Patents Assigned to Applied Biosystem, LLC
  • Methods and kits using extended rhodamine dyes
    Patent number: 9309561
    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: December 5, 2013
    Date of Patent: April 12, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Joe Y. L. Lam, Scott C. Benson, Steven M. Menchen
  • Axial illumination for capillary electrophoresis
    Patent number: 9285316
    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. The system for analyzing samples comprising: a light source that provides a non-coherent excitation light; at least one housing, wherein the housing transports samples and propagates the non-coherent excitation light by total internal reflection; a coupling optical element configured to introduce the non-coherent excitation light into the at least one housing through a wall of the at least one housing; and at least one NA enhancing optical element to collect an emitted fluorescence, wherein the NA enhancing optical element is constructed of a first material and the housing is constructed of a second material, wherein the first material has a greater index of refraction than the second material.
    Type: Grant
    Filed: July 24, 2014
    Date of Patent: March 15, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Richard Reel, Eric Nordman
  • Optical instrument including excitation source
    Patent number: 9285318
    Abstract: An optical instrument is provided for simultaneously illuminating two or more spaced-apart reaction regions with an excitation beam generated by a light source. A collimating lens can be disposed along a beam path between the light source and the reaction regions to form bundles of collimated excitation beams, wherein each bundle corresponds to a respective reaction region. Methods of analysis using the optical instrument are also provided.
    Type: Grant
    Filed: September 14, 2012
    Date of Patent: March 15, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Steven J. Boege, Mark F. Oldham, Eugene F. Young
  • Device, system, and method for depositing processed immiscible-fluid-discrete-volumes
    Patent number: 9285297
    Abstract: Various embodiments relate to systems and/or methods for sample preparation that can be used for biochemical and/or molecular biology procedures involving small volumes, for example, micro volumes or smaller. Methods and systems that can reduce sample size requirements and increase the number of samples on a substrate are provided. Samples can be applied to a plate or other appropriate substrate and can be used for, inter alia, sequencing reactions. In some embodiments, apparatuses, systems, and/or methods for charged analyte collection are provided. Charged analytes in a sample can be electrokinetically collected or extracted from a conduit through a hole formed in a sidewall of the conduit, by application of an electric field that causes the charged analytes to migrate in a direction that is transverse to the conduit.
    Type: Grant
    Filed: August 22, 2006
    Date of Patent: March 15, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Benjamin G. Schroeder, David M. Cox, Mark F. Oldham, Richard T. Reel, Willy Wiyatno
  • Synthesis of oligomers in arrays
    Patent number: 9283535
    Abstract: Systems, including apparatus and methods, for synthesis of oligomers in arrays.
    Type: Grant
    Filed: November 6, 2012
    Date of Patent: March 15, 2016
    Assignee: Applied Biosystems, LLC
    Inventor: John H. Butler
  • RNAi sequence-independent modification formats, and stabilized forms thereof
    Patent number: 9284551
    Abstract: Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.
    Type: Grant
    Filed: March 1, 2013
    Date of Patent: March 15, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Nitin Puri, Irudaya Charles, Susan Magdaleno, Alexander Vlassov, Chris Burnett
  • Sample preparation for in situ nucleic acid analysis, methods and compositions therefor
    Patent number: 9279152
    Abstract: Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms.
    Type: Grant
    Filed: August 14, 2014
    Date of Patent: March 8, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Richard Fekete, Annalee Nguyen
  • SiRNA sequence-independent modification formats for reducing off-target phenotypic effects in RNAi, and stabilized forms thereof
    Patent number: 9273312
    Abstract: Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.
    Type: Grant
    Filed: August 23, 2013
    Date of Patent: March 1, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Nitin Puri, Irudaya Charles, Susan Magdaleno, Alexander Vlassov, Christopher Burnett
  • Polypeptides having nucleic acid binding activity and compositions and methods for nucleic acid amplification
    Patent number: 9267130
    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: Grant
    Filed: September 13, 2012
    Date of Patent: February 23, 2016
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Patrick K. Martin, David A. Simpson, Christine D. Hardy
  • System and method for electroporating a sample
    Patent number: 9260690
    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: November 17, 2014
    Date of Patent: February 16, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Richard Jarvis, Mike Byrom, Dmitriy Ovcharenko
  • Nanowire-based system for analysis of nucleic acids
    Patent number: 9238835
    Abstract: System for detection and/or analysis of nucleic acids using nanowires to detect covalent modification of nucleic acids.
    Type: Grant
    Filed: March 11, 2014
    Date of Patent: January 19, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Hongye Sun, Steven Fung, Sam Lee Woo
  • Methods for bead-based sequencing
    Patent number: 9217177
    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 beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages.
