Patents Assigned to Applied Biosystems
  • Poly and Copoly(N-vinylamide)s and Their Use In Capillary Electrophoresis
    Publication number: 20140209461
    Abstract: The invention relates generally to polymers and copolymers comprising N-vinylamide-type monomers, their preparation, and compositions, such as electrophoresis separation media, containing the same; to supports, such as capillaries, containing these polymers; and methods for separating a mixture of biomolecules, especially polynucleotides, using capillary electrophoresis. Separation media comprising such polymers yield advantageous performance in the analysis and separation of biomolecules by capillary electrophoresis.
    Type: Application
    Filed: January 6, 2014
    Publication date: July 31, 2014
    Applicant: Applied Biosystems, LLC
    Inventor: Aldrich N.K. LAU
  • Methods for the reduction of stutter in microsatellite amplification
    Patent number: 8785126
    Abstract: 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: Grant
    Filed: September 12, 2012
    Date of Patent: July 22, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Sulekha Rao Coticone, William Bloch
  • Graft copolymers, their preparation and use in capillary electrophoresis
    Patent number: 8784627
    Abstract: The invention relates to graft copolymers, their preparation, and compositions, such as electrophoresis separation media, containing the same; also to ultra-high molecular weight poly(N,N-dimethylacrylamide) (“poly(DMA)”) polymers, their preparation, and compositions, such as electrophoresis separation media, containing the same; and more particularly to supports, such as capillaries, containing these polymers and methods for separating biomolecules, especially polynucleotides, using capillary electrophoresis. The graft copolymers can be prepared by, e.g., grafting polyacrylamide units onto a poly(DMA) backbone. Separation media comprising such graft copolymers or ultra-high molecular weight poly(DMA) polymers yield superior performance in the analysis and separation of biomolecules by capillary electrophoresis.
    Type: Grant
    Filed: September 23, 2009
    Date of Patent: July 22, 2014
    Assignee: Applied Biosystems, LLC
    Inventor: Aldrich N. Lau
  • AXIAL ILLUMINATION FOR CAPILLARY ELECTROPHORESIS
    Publication number: 20140192532
    Abstract: System and method for fluorescent light excitation and detection from samples to enhance the numerical aperture and/or reduce the cross-talk of the fluorescent light.
    Type: Application
    Filed: December 16, 2013
    Publication date: July 10, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Richard Reel, Eric Nordman
  • NANOWIRE-BASED SYSTEM FOR ANALYSIS OF NUCLEIC ACIDS
    Publication number: 20140193820
    Abstract: System for detection and/or analysis of nucleic acids using nanowires to detect covalent modification of nucleic acids.
    Type: Application
    Filed: March 11, 2014
    Publication date: July 10, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Hongye SUN, Steven FUNG, Sam Lee WOO
  • Methods for Analyzing Short Tandem Repeats and Single Nucleotide Polymorphisms
    Publication number: 20140186830
    Abstract: Methods for genotyping a sample comprising nucleic acid are provided. The methods comprise analyzing STR and SNP loci.
    Type: Application
    Filed: August 28, 2013
    Publication date: July 3, 2014
    Applicant: Applied Biosystems, LLC
    Inventor: Lori K. HENNESSY
  • Apparatus and Method for Specific Release of Captured Extension Products
    Publication number: 20140187429
    Abstract: Apparatus and methods for separating different polynucleotide populations in a mixture are provided, wherein different polynucleotides or polynucleotide populations are captured on different solid support. After hybridization, polynucleotides are selectively released from a selected support by altering a physical property of that support. The released polynucleotides can be eluted from a common flow path and isolated.
    Type: Application
    Filed: January 3, 2014
    Publication date: July 3, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: John SHIGEURA, Jer-Kang CHEN
  • PNA probes, mixtures, methods and kits pertaining to the determination of and related
    Patent number: 8753821
    Abstract: This invention is related to PNA probes, probe sets, mixtures, methods and kits pertaining to the determination of Mycoplasma and related Mollicutes.
