Patents Assigned to Applied Biosystems
  • Enrichment through heteroduplexed molecules
    Patent number: 7851158
    Abstract: The present invention relates to the enrichment of specific target sequences. Enrichment can be achieved through the formation of a heteroduplex that includes the specific target sequence and then the specific cleavage of the heteroduplex. A binding moiety is then added to the cleaved heteroduplex, allowing for the subsequent manipulation of the specific target sequence in the heteroduplex.
    Type: Grant
    Filed: December 28, 2007
    Date of Patent: December 14, 2010
    Assignee: Applied Biosystems, LLC
    Inventor: Kevin J. McKernan
  • Method and apparatus for reducing space charge in an ion trap
    Patent number: 7847248
    Abstract: Ion trap apparatus and methods for efficiently addressing the effects of charge space caused by ion trap overfilling, useful in linear ion traps of mass spectrometers.
    Type: Grant
    Filed: November 18, 2008
    Date of Patent: December 7, 2010
    Assignees: MDS Analytical Technologies, a business unit of MDS Inc., Applied Biosystems, Inc.
    Inventor: Bruce A. Collings
  • Automatic threshold setting for quantitative polymerase chain reaction
    Patent number: 7848892
    Abstract: Disclosed are systems and methods for identifying and quantitating the presence of one or more DNA species in a sample population through PCR amplification. DNA species quantitation includes a determination of a threshold fluorescence value used in the assessment of the PCR amplification reaction. Various embodiments of the present invention incorporate an enhancement function useful in selecting appropriate threshold fluorescence values and facilitate the determination of DNA concentrations by quantitative PCR based methodologies.
    Type: Grant
    Filed: December 28, 2006
    Date of Patent: December 7, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Lesley Ward, Adrian Jensen, Justin Lyon, Cameron McLeman, Bryan Tysinger
  • DUAL ELECTRODE INJECTION OF ANALYTE INTO A CAPILLARY ELECTROPHORETIC DEVICE
    Publication number: 20100300879
    Abstract: An injection system including a first electrical circuit for concentration of an analyte and a second electrical circuit for injection of the concentrated analyte into an electrophoretic device is described, as well as methods of using the injection system.
    Type: Application
    Filed: July 29, 2010
    Publication date: December 2, 2010
    Applicant: Applied Biosystems, LLC
    Inventors: Charles S. Vann, Timothy Z. Liu
  • MICROFLUIDIC SIZE-EXCLUSION DEVICES, SYSTEMS, AND METHODS
    Publication number: 20100298172
    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: August 4, 2010
    Publication date: November 25, 2010
    Applicant: Applied Biosystems, LLC
    Inventors: Sean M. DESMOND, Zbigniew T. BRYNING, John SHIGEURA, Gary LIM, Adrian FAWCETT, Jacob K. FREUDENTHAL, Gary BORDENDIRCHER
  • Minimizing effects of dye crosstalk
    Patent number: 7839507
    Abstract: Methods and systems for processing signals to minimize the effects of dye crosstalk. Deconvolution of multiplexed dye signals can include corrections for residual error determined from experimental measurements. Residual error corrections can account for reaction or assay specific factors and modify the subsequent filtering of signals. Correction values can be determined for specific dye-probe conjugates to minimize dye crosstalk and may be combined with residual error correction to further minimize errors in spectral deconvolution. Apparatus, systems, and computer-readable media can process signals and modify filters based on values obtained using the methods.
    Type: Grant
    Filed: June 28, 2007
    Date of Patent: November 23, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Stephen J. Gunstream, David C. Woo, John P. Bodeau, Mark A. McCoy
  • Dye-labeled ribonucleotide triphosphates
    Publication number: 20100292457
    Abstract: 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: Application
    Filed: January 25, 2010
    Publication date: November 18, 2010
    Applicant: Applied Biosystems, LLC
    Inventors: Peter Virgil Fisher, Paolo Vatta, Shaheer H. Khan
  • Device and method for multiple analyte detection
    Patent number: 7833711
    Abstract: The invention is directed to a method and device for simultaneously testing a sample for the presence, absence, and/or amounts of one or more of a plurality of selected analytes. The invention includes, in one aspect, a device for detecting or quantitating a plurality of different analytes in a liquid sample. Each chamber may include an analyte-specific reagent effective to react with a selected analyte that may be present in the sample, and detection means for detecting the signal. Also disclosed are methods utilizing the device.
