abstract: 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: GrantFiled: October 11, 2001Date of Patent: November 2, 2004Assignee: Applera CorporationInventors: Meng Taing, Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Publication number: 20040096397Abstract: Sulfonated diarylrhodamine compounds are useful as fluorescent labels of nucleosides, nucleotides, polynucleotides, and polypeptides. The compounds find particular application in the area of fluorescent nucleic acid analysis, e.g., automated DNA sequencing and fragment analysis, detection of probe hybridization in hybridization arrays, detection of nucleic acid amplification products, and the like.Type: ApplicationFiled: June 24, 2003Publication date: May 20, 2004Applicant: Applera CorporationInventors: Steven M. Menchen, Scott C. Benson, Joe Y.L. Lam, Weiguo Zhen, Daqing Sun, Barnett B. Rosenblum, Shaheer H. Khan, Meng Taing
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Patent number: 6716994Abstract: 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: GrantFiled: January 4, 2000Date of Patent: April 6, 2004Assignee: Applera CorporationInventors: Steven M. Menchen, Scott C. Benson, Barnett B. Rosenblum, Shaheer H. Khan
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Patent number: 6653462Abstract: A nucleoside/tide compound having the structure: NUC-L-S-LB/LG is described wherein NUC is a nucleoside/tide having a nucleobase portion B, L is a rigid linkage, S is a spacer; and LB/LG is a member of a linkage pair or a label. NUC is attached to L through B such that when B is a purine, L is attached to the 8-position of the purine, when B is 7-deazapurine, L is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, L is attached to the 5-position of the pyrimidine. In an important aspect of the invention, L has the structure: wherein each of n, o and p are integers ranging from 0 to 3, and the sum of n, o and p is at least 2, and each of W, X, Y and Z is selected from the group consisting of carbon and nitrogen. The invention further includes polynucleotide compounds comprising the nucleoside/tide, and primer extension methods utilizing the nucleoside/tide, particularly when used in combination with certain mutant polymerase enzymes.Type: GrantFiled: February 26, 2002Date of Patent: November 25, 2003Assignee: Applera CorporationInventors: Shaheer H. Khan, Barnett B. Rosenblum, Weiguo Zhen, Steven M. Menchen
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Patent number: 6649769Abstract: 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: GrantFiled: August 21, 2002Date of Patent: November 18, 2003Assignee: Applera CorporationInventors: Linda G. Lee, Meng C. Taing, Barnett B. Rosenblum
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Publication number: 20030191303Abstract: Methods and compositions to label oligonucleotides and analogs directly on a solid-support having the structure 1Type: ApplicationFiled: February 20, 2003Publication date: October 9, 2003Applicant: Applera CorporationInventors: Ravi S. Vinayak, Linda G. Lee, Khairuzzaman B. Mullah, Barnett B. Rosenblum
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Publication number: 20030148470Abstract: Propargylethoxyamino nucleosides are disclosed having the structure 1Type: ApplicationFiled: July 9, 2002Publication date: August 7, 2003Applicant: PE Corporation (NY)Inventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Publication number: 20030119040Abstract: 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: November 7, 2002Publication date: June 26, 2003Inventor: Barnett B. Rosenblum
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Patent number: 6583168Abstract: Sulfonated diarylrhodamine compounds are useful as fluorescent labels of nucleosides, nucleotides, polynucleotides, and polypeptides. The compounds find particular application in the area of fluorescent nucleic acid analysis, e.g., automated DNA sequencing and fragment analysis, detection of probe hybridization in hybridization arrays, detection of nucleic acid amplification products, and the like.Type: GrantFiled: November 28, 2000Date of Patent: June 24, 2003Assignee: Applera CorporationInventors: Steven M. Menchen, Scott C. Benson, Joe Y. L. Lam, Weiguo Zhen, Daqing Sun, Barnett B. Rosenblum, Shaheer H. Khan, Meng Taing
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Publication number: 20030055243Abstract: 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: August 21, 2002Publication date: March 20, 2003Applicant: PE Corporation (NY)Inventors: Linda G. Lee, Meng C. Taing, Barnett B. Rosenblum
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Patent number: 6525183Abstract: 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: GrantFiled: November 7, 2001Date of Patent: February 25, 2003Assignee: PE Corporation (NY)Inventors: Ravi S. Vinayak, Linda G. Lee, Khairuzzaman B. Mullah, Barnett B. Rosenblum