Patents Assigned to Applied Biosystems, LLC.
  • Modified oligonucleotides and applications thereof
    Patent number: 8431366
    Abstract: Disclosed, among other things, are primers containing certain modified nucleobases in the 3? terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof.
    Type: Grant
    Filed: March 21, 2011
    Date of Patent: April 30, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Khairuzzaman Bashar Mullah, Zhaochun Ma, Wanli Bi
  • Reagents, methods, and libraries for bead-based sequencing
    Patent number: 8431691
    Abstract: The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled probes containing phosphorothiolate linkages.
    Type: Grant
    Filed: July 21, 2008
    Date of Patent: April 30, 2013
    Assignee: Applied Biosystems LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Modified surfaces as solid supports for nucleic acid purification
    Patent number: 8426126
    Abstract: The invention relates to methods of separating polynucleotides, such as DNA, RNA and PNA, from solutions containing polynucleotides by reversibly binding the polynucleotides to a solid surface, such as a magnetic microparticle.
    Type: Grant
    Filed: September 30, 2004
    Date of Patent: April 23, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Gary J. Latham, Xingwang Fang, Richard C. Conrad, Jon A. Kemppainen, Robert A. Setterquist, Brittan L. Pasloske
  • MULTIPLEX AMPLIFICATION OF POLYNUCLEOTIDES
    Publication number: 20130096014
    Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.
    Type: Application
    Filed: October 4, 2012
    Publication date: April 18, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: APPLIED BIOSYSTEMS, LLC
  • Polypeptides Having Nucleic Acid Binding Activity and Compositions and Methods For Nucleic Acid Amplification
    Publication number: 20130089895
    Abstract: Polypeptides having nucleic acid binding activity are provided. Methods of using polypeptides having nucleic acid binding activity are provided. Fusion proteins and methods of using fusion proteins are provided. Fusion proteins comprising a polymerase and a nucleic acid binding polypeptide are provided. Fusion proteins comprising a reverse transcriptase and a nucleic acid binding polypeptide are provided. Methods are provided for amplifying a nucleic acid sequence using a fusion protein comprising a nucleic acid binding polypeptide and a polymerase. Methods are provided for amplifying a nucleic acid sequence using a fusion protein comprising a nucleic acid binding polypeptide and a reverse transcriptase.
    Type: Application
    Filed: September 13, 2012
    Publication date: April 11, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Patrick K. MARTIN, David A. Simpson, Christine D. Hardy
  • METHODS AND SYSTEMS FOR USING RFID IN BIOLOGICAL FIELD
    Publication number: 20130088321
    Abstract: Biological reagent carrier devices and methods are disclosed, which employ RFID techniques to associate information with biological reagents.
    Type: Application
    Filed: November 29, 2012
    Publication date: April 11, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: Applied Biosystems, LLC
  • METHODS AND SYSTEMS FOR USING RFID IN BIOLOGICAL FIELD
    Publication number: 20130088322
    Abstract: Biological reagent carrier devices and methods are disclosed, which employ RFID techniques to associate information with biological reagents.
    Type: Application
    Filed: November 29, 2012
    Publication date: April 11, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: APPLIED BIOSYSTEMS, LLC
  • THERMUS BROCKIANUS NUCLEIC ACID POLYMERASES
    Publication number: 20130089865
    Abstract: The invention provides nucleic acids and polypeptides for nucleic acid polymerases from a thermophilic organism, Thermus brockianus. The invention also provides methods for using these nucleic acids and polypeptides.
    Type: Application
    Filed: September 13, 2012
    Publication date: April 11, 2013
    Applicant: Applied Biosystems, LLC
    Inventors: Elena V. BOLCHACOVA, James Rozzelle
  • Thermal Cycler For PCR
    Publication number: 20130078713
    Abstract: An assembly for cycling vials of reaction mixtures through a series of temperature excursions is provided. The assembly can include a sample block for receiving the vials, a plurality of thermoelectric devices, a heat sink, and a clamping mechanism positioned to clamp the thermoelectric devices between the sample block and heatsink. The assembly can also include a thermal connector having a first end and a second end, the first end in close contact with the sample block and the second end in close contact with the heatsink to provide a thermal path between the sample block and the heatsink, the thermal connector being positioned to reduce thermal gradients across the sample block. The assembly can further include means for connecting the assembly to a computing apparatus for controlling the temperature excursions of the assembly.
    Type: Application
    Filed: September 14, 2012
    Publication date: March 28, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: John G. ATWOOD, Adrian FAWCETT, Keith S. FERRARA, Paul M. HETHERINGTON, Richard W. NOREIKS, Douglas E. OLSEN, John R. WIDOMSKI, Charles M. WITTMER
  • Methods and compositions for isolating small RNA molecules
    Patent number: 8404439
    Abstract: The present invention concerns the use of methods and compositions for the isolation of small RNA molecules (100 nucleotides or fewer), such as microRNA and siRNA molecules. Such molecules are routinely lost in commonly used isolation procedures and therefore the present invention allows for a much higher level of enrichment or isolation of these small RNA molecules.