    Type: Grant
    Filed: April 7, 2006
    Date of Patent: November 16, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Timothy M. Woudenberg, Michael Albin, Reid B. Kowallis, Yefim Raysberg, Robert P. Ragusa, Emily S. Winn-Deen
  • Methods of labelling polynucleotides with dibenzorhodamine dyes
    Patent number: 7833756
    Abstract: Dibenzorhodamine compounds having the structure are disclosed, including nitrogen- and aryl-substituted forms thereof. In addition, two intermediates useful for synthesizing such compounds are disclosed, a first intermediate having the structure including nitrogen- and aryl-substituted forms thereof, and a second intermediate having the structure including nitrogen- and aryl-substituted forms thereof, wherein substituents at positions C-14 to C18 taken separately are selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, carboxylic acid, sulfonic acid, —CH2OH, alkoxy, phenoxy, linking group, and substituted forms thereof. The invention further includes energy transfer dyes comprising the dibenzorhodamine compounds, nucleosides labeled with the dibenzorhodamine compounds, and nucleic acid analysis methods employing the dibenzorhodamine compounds.
    Type: Grant
    Filed: July 8, 2008
    Date of Patent: November 16, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Scott C. Benson, Joe Y. L. Lam, Steven Michael Menchen
  • Oligonucleotides and analogs labeled with energy transfer dyes
    Patent number: 7825237
    Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers facilitate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R28 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.
    Type: Grant
    Filed: September 4, 2009
    Date of Patent: November 2, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
  • Reversible terminator nucleotides and methods of use
    Patent number: 7824887
    Abstract: Disclosed herein a reversible terminator nucleotides and methods of use.
    Type: Grant
    Filed: June 26, 2009
    Date of Patent: November 2, 2010
    Assignee: Applied Biosystems LLC
    Inventors: Linda Lee, Gerald Zon
  • Sequencing System With Memory
    Publication number: 20100262379
    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: Application
    Filed: May 19, 2010
    Publication date: October 14, 2010
    Applicant: Applied Biosystems, LLC
    Inventor: Jeffery D. Frazier
  • DUAL-SIDED THERMAL CYCLER
    Publication number: 20100233763
    Abstract: A device, system, and method are provided for thermally treating a fluid processing device. According to various embodiments, a system is provided that can include a thermal device and a fluid processing device holder. The thermal device can include a first block having a thermal conductivity greater than 0.5 Watt per centimeter Kelvin (W/cm·K), a second block having a thermal conductivity greater than 0.5 W/cm·K, and a heat-pump device disposed between the first block and the second block. The heat-pump device can transfer thermal energy from at least one of the first block and the second block to the other of the first block and the second block. The fluid processing device holder can hold a fluid processing device in a heat-transfer position with respect to the first block and the second block. The fluid processing device can be a microfluidic device.
    Type: Application
    Filed: May 24, 2010
    Publication date: September 16, 2010
    Applicant: Applied Biosystems, LLC
    Inventors: John S. SHIGEURA, Janice G. SHIGEURA, Sean M. DESMOND, David M. COX
  • Water-soluble rhodamine dye conjugates
    Patent number: 7795042
    Abstract: The present invention provides novel, water-soluble, red-emitting fluorescent rhodamine dyes and red-emitting fluorescent energy-transfer dye pairs, as well as labeled conjugates comprising the same and methods for their use. The dyes, energy-transfer dye pairs and labeled conjugates are useful in a variety of aqueous-based applications, particularly in assays involving staining of cells, protein binding, and/or analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing.