    Type: Grant
    Filed: January 9, 2013
    Date of Patent: December 22, 2015
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Polypeptides having nucleic acid binding activity
    Patent number: 9212352
    Abstract: Polynucleotides having nucleic acid binding activity are provided. Methods of stabilizing a nucleic acid duplex are provided. Methods of promoting the annealing of complementary nucleic acid strands are provided. Methods of increasing the processivity of a DNA polymerase are provided. Methods of enhancing the activity of a nucleic acid modification enzyme are provided. Fusion proteins are provided. Methods of using fusion proteins are provided. Kits are provided.
    Type: Grant
    Filed: September 14, 2012
    Date of Patent: December 15, 2015
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Patrick K. Martin, David A. Simpson
  • Vacuum assist for a microplate
    Patent number: 9213042
    Abstract: A vacuum assist apparatus can comprise a microplate. The microplate can comprise a first surface and an opposing second surface. A plurality of wells can be formed in the first surface of the microplate. Each of the plurality of wells can be sized to receive an assay therein. A support base can comprise a fluid passage. The microplate can be positioned adjacent and in contact with the support base. A pressure device, in fluid communication with the fluid passage, can exert a vacuum within the fluid passage to actively retain the microplate in the contact with the support base.
    Type: Grant
    Filed: July 8, 2014
    Date of Patent: December 15, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Mark F. Oldham, Adrian Fawcett
  • Methods for multiplexing amplification reactions
    Patent number: 9206475
    Abstract: A two-step multiplex amplification reaction includes a first step which truncates the standard initial multiplex amplification round to “boost” the sample copy number by only a 100-1000 fold increase in the target. Following the first step the product is divided into optimized secondary single amplification reactions, each containing one of the primer sets that were used previously in the first or multiplexed booster step. The booster step can occur using an aqueous target nucleic acid or using a solid phase archived nucleic acid. In particular, nucleic acid sequences that uniquely identify E. Coli were identified using the multiplex amplification method.
    Type: Grant
    Filed: January 5, 2015
    Date of Patent: December 8, 2015
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: John C. Gerdes, Elaine Best, Jeffrey M. Marmaro
  • Methods and compositions for isolating small RNA molecules
    Patent number: 9193748
    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: February 27, 2013
    Date of Patent: November 24, 2015
    Assignee: Applied Biosystems, LLC
    Inventor: Richard Conrad
  • Apparatus, system, and method using immiscible-fluid-discrete-volumes
    Patent number: 9194772
    Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.
    Type: Grant
    Filed: September 10, 2009
    Date of Patent: November 24, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Linda Lee, Sam Woo, Congcong Ma, Richard Reel, Mark Oldham, David Cox, Benjamin Schroeder, Jon Sorenson, Willy Wiyatno
  • Caps for sample wells and microcards for biological materials
    Patent number: 9175333
    Abstract: A cover for a biological sample well tray, comprising a cap for sealing a sample well. The cap comprises a well lens for focusing light into the sample well and collecting light from the sample. In another aspect, the cap comprises an elongate portion configured to permit incoming light to pass into the sample well and out of the sample well. Various other aspects comprise a microcard for biological material, and an apparatus for a plurality of sample well strips. A method for testing a biological sample is also provided.
    Type: Grant
    Filed: November 22, 2013
    Date of Patent: November 3, 2015
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Eugene Young, Steven Boege, Donald Sandell
  • Achromatic lens array
    Patent number: 9157860
    Abstract: A luminescence detection system may include an excitation light source, a single element achromat, and a detector. The single element achromat may be configured to regulate the excitation light from the light source and direct the regulated light to a target, and the detector may be configured to detect luminescence generated by the target. The single element achromat may be configured to regulate the emission light from the target and direct the regulated light to a detector, and the excitation light source may be configured to direct the excitation light to the target. The single element achromat may be configured to regulate both the excitation light from the light source and the emission light from the target and direct the regulated light to, respectively, the target and a detector.
    Type: Grant
    Filed: September 13, 2005
    Date of Patent: October 13, 2015
    Assignee: Applied Biosystems, LLC
    Inventor: Steven J. Boege
  • Compositions, systems, and methods for immiscible fluid discrete volume manipulation
    Patent number: 9152150
    Abstract: Systems and methods of manipulating discrete volumes of a first fluid in a second fluid are provided. In some embodiments, discrete volumes can be formed in a conduit. In other embodiments, addition fluid can be added to a discrete volume in a first conduit by injecting the addition fluid at a relatively higher pressure. In some embodiments, discrete volumes that normally would not coalesce can be manipulated to be merged together.
    Type: Grant
    Filed: February 22, 2008
    Date of Patent: October 6, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Linda G. Lee, Mark F. Oldham, Sam L. Woo, David M. Cox, Richard T. Reel, Peter N. Ma, Ben F. Johnson, Dennis Letho