    Type: Grant
    Filed: February 20, 2012
    Date of Patent: June 17, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Jens Hyldig-Nielsen, Susan Rigby, Michael Tanner, Ditte Lee, Byron Brehm-Stecher
  • COMPOSITIONS, METHODS, AND KITS FOR (MIS)LIGATING OLIGONUCLEOTIDES
    Publication number: 20140162258
    Abstract: Methods, reagents, and kits for (mis)ligating oligonucleotide probes or for identifying at least one target nucleotide are disclosed. One can enhance the generation of misligation product using a ligase under reaction conditions and with reagents where that particular ligase is prone to misligation. Alternatively, one can decrease or avoid generating misligation products using a particular ligase under reaction conditions and using reagents where that ligase is at least less prone to misligation. In certain embodiments, the recombinant ligase from Archaeoglobus fulgidus (Afu) is employed due to its unique misligation properties.
    Type: Application
    Filed: October 21, 2013
    Publication date: June 12, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Achim KARGER, James Rozzelle, Chien-Wei Chang, Elena Bolchakova
  • Methods for normalizing and for identifying small nucleic acids
    Patent number: 8741569
    Abstract: The present teachings are generally directed to methods for normalizing at least one species of small nucleic acid that is present in a population of small nucleic acid species, wherein the relative concentration of at least one small nucleic acid species is substantially greater than the relative concentration of at least one other small nucleic acid species in the population. At least one small nucleic acid species is normalized using a multiplicity of primers comprising degenerate sequences. In some embodiments, a small nucleic acid species is identified by inserting at least part of an extension product from a normalized population into a vector and subsequently sequencing the insert. In some embodiments, a small nucleic acid species is identified by determining the sequence of at least part of an extension product.
    Type: Grant
    Filed: October 23, 2009
    Date of Patent: June 3, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Lao, Neil Straus, John Burns
  • Fluorescent Polymeric Materials Containing Lipid Soluble Rhodamine Dyes
    Publication number: 20140145115
    Abstract: Fluorescent polymeric materials are disclosed comprising a polymer and one or more lipid soluble rhodamine dyes. The materials are especially useful in the preparation of multicolored microparticles, especially multicolored polystyrene microparticle, for use in the multiplexed analysis of a plurality of analytes in a single sample. When excited by a light source, the materials give off a unique emission based on the nature, concentration and ratio of the dyes therein. Methods of preparing and using said materials are also disclosed.
    Type: Application
    Filed: November 26, 2013
    Publication date: May 29, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Joe Y.L. LAM, Steven Menchen, Ruiming Zou, Scott Benson
  • High speed, high resolution compositions, methods, and kits for capillary electrophoresis
    Patent number: 8734630
    Abstract: The invention provides compositions, methods and kits for high speed, high resolution of analytes by capillary electrophoresis starting with uncoated capillaries. The compositions comprise a sieving component, comprising a non-crosslinked acrylamide polymer, and a surface interaction component, comprising at least one uncharged and non-crosslinked water-soluble silica-adsorbing polymer. Methods for employing the novel compositions in capillary electrophoresis are provided. Kits comprising the novel compositions for use in the novel methods are also provided.
    Type: Grant
    Filed: September 13, 2012
    Date of Patent: May 27, 2014
    Assignee: Applied Biosystems, LLC.
    Inventors: Karl O. Voss, Aldrich N. K. Lau
  • Fluorescent dye compounds, conjugates and uses thereof
    Patent number: 8729267
    Abstract: The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof.
    Type: Grant
    Filed: June 21, 2011
    Date of Patent: May 20, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Ronald Graham, Ruiming Zou, Krishna G. Upadhya, Scott C. Benson
  • Device for the carrying out of chemical or biological reactions
    Patent number: 8721972
    Abstract: The invention relates to a device for performing biological reactions in a nucleic acid sample. The device can comprise a reaction vessel receiving element that includes a plurality of reaction vessel holders and a gastight jacket or equalization plate containing a fluid changeable between liquid and gaseous states. The gastight jacket or equalization plate can be configured to provide temperature equalization among the reaction vessel holders. The reaction vessel receiving element can also include at least one Peltier element, a cooling element, and a controller configured to cycle the device through a predetermined time-temperature profile via heating and cooling.
