Abstract: Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.
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:
October 14, 2016
Date of Patent:
October 23, 2018
Assignee:
Applied Biosystems, LLC
Inventors:
John Gerdes, Elaine Best, Jeffrey M. Marmaro
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:
October 28, 2015
Date of Patent:
August 7, 2018
Assignee:
Applied Biosystems, LLC
Inventors:
Linda G. Lee, Sam L. Woo, Congcong Ma, Richard T. Reel, Mark F. Oldham, David M. Cox, Benjamin G. Schroeder, Jon M. Sorenson, Willy Wiyatno
Abstract: The invention relates to methods for the detection of a specific sequence of RNA in a cell or tissue sample. The invention also relates to methods to enzymatically manipulate the RNA in a crude cell lysate in a number of applications.
Abstract: An apparatus and method for rapid thermal cycling including a thermal diffusivity plate. The thermal diffusivity plate can provide substantial temperature uniformity throughout the thermal block assembly during thermal cycling by a thermoelectric module. An edge heater can provide substantial temperature uniformity throughout the thermal block assembly during thermal cycling.
Type:
Grant
Filed:
October 10, 2014
Date of Patent:
July 3, 2018
Assignee:
Applied Biosystems, LLC
Inventors:
Hon Siu Shin, Jew Kwee Ngui, Chee Kiong Lim, Ching Ong Lau, Lim Hi Tan, Yang Hooi Kee
Abstract: Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.
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.
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 2, 2015
Date of Patent:
March 13, 2018
Assignee:
Applied Biosystems, LLC
Inventors:
Eugene F. Young, Steven J. Boege, Donald R. Sandell
Abstract: The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.
Type:
Application
Filed:
September 1, 2017
Publication date:
March 1, 2018
Applicant:
Applied Biosystems, LLC
Inventors:
Scott C. Benson, Ruiming N. Zou, Krishna G. Upadhya, Paul M. Kenney, Jonathan M. Cassel
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.
Abstract: The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.
Type:
Grant
Filed:
May 1, 2015
Date of Patent:
October 10, 2017
Assignee:
Applied Biosystems, LLC
Inventors:
Scott C. Benson, Ruiming N. Zou, Krishna G. Upadhya, Paul M. Kenney, Jonathan M. Cassel
Abstract: Systems and methods are provided that comprise calibration techniques and associated systems that identify the two-dimensional position, or other alignment or positioning, of sample wells or other calibration objects located in a sample well plate, or other surface or area of interest. In some embodiments, calibration of the plate and/or positioning and/or alignment with respect to detection optics can be performed in multiple stages for two or more dimensions.
Type:
Grant
Filed:
September 3, 2010
Date of Patent:
October 10, 2017
Assignee:
Applied Biosystems, LLC
Inventors:
Alan R. Stanford, David C. Woo, John David Morgenthaler
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.
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:
March 28, 2014
Date of Patent:
August 29, 2017
Assignee:
Applied Biosystems, LLC
Inventors:
Ronald Graham, Ruiming Zou, Krishna Upadhya, Scott Benson
Abstract: An apparatus and method are provided for differentiating multiple detectable signals by excitation wavelength. The apparatus can include a light source that can emit respective excitation light wavelengths or wavelength ranges towards a sample in a sample retaining region, for example, in a well. The sample can contain two or more detectable markers, for example, fluorescent dyes, each of which can be capable of generating increased detectable emissions when excited in the presence of a target component. The detectable markers can have excitation wavelength ranges and/or emission wavelength ranges that overlap with the ranges of the other detectable markers. A detector can be arranged for detecting an emission wavelength or wavelength range emitted from a first marker within the overlapping wavelength range of at least one of the other markers.
Type:
Grant
Filed:
June 16, 2015
Date of Patent:
August 1, 2017
Assignee:
Applied Biosystems, LLC
Inventors:
Howard G. King, Steven J. Boege, Eugene F. Young, Mark F. Oldham
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.
Abstract: A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.
Type:
Grant
Filed:
August 4, 2015
Date of Patent:
June 6, 2017
Assignee:
Applied Biosystems, LLC
Inventors:
Charles S. Vann, Debjyoti Banerjee, Timothy G. Geiser, James C. Nurse, Nigel P. Beard
Abstract: The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3? target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3? target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.
Type:
Grant
Filed:
January 28, 2016
Date of Patent:
May 23, 2017
Assignee:
Applied Biosystems, LLC
Inventors:
Caifu Chen, Dana Ridzon, Zhaohui Zhou, Kai Qin Lao, Neil A. Straus
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:
September 30, 2014
Date of Patent:
January 23, 2018
Assignee:
Applied Biosystems, LLC
Inventors:
Barnett Rosenblum, Steven Menchen, Shaheer Khan, Paul Kenney