    Type: Grant
    Filed: March 12, 2009
    Date of Patent: September 14, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Linda G. Lee, Ronald J. Graham, William E. Werner, Elana Swartzman, Lily Lu
  • Methods and kits using extended rhodamine dyes
    Patent number: 7776568
    Abstract: Extended rhodamine compounds exhibiting favorable fluorescence characteristics having the structure are disclosed. In addition, novel intermediates for synthesis of these dyes are disclosed, such intermediates having the structure In addition, methods of making and using the dyes as fluorescent labels are disclosed.
    Type: Grant
    Filed: August 24, 2004
    Date of Patent: August 17, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Joe Y. L. Lam, Scott C. Benson, Steven M. Menchen
  • Two-color Real-time/End-point Quantitation of MicroRNAs (miRNAs)
    Publication number: 20100203545
    Abstract: The present invention is directed to methods, reagents, kits, and compositions for detecting target polynucleotide sequences, especially small target polynucleotides such as miRNAs, between two samples. A pair of linker probes can be employed in two different reactions to query a particular species of target polynucleotide. A pair of detector probes, a single forward primer specific for the target polynucleotide, and a reverse primer can be employed in an amplification reaction to query the difference in expression level of the target polynucleotide between the two samples. In some embodiments a plurality of small miRNAs are queried with a plurality of linker probes. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.
    Type: Application
    Filed: April 14, 2010
    Publication date: August 12, 2010
    Applicant: Applied Biosystems, LLC
    Inventors: Andrew K. Finn, Caifu Chen
  • Methods for improving the performance of a detector
    Patent number: 7764378
    Abstract: A system and method for allowing adjustments of various parameters associated with the operation of charge-coupled devices adapted for use in biological analysis devices. Gate voltage signal applied to the CCDs can be adjusted to advantageously affect the manner in which charge is transferred from pixels. The manner in which transferred charges from the pixels are processed in a readout process can also be adjusted to advantageously change the speed of the CCD based detector. Various methods of performing such adjustments are disclosed.
    Type: Grant
    Filed: June 12, 2008
    Date of Patent: July 27, 2010
    Assignee: Applied Biosystems, LLC
    Inventor: Mark F. Oldham
  • System and methods for improving signal/noise ratio for signal detectors
    Patent number: 7759636
    Abstract: A method and system for characterizing and quantifying various error and calibration components of signals associated with photo-detectors. By varying the detector operational parameters such as input light intensity and integration times, measured signals can be analyzed to separate out and quantify various components of the measured signals. The various components thus determined may be categorized according to their dependencies on the operational parameters. Such component characterization allows better understanding of the detector system and ways in which such system can be improved so as to yield an improved measurement result for which the detector is being utilized.
    Type: Grant
    Filed: January 6, 2009
    Date of Patent: July 20, 2010
    Assignee: Applied Biosystems, LLC
    Inventor: Dmitry M. Sagatelyan
  • Analyzing messenger RNA and micro RNA in the same reaction mixture
    Patent number: 7745122
    Abstract: The present teachings provide methods, compositions, and kits for performing primer extension reactions on at least two target polynucleotides in the same reaction mixture. In some embodiments, a reverse transcription reaction is performed on a first target polynucleotide with a hot start primer comprising a self-complementary stem and a loop, and extension products form at high temperatures but extension products form less so at low temperatures since the self-complementary stem of the hot start primer prevents hybridization of the target specific region to the target. However, non-hot start primers with free target specific regions can hybridize to their corresponding targets at the low temperature and extension can happen at the low temperature.
    Type: Grant
    Filed: July 17, 2006
    Date of Patent: June 29, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Qin Lao, Neil A. Straus
  • Luminescence reference standards
    Patent number: 7742164
    Abstract: The present teachings provide for systems, and components thereof, for detecting and/or analyzing light. These systems can include, among others, optical reference standards utilizing luminophores, such as nanocrystals, for calibrating, validating, and/or monitoring light-detection systems, before, during, and/or after sample analysis.
    Type: Grant
    Filed: December 18, 2008
    Date of Patent: June 22, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: J. Michael Phillips, Aldrich N. K. Lau, Mark F. Oldham, Kevin S. Bodner, Steven J. Boege, Donald R. Sandell, David H. Tracy