Patents by Inventor Shaheer H. Khan
Shaheer H. Khan 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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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: 6887690Abstract: The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.Type: GrantFiled: June 22, 2001Date of Patent: May 3, 2005Assignee: PE CorporationInventors: Peter Virgil Fisher, Paolo Vatta, Shaheer H. Khan
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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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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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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: 20030013089Abstract: The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.Type: ApplicationFiled: June 22, 2001Publication date: January 16, 2003Inventors: Peter Virgil Fisher, Paolo Vatta, Shaheer H. Khan
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Patent number: 6504024Abstract: 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. Additionally, a primer extension method is provided employing the above propargylethoxyamino nucleosides.Type: GrantFiled: June 14, 2001Date of Patent: January 7, 2003Assignee: PE Corporation (NY)Inventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Publication number: 20020151711Abstract: A nucleoside/tide compound having the structureType: ApplicationFiled: February 26, 2002Publication date: October 17, 2002Applicant: PE Corporation (NY)Inventors: Shaheer H. Khan, Barnett B. Rosenblum, Weiguo Zhen, Steven M. Menchen
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Publication number: 20020102590Abstract: 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 11, 2001Publication date: August 1, 2002Applicant: PE Corporation (NY)Inventors: Meng Taing, Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Publication number: 20020045180Abstract: Propargylethoxyamino nucleosides are disclosed having the structure 1Type: ApplicationFiled: June 14, 2001Publication date: April 18, 2002Applicant: The Perkin-Elmer CorporationInventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Patent number: 6248568Abstract: 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: June 18, 1998Date of Patent: June 19, 2001Assignee: The Perkin-Elmer CorporationInventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Patent number: 6197555Abstract: 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: December 14, 1999Date of Patent: March 6, 2001Assignee: The Perkin-Elmer CorporationInventors: Shaheer H. Khan, Barnett B. Rosenblum, Weiguo Zhen, Steven M. Menchen
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Patent number: 6096875Abstract: A nucleoside/tide compound having the structureNUC--L--S--LB/LGis 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 ##STR1## 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: October 14, 1998Date of Patent: August 1, 2000Assignee: The Perlein-Elmer CorporationInventors: Shaheer H. Khan, Barnett B. Rosenblum, Weiguo Zhen, Steven M. Menchen
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Patent number: 5948648Abstract: A nucleoside/tide compound having the structureNUC--L--S--LB/LGis 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 ##STR1## 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 nuclcoside/tide, and primer extension methods utilizing the nucleoside/tide, particularly when used in combination with certain mutant polymerase enzymes.Type: GrantFiled: May 29, 1998Date of Patent: September 7, 1999Inventors: Shaheer H. Khan, Barnett B. Rosenblum, Weiguo Zhen, Steven M. Menchen
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Patent number: 5821356Abstract: Propargylethoxyamino nucleosides are disclosed having the structure ##STR1## wherein R.sub.1 and R.sub.2 are --H, lower alkyl, or label; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; W.sub.1 is --H or --OH; W.sub.2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W.sub.3 is --PO.sub.4, --P.sub.2 O.sub.7, --P.sub.3 O.sub.10, phosphate analog, or --OH. Additionaly, a primer extension method is provided employing the above propargylethoxyamino nucleosides.Type: GrantFiled: August 13, 1996Date of Patent: October 13, 1998Assignee: The Perkin Elmer CorporationInventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Patent number: 5798032Abstract: Methods and apparatus are disclosed for improved mapping and sequencing of carbohydrate polymers. In one aspect, the improvement includes a means for coupling two capillary electrophoresis (CE) tubes in such a way so as to (i) efficiently transfer a selected sample component from a first CE capillary to a second CE capillary or, (ii) introduce a supplementary reagent into the separation path between the two capillaries, e.g., an internal standard, binding agent, enzyme, and the like. In an additional aspect, the invention includes improved apparatus and methods for electrophoresis of labeled carbohydrates in which a sample carbohydrate labeled with a first label is separated by CE and its migration behavior is compared with an internal standard labeled with one or more second labels which are distinguishable from the first label.Type: GrantFiled: November 13, 1995Date of Patent: August 25, 1998Assignee: The Perkin-Elmer CorporationInventors: Shaheer H. Khan, Roger A. O'Neill, Louis B. Hoff
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Patent number: 5770716Abstract: Substituted propargylethoxyamido nucleosides are disclosed having the structure ##STR1## wherein X is selected from the group consisting of amino alkanoic acid, alkylamino benzoic acid, .alpha.-amino acid, and 4-amino-2-butynoic acid. R.sub.1 and R.sub.2 taken separately are selected from the group consisting of --H, lower alkyl, protecting group, and label; R.sub.3 is selected from the group consisting of --H and lower alkyl. B is a 7-deazapurine, purine, or pyrimidine nucleoside base. When B is purine or 7-deazapurine, the sugar moiety is attached at the N.sup.9 -position of the purine or deazapurine, and when B is pyrimidine, the sugar moiety is attached at the N.sup.1 -position of the pyrimidine.Type: GrantFiled: April 10, 1997Date of Patent: June 23, 1998Assignee: The Perkin-Elmer CorporationInventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum