Patents by Inventor Neil Straus

Neil Straus has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20170292158
    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: Application
    Filed: April 18, 2017
    Publication date: October 12, 2017
    Inventors: Caifu CHEN, Dana RIDZON, Zhaohui ZHOU, Kai Qin LAO, Neil A. STRAUS
  • Patent number: 9657346
    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
  • Publication number: 20170107567
    Abstract: The present disclosure relates to the amplification of target nucleic acid sequences for various sequencing and/or identification techniques. The use of these primers, as described herein, allows for the reduction in the amplification of nonspecific hybridization events (such as primer dimerization) while allowing for the amplification of the target nucleic acid sequences.
    Type: Application
    Filed: August 15, 2016
    Publication date: April 20, 2017
    Inventors: Kai LAO, Neil STRAUS, Nanlan XU
  • Patent number: 9574234
    Abstract: The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein.
    Type: Grant
    Filed: January 9, 2015
    Date of Patent: February 21, 2017
    Assignee: ILLUMINA, INC.
    Inventors: Neil A. Straus, Shengrong Lin, Helmy A. Eltoukhy, Kevin L. Gunderson
  • Patent number: 9567635
    Abstract: The present teachings provide methods, compositions, and kits for performing primer extension reactions. In some embodiments, a reverse transcription reaction is performed on a target polynucleotide with a hot start primer comprising a blunt-ended self-complementary stem, and a loop, and extension products form at high temperatures but reduce extension product formation at low temperatures.
    Type: Grant
    Filed: March 12, 2015
    Date of Patent: February 14, 2017
    Assignee: Life Technologies Corporation
    Inventors: Kai Lao, Neil Straus, Kenneth Livak
  • Patent number: 9528147
    Abstract: The present disclosure relates to the amplification of target nucleic acid sequences. This can be accomplished via the use of various primers. The use of these primers, as described herein, results in nucleic acid structures that can reduce the amplification of nonspecific hybridization events (such as primer dimerization) while allowing the amplification of the target nucleic acid sequences.
    Type: Grant
    Filed: May 27, 2015
    Date of Patent: December 27, 2016
    Assignee: Life Technologies Corporation
    Inventors: Kai Lao, Neil Straus
  • Patent number: 9447463
    Abstract: The present disclosure relates to the amplification of target nucleic acid sequences for various sequencing and/or identification techniques. The use of these primers, as described herein, allows for the reduction in the amplification of nonspecific hybridization events (such as primer dimerization) while allowing for the amplification of the target nucleic acid sequences.
    Type: Grant
    Filed: December 9, 2013
    Date of Patent: September 20, 2016
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Kai Lao, Neil Straus, Nanlan Xu
  • Patent number: 9422603
    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: February 20, 2015
    Date of Patent: August 23, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Qin Lao, Neil A. Straus
  • Publication number: 20160215336
    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: Application
    Filed: January 28, 2016
    Publication date: July 28, 2016
    Inventors: Caifu CHEN, Dana RIDZON, Zhaohui ZHOU, Kai Qin LAO, Neil A. STRAUS
  • Publication number: 20150322504
    Abstract: The present disclosure relates to the amplification of target nucleic acid sequences. This can be accomplished via the use of various primers. The use of these primers, as described herein, results in nucleic acid structures that can reduce the amplification of nonspecific hybridization events (such as primer dimerization) while allowing the amplification of the target nucleic acid sequences.
    Type: Application
    Filed: May 27, 2015
    Publication date: November 12, 2015
    Inventors: Kai LAO, Neil STRAUS
  • Publication number: 20150252418
    Abstract: The present teachings provide methods, compositions, and kits for performing primer extension reactions. In some embodiments, a reverse transcription reaction is performed on a target polynucleotide with a hot start primer comprising a blunt-ended self-complementary stem, and a loop, and extension products form at high temperatures but reduce extension product formation at low temperatures.
    Type: Application
    Filed: March 12, 2015
    Publication date: September 10, 2015
    Inventors: Kai LAO, Neil Straus, Kenneth Livak
  • Publication number: 20150232918
    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: Application
    Filed: February 20, 2015
    Publication date: August 20, 2015
    Inventors: Kai Qin LAO, Neil A. STRAUS
  • Patent number: 9068222
    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: August 18, 2009
    Date of Patent: June 30, 2015
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Caifu Chen, Dana Ridzon, Zhaohui Zhou, Kai Qin Lao, Neil A. Straus
  • Publication number: 20150141295
    Abstract: The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein.
    Type: Application
    Filed: January 9, 2015
    Publication date: May 21, 2015
    Applicant: ILLUMINA, INC.
    Inventors: Neil A. Straus, Shengrong Lin, Helmy A. Eltoukhy, Kevin Gunderson
  • Patent number: 8993240
    Abstract: The present teachings provide methods, compositions, and kits for performing primer extension reactions. In some embodiments, a reverse transcription reaction is performed on a target polynucleotide with a hot start primer comprising a blunt-ended self-complementary stem, and a loop, and extension products form at high temperatures but reduce extension product formation at low temperatures.
    Type: Grant
    Filed: July 16, 2009
    Date of Patent: March 31, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Qin Lao, Neil A. Straus, Kenneth J. Livak
  • Patent number: 8962254
    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 15, 2013
    Date of Patent: February 24, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Lao, Neil Straus
  • Patent number: 8951940
    Abstract: The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein.
    Type: Grant
    Filed: March 16, 2011
    Date of Patent: February 10, 2015
    Assignee: Illumina, Inc.
    Inventors: Neil A. Straus, Shengrong Lin, Helmy A. Eltoukhy, Kevin Gunderson
  • Publication number: 20140349301
    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: Application
    Filed: June 2, 2014
    Publication date: November 27, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Kai LAO, Neil Straus, John Burns
  • Publication number: 20140303017
    Abstract: The present teachings provide methods, compositions, and kits for reverse transcribing and amplifying small nucleic acids such as micro RNAs. High levels of multiplexing are provided by the use of a zip-coded stem-loop reverse transcription primer, along with a PCR-based pre-amplification reaction that comprises a zip-coded forward primer. Detector probes in downstream decoding PCRs can take advantage of the zip-code introduced by the stem-loop reverse transcription primer. In some embodiments, further amplification is achieved by cycling the reverse transcription reaction. The present teachings also provide compositions and kits useful for performing the reverse transcription and amplification reactions described herein.
    Type: Application
    Filed: March 6, 2014
    Publication date: October 9, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Kai LAO, Kenneth Livak, Neil Straus
  • Publication number: 20140235845
    Abstract: The present disclosure relates to the amplification of target nucleic acid sequences. This can be accomplished via the use of various primers. The use of these primers, as described herein, results in nucleic acid structures that can reduce the amplification of nonspecific hybridization events (such as primer dimerization) while allowing the amplification of the target nucleic acid sequences.
    Type: Application
    Filed: February 10, 2014
    Publication date: August 21, 2014
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: KAI LAO, NEIL STRAUS