Abstract: This invention provides compositions, methods, and systems for characterizing, resolving, and quantitating single stranded and double stranded DNA and RNA in-situ. Paired sense and anti-sense probes can signal the presence of double stranded nucleic acids. DNA and RNA can be distinguished in cell and tissue samples by hybridizing with probe sets adapted to highlight differences in these targets in-situ.
Type:
Grant
Filed:
January 20, 2016
Date of Patent:
April 23, 2019
Inventors:
Quan Nguyen, Yunqing Ma, Audrey Lin, Shauna Levinson, Chunfai Lai
Abstract: Methods and kits for joining three or more polynucleotides to form a product polynucleotide are provided. Such a method includes forming a reaction mixture comprising (i) a vector fragment whose ends have four base overhangs resulting from cleavage of a vector with a first type IIs enzyme, (ii) a first insert nucleic acid with a four base overhang at one end resulting from cleavage by the first type IIs enzyme and a three base overhang at the other end resulting from cleavage by the second type IIs enzyme; and (iii) a second insert nucleic acid with a four base overhang at one end resulting from cleavage by the first type IIs enzyme and a three base overhang at the other end resulting from cleavage by the second type IIs enzyme, and (iv) a ligase.
Abstract: A method of screening for at least one biological entity of interest using a microfabricated device which has a top surface defining an array of microwells. A sample is loaded onto the microfabricated device such that at least one microwell of the array of microwells includes at least one cell and an amount of a nutrient. A membrane is applied to the microfabricated device to retain the at least one cell and the nutrient. Without furnishing additional nutrient to the microwells, the microfabricated device is incubated to grow a plurality of cells from the at least one cell in the at least one microwell of the array of microwells. The plurality of cells is then analyzed to determine a presence or absence of a biological entity of interest.
Type:
Grant
Filed:
September 30, 2017
Date of Patent:
March 12, 2019
Assignee:
GENERAL AUTOMATION LAB TECHNOLOGIES, INC.
Inventors:
Paul C. Blainey, Michael W. Seely, Roman Stocker, Karsten Zengler, Scott Conradson, Peter Christey, Alexander Hallock
Abstract: This disclosure relates to analyzing the end-to-end sequence and the relative distributions in heterogeneous mixtures of polynucleotides and methods and enabling reagents related thereto. In certain embodiments this method relates to the complete full length sequencing and quantitative profiling of mRNAs present in the transcriptomes of cells or tissues of but not limited to, higher multicellular organisms that possess interrupted genes subject to complex post-transcriptional RNA processing.
Type:
Grant
Filed:
February 17, 2014
Date of Patent:
March 12, 2019
Assignees:
Emory University, The Johns Hopkins University
Abstract: Provided are a PNA probe for detecting nucleotide polymorphism of a target gene, a melting curve analysis method for detecting the nucleotide polymorphism of the target gene using the same, a nucleotide polymorphism analysis method of a target gene including the melting curve analysis method, and a kit for detecting the nucleotide polymorphism of the target gene containing the PNA probe. It is characterized that the PNA probe according to the present invention contains negative charge molecules. The modified PNA probe according to the present invention contains the negative charge molecules to have a high recognition ability with respect to a target DNA and a high coupling ability to the target DNA and to be rapidly dissociated by heat, such that the nucleotide polymorphism analysis may be relatively easily performed even in a heterozygous sample showing two melting curve graphs, and two or more adjacent single nucleotide polymorphisms may be simultaneously analyzed.
Type:
Grant
Filed:
April 4, 2014
Date of Patent:
March 12, 2019
Assignee:
PANAGENE INC.
Inventors:
Goon Ho Joe, Sung-Kee Kim, Heekyung Park, Chwang Siek Park, Se Ryun Kim, Yongtae Kim, Su Nam Kim
Abstract: The subject innovation relates to a RNA binding buffer comprising (a) at least one chaotropic agent; and (b) an organic solvent selected from the group consisting of ethylene carbonate, ethylene glycol diacetate and 2-pyrrolidone or combinations thereof. The subject innovation further relates to a method of binding RNA to a solid support and to a method of isolating RNA both making use of the binding buffer of the subject innovation. The subject innovation finally relates to a kit comprising the RNA binding buffer or the organic solvent as relevant substance therein.
