Patents Assigned to Applera Corporation Applied Biosystems Group
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Publication number: 20090246763Abstract: Disclosed are tri-nuclear metal complexes and salts thereof, such as tri-nuclear osmium or ruthenium complexes or salts thereof, suitable for use as electrochemical labels. Also disclosed are oligonucleotide probes with an attached electrochemical label, methods of nucleic acid amplification, methods of sequencing, and kits for nucleic acid amplification and sequencing having oligonucleotide probes including an electrochemical label. The electrochemical labels are synthesized from siderophores.Type: ApplicationFiled: March 31, 2008Publication date: October 1, 2009Applicant: APPLERA CORPORATION, APPLIED BIOSYSTEMS GROUPInventor: Robert G. Eason
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Publication number: 20090246762Abstract: Disclosed are methods and kits applicable to sequencing methods, such as Sanger dideoxy sequencing methods. The methods and kits disclosed utilize a cationically charged nucleic acid terminator in combination with a discriminatory polymerase.Type: ApplicationFiled: March 31, 2008Publication date: October 1, 2009Applicant: APPLERA CORPORATION, APPLIED BIOSYSTEMS GROUPInventors: Barnett B. Rosenblum, Steven M. Menchen
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Publication number: 20090047688Abstract: Reagents, kits and methods for detecting biological molecules by energy transfer from an activated chemiluminescent substrate to an energy acceptor dye such as a J-aggregated dye are described.Type: ApplicationFiled: May 23, 2008Publication date: February 19, 2009
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Publication number: 20080241838Abstract: Methods and kits for detecting a target nucleic acid in a sample are described. In some embodiments, the sample to be analyzed includes a primer which hybridizes to at least a portion of the target nucleic acid, a probe having a first region which hybridizes to at least a portion of the target nucleic acid and a second region having a detectable label, a polymerase which extends the hybridized primer and an enzyme comprising nuclease activity that can cleave the hybridized hybridization probe to thereby release a labeled probe fragment. In some embodiments, the sample can then be contacted with a solid support comprising surface bound capture probes which can hybridize to the labeled probe fragment(s). These capture probes more readily bind to the probe fragment(s) than to the intact hybridization probe. The label can then be detected on the support surface. In this manner, improved discrimination between the probe fragments and the intact hybridization probes can be achieved.Type: ApplicationFiled: December 28, 2007Publication date: October 2, 2008Applicant: APPLERA CORPORATION, APPLIED BIOSYSTEMS GROUPInventors: Kristian Scaboo, Vissarion Aivazachvili, Timothy Liu, Robert Eason, Konrad Faulstich
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Publication number: 20080193940Abstract: A method and kit for detecting a target nucleic acid in a sample is described. The sample to be analyzed may include a primer which hybridizes to at least a portion of the target nucleic acid, a probe having a first region which hybridizes to at least a portion of the target nucleic acid and a second region having a detectable label, a polymerase which extends the hybridized primer and an enzyme comprising exonuclease activity that can cleave the hybridized hybridization probe to thereby generate a labeled probe fragment. At least one portion of the hybridization probe hybridizes to another portion of the hybridization probe to thereby form a folded structure. The method can involve melting the sample, reducing the temperature of the sample to allow primer and probe to each hybridize to at least a portion of single stranded target nucleic acid in the sample, elongating the primer and releasing the labeled probe fragment.Type: ApplicationFiled: December 28, 2007Publication date: August 14, 2008Applicant: APPLERA CORPORATION, APPLIED BIOSYSTEMS GROUPInventors: Vissarion Aivazachvili, Kristian Scaboo, Eugene Spier
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Publication number: 20080176761Abstract: Intermediates and methods for forming passivated surfaces on oxide layers and articles produced thereby are described. Hydroxyl or hydroxide groups on the oxide surfaces are reacted with a metal reagent of the formula Y(L-Pol)m, where Y is a transition metal, magnesium or aluminum, L is oxygen, sulfur, selenium or an amine, and “Pol” represents a passivating agent such as a polyethylene glycol, a hydrocarbon, or a fluorocarbon. The resulting modified surface can be further reacted with a passivating agent having a phosphate functional group or a polyvalent reagent comprising a passivating moiety and a plurality of functional groups that are reactive with or that form complexes with Y. The passivating agent can also include a functional group such as biotin to provide surfaces with a desired functionality. The passivated surfaces exhibit minimal binding to bio-molecules and can be used in single-molecule detection schemes.Type: ApplicationFiled: November 21, 2007Publication date: July 24, 2008Applicant: APPLERA CORPORATION, APPLIED BIOSYSTEMS GROUPInventors: Steven M. Menchen, Christina E. Inman, Meng Taing, Khai Luong, Handong Li
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Publication number: 20070254298Abstract: 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: April 9, 2007Publication date: November 1, 2007Applicant: APPLERA CORPORATION, Applied Biosystems GroupInventors: Linda Lee, Meng Taing, Barnett Rosenblum