    Type: Grant
    Filed: November 2, 2009
    Date of Patent: March 26, 2013
    Assignee: Applied Biosystems, LLC
    Inventor: Richard C. Conrad
  • nucleic acid polymerases
    Patent number: 8399231
    Abstract: The invention provides novel nucleic acid polymerases from strains GK24 and RQ-1 of Thermus thermophilus, and nucleic acids encoding those polymerases, as well as methods for using the polymerases and nucleic acids.
    Type: Grant
    Filed: October 14, 2010
    Date of Patent: March 19, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Elena Bolchakova, James Rozzelle
  • Methods and systems for using RFID in biological field
    Patent number: 8400304
    Abstract: Biological reagent carrier devices and methods are disclosed, which employ RFID techniques to associate information with biological reagents.
    Type: Grant
    Filed: October 5, 2011
    Date of Patent: March 19, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Richard D. Morris, Jerome A. Mack
  • METHODS AND SYSTEMS FOR USING RFID IN BIOLOGICAL FIELD
    Publication number: 20130063252
    Abstract: Biological reagent carrier devices and methods are disclosed, which employ RFID techniques to associate information with biological reagents.
    Type: Application
    Filed: September 13, 2012
    Publication date: March 14, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Richard D. MORRIS, Jerome A. MACK
  • Non-contact radiant heating and temperature sensing device for a chemical reaction chamber
    Patent number: 8388901
    Abstract: An apparatus and methods are provided for heating and sensing the temperature of a chemical reaction chamber without direct physical contact between a heating device and the reaction chamber, or between a temperature sensor and the reaction chamber. A plurality of chemical reaction chambers can simultaneously or sequentially be heated independently and monitored separately.
    Type: Grant
    Filed: May 24, 2012
    Date of Patent: March 5, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: John S. Shigeura, Janice G. Shigeura
  • Nucleic acid terminators incorporating a cationic moiety and methods for their use
    Patent number: 8389699
    Abstract: 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: Grant
    Filed: October 15, 2009
    Date of Patent: March 5, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Barnett Rosenblum, Steven Menchen
  • Device for the carrying out of chemical or biological reactions
    Patent number: 8389288
    Abstract: The invention relates to a device for the carrying out of chemical or biological reactions with a reaction vessel receiving element for receiving a microtiter plate with several reaction vessels, wherein the reaction vessel receiving element has several recesses arranged in a regular pattern to receive the respective reaction vessels, a heating device for heating the reaction vessel receiving element, and a cooling device for cooling the reaction vessel receiving element. The invention is characterized by the fact that the reaction vessel receiving element is divided into several segments. The individual segments are thermally decoupled from one another, and each segment is assigned a heating device which may be actuated independently of the others. By means of the segmentation of the reaction vessel receiving element, it is possible for zones to be set and held at different temperatures.
    Type: Grant
    Filed: January 18, 2010
    Date of Patent: March 5, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Wolfgang Heimberg, Thomas Herrmann, Matthias Knulle, Markus Schurf, Tilmann Wagner
  • System and method for electroporating a sample
    Patent number: 8383394
    Abstract: A system and method are described for electroporating a sample that utilizes one or more sets of electrodes that are spaced apart in order to hold a surface tension constrained sample between the electrodes. The first electrode is connected to the lower body of the system while the second electrode is connected to the upper body. Both electrodes are connected to a pulse generator. Each electrode has a sample contact surface such that the first electrode and the second electrode may be positioned to hold a surface tension constrained sample between the two sample contact surfaces and the sample may receive a selected electric pulse.
    Type: Grant
    Filed: April 14, 2010
    Date of Patent: February 26, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Richard Jarvis, Mike Byrom, Dmitriy Ovcharenko
  • DNA sequencing system
    Patent number: 8384898
    Abstract: An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector.
    Type: Grant
    Filed: April 9, 2012
    Date of Patent: February 26, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Mark Oldham, Eric Nordman, Richard Reel, Janice Shigeura
  • DNA sequencing system
    Patent number: 8384899
    Abstract: An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector.
    Type: Grant
    Filed: April 9, 2012
    Date of Patent: February 26, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Mark Oldham, Eric Nordman, Richard Reel, Janice Shigeura
  • Phenyl xanthene dyes
    Patent number: 8383841
    Abstract: Fluorescent phenyl xanthene dyes are described that comprise any fluorescein, rhodamine or rhodol comprising a particular C9 phenyl ring. One or both of the ortho groups on the lower C9 phenyl ring is ortho substituted with a group selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, mercapto, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitroso, nitro, azido, sulfeno, sulfinyl, and sulfino. In one embodiment, halo and/or hydroxy groups are used. Optimal dyes contain a lower C9 phenyl ring in which both ortho groups are the same and the lower ring exhibits some form a symmetry relative to an imaginary axis running from the phenyl rings point of attachment to the remainder of the xanthene dye through a point para to the point of attachment. The phenyl xanthene dyes may be activated. Furthermore, the phenyl xanthene dyes may be conjugated to one or more substances including other dyes.
    Type: Grant
    Filed: January 9, 2009
    Date of Patent: February 26, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Joe Y. L. Lam, Steven M. Menchen, Ruiming Zou, Scott C. Benson