Abstract: The invention provides methods and compositions for separately denaturing a probe and target in hybridization applications. The invention may, for example, eliminate the use of or reduce the dependence on formamide in hybridization applications. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.
Abstract: Small molecule fluorescent probes for established drug targets such as nucleic acids including DNA and RNA has been developed and disclosed herein. These nucleic acid probes bind to multiple DNA and RNA structures, and to sites crucial for nucleic acid function, such as DNA and RNA major grooves. Displacement of the probes by other binders such as small molecule compounds and/or proteins illicits a fluorescence change in the probe that once detected and analyzed provide binding information of these other binders of interest. Similarly, changes in fluorescence upon binding of the probes to nucleic acid have been applied to screen nucleic acid of different sequence and conformation. The nucleic acid probes and method of uses disclosed herein are advantageously suitable for high-through put screening of libraries of small molecule compounds, proteins, and nucleic acids.
Type:
Grant
Filed:
March 31, 2016
Date of Patent:
February 12, 2019
Assignee:
Nubad, LLC
Inventors:
Dev P. Arya, Frank Anderson Norris, Jason Derrick Watkins
Abstract: Provided are methods for labeling transfer RNA comprising replacing the uracil component of a dihydrouridine of said transfer RNA with a fluorophore. The disclosed methods may comprise fluorescent labeling of natural tRNAs (i.e., tRNAs that have been synthesized in a cell, for example, in a bacterium, a yeast cell, or a vertebrate cell) at dihydrouridine (D) positions, or fluorescent labeling of synthetic tRNAs. In another aspect, the present invention provides methods for assessing protein synthesis in a translation system comprise providing a tRNA having a fluorophore substitution for the uracil component of a dihydrouridine in a D loop of the tRNA; introducing the labeled tRNA into the translation system; irradiating the translation system with electromagnetic radiation, thereby generating a fluorescence signal from the fluorophore; detecting the fluorescence signal; and, correlating the fluorescence signal to one or more characteristics of the protein synthesis in the translation system.
Type:
Grant
Filed:
February 9, 2017
Date of Patent:
February 12, 2019
Assignees:
The Trustees of the University of Pennsylvania, Anima Cell Metrology
Inventors:
Barry S. Cooperman, Zeev Smilansky, Yale E. Goldman, Dongli Pan
Abstract: Provided herein are improved methods, compositions, and kits for analysis of nucleic acids. The improved methods, compositions, and kits can enable copy number estimation of a nucleic acid in a sample. Also provided herein are methods, compositions, and kits for determining the linkage of two or more copies of a target nucleic acid in a sample (e.g. whether the two or more copies are on the same chromosome or different chromosomes) or for phasing alleles.
Type:
Grant
Filed:
September 8, 2015
Date of Patent:
January 1, 2019
Assignee:
Bio-Rad Laboratories, Inc.
Inventors:
John F. Regan, Serge Saxonov, Michael Y. Lucero, Benjamin J. Hindson, Phillip Belgrader, Simant Dube, Austin P. So, Jeffrey C. Mellen, Nicholas J. Heredia, Kevin D. Ness, Billy W. Colston, Jr.
Abstract: The present invention provides a novel method that can analyze a target easily utilizing binding nucleic acid molecules and an analysis kit for use in the method. The analysis method of the present invention includes: a complex formation step of causing a binding nucleic acid molecule that binds to the target and a sample to come into contact with each other to form a complex of the binding nucleic acid molecule and the target in the sample; a nuclease treatment step of releasing a nucleic acid monomer from at least one of a complex fraction and a non-complex fraction by a nuclease treatment; an enzyme treatment step of reacting the released nucleic acid monomer with an enzyme for which the nucleic acid monomer is a substrate; a detection step of detecting the enzyme reaction; and an analysis step of analyzing the target that has formed the complex from the result of detecting the enzyme reaction.
Abstract: The present invention provides, among other things, methods of purifying messenger RNA (mRNA) including the steps of (a) precipitating mRNA from an impure preparation; (b) subjecting the impure preparation comprising precipitated mRNA to a purification process involving membrane filtration such that the precipitated mRNA is captured by a membrane; and (c) eluting the captured precipitated mRNA from the membrane by re-solubilizing the mRNA, thereby resulting in a purified mRNA solution. In some embodiments, a purification process involving membrane filtration suitable for the present invention is tangential flow filtration.