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Publication number: 20070100569Abstract: Method and system providing an automated workflow for installing and/or calibrating laboratory equipment. The workflow empowers an end user to perform installation and calibration thereby reducing the costs associated with such activities. The automated workflow taught herein, can greatly reduce the incidence of calibration error by providing for verification of certain events during the calibration process.Type: ApplicationFiled: August 31, 2006Publication date: May 3, 2007Applicant: APPLERA CORPORATION, APPLIED BIOSYSTEMS GROUPInventors: Bruce DeSimas, Leslie Dow
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Publication number: 20070038387Abstract: The present teachings relate to a method of filtering mass spectrometer data using a variable filter window. The width of the window can depend on the mass itself and the mass defects for a family of compounds. The teachings can be used with a plurality of compounds including but not limited to peptides and can be utilized on a brood range of mass spectrometers.Type: ApplicationFiled: June 23, 2006Publication date: February 15, 2007Applicants: Applera Corporation; Applied Biosystems Group, MDS Inc.; MDS Sciex DivisionInventors: Xunming Chen, Philip Savickas, Marvin Vestal
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Publication number: 20060292438Abstract: Methods, compositions and kits are disclosed that utilize heteroconfigurational polynucleotide comprising a D-form polynucleotide sequence portion and an L-form polynucleotide sequence portion that is covalently linked to the D-form polynucleotide sequence portion.Type: ApplicationFiled: June 22, 2006Publication date: December 28, 2006Applicant: Applera Corporation; Applied Biosystems GroupInventors: I. Greenfield, Stefan Matysiak, Benjamin Shroeder, Ravi Vinayak
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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: 20060286581Abstract: Methods, compositions and kits are disclosed that utilize heteroconfigurational polynucleotide comprising a D-form polynucleotide sequence portion and an L-form polynucleotide sequence portion that is covalently linked to the D-form polynucleotide sequence portion.Type: ApplicationFiled: June 22, 2006Publication date: December 21, 2006Applicant: APPLERA CORPORATION; APPLIED BIOSYSTEMS GROUPInventors: Stefan Matysiak, Benjamin Schroeder, Ravi Vinayak, I. Greenfield
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Publication number: 20060063189Abstract: The invention provides for the use of sulfur nucleophiles in analyzing methylated DNA and novel sulfur nucleophiles suitable for such us.Type: ApplicationFiled: September 21, 2005Publication date: March 23, 2006Applicant: Applera Corporation Applied Biosystems GroupInventor: Gerald Zon
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Patent number: 7006215Abstract: A method and apparatus to illuminate a target. The apparatus can comprise a first lens configured to receive light from the light source, a diffractive optical element configured to receive the light from the first lens and to regulate the light into regulated light, and second lens configured to receive the regulated light and to direct the regulated light onto a selected area of the target.Type: GrantFiled: May 4, 2004Date of Patent: February 28, 2006Assignee: Applera Corporation Applied Biosystems GroupInventors: Louis B. Hoff, Mark F. Oldham
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Publication number: 20050037361Abstract: The invention provides a method for reducing stutter in the amplification of a microsatellite comprising the steps of providing a sample comprising a microsatellite having a G+C content of 50% or less; contacting the sample with at least one enzyme having nucleic acid polymerase activity; and incubating the sample with the enzyme for a sufficient amount of time and under conditions sufficient to amplify the microsatellite; wherein the incubation is performed in the presence of an amount of betaine, sorbitol or mixtures thereof, effective to reduce stutter relative to the amount of stutter observed in the absence of betaine and/or sorbitol. The invention also provides compositions containing betaine and/or sorbitol, kits for amplifying microsatellites having a G+C content of 50% or less, and methods of using all of the foregoing.Type: ApplicationFiled: August 8, 2003Publication date: February 17, 2005Applicant: Applera Corporation Applied Biosystems GroupInventors: Sulekha Rao Coticone, Will Bloch
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Patent number: 6841349Abstract: The invention provides a method for reducing stutter in the amplification of a microsatellite comprising the steps of providing a sample comprising a microsatellite having a G+C content of 50% or less; contacting the sample with at least one enzyme having nucleic acid polymerase activity; and incubating the sample with the enzyme for a sufficient amount of time and under conditions sufficient to amplify the microsatellite; wherein the incubation is performed in the presence of an amount of betaine, sorbitol or mixtures thereof, effective to reduce stutter relative to the amount of stutter observed in the absence of betaine and/or sorbitol. The invention also provides compositions containing betaine and/or sorbitol, kits for amplifying microsatellites having a G+C content of 50% or less, and methods of using all of the foregoing.Type: GrantFiled: May 7, 2001Date of Patent: January 11, 2005Assignee: Applera Corporation Applied Biosystems GroupInventors: Sulekha Rao Coticone, Will Bloch