    Type: Grant
    Filed: May 14, 2012
    Date of Patent: May 13, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Wolfgang Heimberg, Thomas Herrmann, Matthias Knulle, Markus Schurf, Tilmann Wagner
  • Method to quantify siRNAs, miRNAs and polymorphic miRNAs
    Patent number: 8710208
    Abstract: The present teachings provide methods, compositions, and kits for quantifying target polynucleotides. In some embodiments, a reverse stem-loop ligation probe is ligated to the 3? end of a target polynucleotide, using a ligase that can ligate the 3? end of RNA to the 5? end of DNA using a DNA template, such as T4 DNA ligase. Following digestion to form an elongated target polynucleotide with a liberated end, a reverse transcription reaction can be performed, followed by a PCR. In some embodiments, the methods of the present teachings can discriminate between polymorphic polynucleotides that vary by as little as one nucleotide.
    Type: Grant
    Filed: April 26, 2012
    Date of Patent: April 29, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Ruoying Tan, Caifu Chen, Karl J. Guegler
  • Multi-Chromophoric Quencher Constructs for Use in High Sensitivity Energy Transfer Probes
    Publication number: 20140114048
    Abstract: Dark quencher constructs, termed “multi-chromophoric quenchers” are described herein that comprise at least two dark quenching moieties, which can be the same or different, linked together by at least one multivalent linking moiety. The structure of the multi-chromophoric quenchers can be varied to selectively enhance quenching within a specific range of reporter emission wavelengths, to quench a broader range of reporter emission wavelengths than previously possible, or can combine both concepts. Multiple types of quenching moieties can be employed to increase the absorption range and a multiple number of each type of quenching moiety can be used to increase the total absorptivity within the absorption range. The multi-chromophoric quenchers can be tethered to probes for biomolecules, insoluble supports and/or fluorescent dyes for use in a wide variety of biomolecular assays.
    Type: Application
    Filed: October 15, 2013
    Publication date: April 24, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Scott BENSON, Steven MENCHEN, Krishna UPADHYA
  • Nanowire-based system for analysis of nucleic acids
    Patent number: 8703497
    Abstract: A system and method for analyzing nucleic acids is presented herein. The system can include a nanowire assembly including a plurality of nanowires. In some embodiments, at least two nanowires can be coupled to a different probe corresponding to a different sequence version of a polymorphism. The system can include a reagent delivery system capable of delivering a template polymorphic nucleotide, an extension nucleic acid, and an enzyme to the nanowire assembly. The system can include an electrical detector configured to measure an electrical characteristic of the nanowire assembly and/or a controller in communication with the reagent delivery system. In some embodiments, the electrical detector can be configured to collect data corresponding to changes in the electrical characteristic in response to contact with the template polymorphic nucleotide, the extension nucleic acid, and the enzyme.
    Type: Grant
    Filed: June 4, 2012
    Date of Patent: April 22, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Hongye Sun, Steven Fung, Sam Woo
  • Microfluidic Size-Exclusion Devices, Systems, and Methods
    Publication number: 20140106364
    Abstract: Microfluidic devices, assemblies, and systems are provided, as are methods of manipulating micro-sized samples of fluids. Microfluidic devices having a plurality of specialized processing features are also provided.
    Type: Application
    Filed: December 20, 2013
    Publication date: April 17, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Sean M. Desmond, Zbigniew T. Bryning, John S. Shigeura, Gary Lim, Adrian Fawcett, Jacob K. Freudenthal, Gary Bordenkircher
  • Methods And Kits For Multiplex Amplification Of Short Tandem Repeat Loci
    Publication number: 20140106353
    Abstract: Methods and materials are disclosed for use in simultaneously amplifying at least 11 specific STR loci of genomic DNA in a single multiplex reaction, as are methods and materials for use in the analysis of the products of such reactions. Included in the present invention are materials and methods for the simultaneous amplification of 16 specific loci in a single multiplex reaction, comprising the 10 AmpFlSTR® SGMplus® STR loci, the Amelogenin locus, and 5 new STR loci, including methods and materials for the analysis of these loci.
    Type: Application
    Filed: October 14, 2013
    Publication date: April 17, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Lori Hennessy, Robert Green
  • Sequencing system with memory
    Patent number: 8697004
    Abstract: The present teachings provide a device including a memory. According to various embodiments, the memory is readable, writable, and rewritable. The present teachings further provide processing stations, e.g., for carrying out electrophoresis, per, genetic analysis, sample preparation, and/or sample cleanup, etc., that are capable of reading from and/or writing/rewriting to such memory.
    Type: Grant
    Filed: May 19, 2010
    Date of Patent: April 15, 2014
    Assignee: Applied Biosystems, LLC
    Inventor: Jeffery D. Frazier