Type:
Grant
Filed:
December 4, 2017
Date of Patent:
December 18, 2018
Assignee:
Translate Bio, Inc.
Inventors:
Frank DeRosa, Anusha Dias, Shrirang Karve, Michael Heartlein
Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
Type:
Grant
Filed:
March 27, 2017
Date of Patent:
December 11, 2018
Assignee:
10X GENOMICS, INC.
Inventors:
Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol, Christopher Hindson, Donald Masquelier, Mirna Jarosz, Michael Schnall-Levin
Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
Type:
Grant
Filed:
August 31, 2017
Date of Patent:
December 11, 2018
Assignee:
10X GENOMICS, INC.
Inventors:
Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol, Christopher Hindson, Donald Masquelier, Mirna Jarosz, Michael Schnall-Levin
Abstract: The present invention provides labeled circular plasmid DNA molecules for studying DNA topology and topoisomerases. The molecules of the present invention also provide tools for high throughput drug screening for inhibitors of DNA gyrases and DNA topoisomerases for anticancer drug discovery and antibiotics discovery.
Type:
Grant
Filed:
December 28, 2017
Date of Patent:
December 11, 2018
Assignee:
THE FLORIDA INTERNATIONAL UNIVERSITY BOARD OF TRUSTEES
Abstract: A method of determining whether a given single nucleotide is methylated or not methylated characterized by the steps of (a) contacting the single nucleotide with one or more hybridization probe types each of which in its unused form; (b) for the relevant probe type causing (i) the single nucleotide to bind to the region resistant to exonucleolytic degradation and the single-stranded region and (ii) the second oligonucleotide to bind to the single nucleotide and the single-stranded nucleotide region; (c) treating the used probe with a methylation-dependent restriction or a methylation-sensitive restriction endonuclease to cleave adjacent the region resistant to exonucleolytic degradation; and thereafter (d) treating the product of step (c) with an exonuclease or a polymerase exhibiting exonuclease activity to liberate either only first or both first and second detectable elements in a detectable state to determine if the single nucleotide is methylated or not.
Type:
Grant
Filed:
February 13, 2015
Date of Patent:
December 4, 2018
Assignee:
BASE4 INNOVATION LTD.
Inventors:
Barnaby Balmforth, Ana Luisa Bras dos Santos Ribeiro da Silva-Weatherley
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.
Abstract: The present invention provides a novel technique by which the redox activity of a nucleic acid molecule can be evaluated. An evaluation method of the present invention includes: a detection step of electrochemically detecting a redox reaction to a substrate, the redox reaction being catalyzed by a nucleic acid molecule to be evaluated, using a device that electrochemically detects a redox reaction; and an evaluation step of evaluating redox activity of the nucleic acid molecule from a result of the detection of the redox reaction. As the device, a device in which a base provided with a detection portion is included, the detection portion includes an electrode system, and the nucleic acid molecule to be evaluated is arranged on the base is used. In the present invention, it is preferred that a plurality of kinds of nucleic acid molecule to be evaluated is arranged on the base, and the plurality of kinds of nucleic acid molecules to be evaluated is evaluated by a single device.
Abstract: Methods and compositions for determining the presence of a polymorphism at a target nucleotide position in a plurality of target nucleic acid sequences is provided.
Type:
Grant
Filed:
September 30, 2014
Date of Patent:
October 16, 2018
Assignee:
President and Fellows of Harvard College
Inventors:
Iain J. Macleod, Christopher F. Rowley, Max Essex
Abstract: The present invention is directed to sequencing of nucleic acids. A method is provided for sequencing based on immobilized nucleic acid on a surface. Advantageously, a long range detection mechanism is used for detecting, whether a nucleotide provided to the substrate of a biochip has been incorporated into the immobilized template nucleic acid. Various different alignment means are provided by the present invention which can be used for facilitating a rigidly locking of the orientation of the DNA complex, which complex comprises the template nucleic acid, the primer and the capture nucleic acid. Various different linker systems may be used to immobilize the DNA complex at a first and a second strand end, such that the desired alignment of the DNA complex is achieved. Also co-adsorbed molecules on the substrate surface can be used for such an aligning measure.
Type:
Grant
Filed:
January 22, 2014
Date of Patent:
September 25, 2018
Assignee:
DYNAMIC BIOSENSORS GMBH
Inventors:
Andreas Langer, Ralf Strasser, Ulrich Rant