公开(公告)号：US20240093317A1

公开(公告)日：2024-03-21

申请号：US17767837

申请日：2020-10-09

Applicant: THE GOVERNING COUNCIL OF THE UNIVERSITY OF TORONTO

Inventor： Margot Karlikow ,  Keith Pardee ,  Peivand Sadat Mousavi

IPC: C12Q1/70 ,  C12Q1/6865 ,  C12Q1/6897

CPC classification number: C12Q1/701 ,  C12Q1/6865 ,  C12Q1/6897

Abstract: Provided are signal-inducing CRISPR-sensitive nucleic acid, optionally DNA, sensors, for example comprising: a) a non-functional CRISPR-sensitive DNA reporter construct comprising a non-functional expression cassette with at least one CRISPR target site inserted, generated by removal or addition of nucleic acids or naturally present in the expression cassette, the non-functional expression cassette having a reporter construct upstream end upstream of the CRISPR target site and a reporter construct downstream end downstream of the CRISPR target site, and b) a function-restoring nucleic acid, the function-restoring nucleic acid comprising an upstream flanking end, a function restoring repair insert and a downstream flanking end, wherein the upstream flanking end interfaces with reporter construct upstream end and/or the downstream flanking end interfaces with the reporter construct downstream end and one or both of the flanking ends are capable of permitting insertion or ligation of the function restoring repair insert into/to the reporter construct when the CRISPR target site is actuated under sensing condition, thereby producing a functional DNA reporter construct and sensor signal. Also provided are cell free and cell based systems, kits, primer pairs and molecular barcodes and methods of use thereof.

公开(公告)号：US11920188B2

公开(公告)日：2024-03-05

申请号：US17332837

申请日：2021-05-27

Applicant: Frederick Henry Eggers ,  Benjamin Alan Katchman ,  Fushi Wen ,  Candy Mavis Rivas ,  Cory Scott Newland ,  Michael Edward Hogan

Inventor： Frederick Henry Eggers ,  Benjamin Alan Katchman ,  Fushi Wen ,  Candy Mavis Rivas ,  Cory Scott Newland ,  Michael Edward Hogan

IPC: C12Q1/68 ,  C12Q1/6848 ,  C12Q1/686 ,  C12Q1/6865

CPC classification number: C12Q1/6848 ,  C12Q1/686 ,  C12Q1/6865

Abstract: Provided herein is a method for detecting the presence of clade variants in the COVID-19 virus in a human sample and/or an environmental sample. Samples are processed to obtain total RNA. The RNA is used as a template in a combined reverse transcription and amplification reaction to obtain fluorescent COVID-19 virus amplicons. These amplicons are hybridized on a microarray with nucleic acid probes having sequences that discriminate among the various clade variants. The microarray is imaged to detect the clade variant. Also provided is a method of distinguishing each clade variant from others by generating an intensity distribution profile from the image, which is unique to each of the clade variants.

公开(公告)号：US20240018578A1

公开(公告)日：2024-01-18

申请号：US17863110

申请日：2022-07-12

Applicant: PerkinElmer Health Sciences, Inc.

Inventor： Yanhong Tong ,  Yali Sun ,  Thomas Perroud

IPC: C12Q1/6865 ,  G01N21/64

CPC classification number: C12Q1/6865 ,  G01N21/6428 ,  G01N2021/6439

Abstract: Provided herein are quantitative assays to evaluate duplex unwinding efficiency or strand exchange efficiency during isothermal amplification.

公开(公告)号：US11859246B2

公开(公告)日：2024-01-02

申请号：US16689018

申请日：2019-11-19

Applicant: ACCURAGEN HOLDINGS LIMITED

Inventor： Li Weng ,  Shengrong Lin ,  Lin Fung Tang

IPC: C12Q1/68 ,  C12Q1/6865 ,  C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6874

CPC classification number: C12Q1/6865 ,  C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6874 ,  C12Q2600/156 ,  C12Q2600/16

Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.

公开(公告)号：US11859238B2

公开(公告)日：2024-01-02

申请号：US16241778

申请日：2019-01-07

Applicant: GEN-PROBE INCORPORATED

Inventor： Norman C. Nelson ,  Lyle J. Arnold, Jr. ,  Lizhong Dai ,  Steven Phelps ,  Jijumon Chelliserry

IPC: C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6848 ,  C12Q1/70 ,  C12P19/34 ,  C12Q1/6865 ,  C12Q1/6825

CPC classification number: C12Q1/6806 ,  C12P19/34 ,  C12Q1/68 ,  C12Q1/6825 ,  C12Q1/6848 ,  C12Q1/6865 ,  C12Q1/70 ,  C12Q1/6865 ,  C12Q2537/101 ,  C12Q2545/10

Abstract: Improved methods for use in nucleic acid amplification, including multiplex amplification, where the amplification is carried out in two or more distinct phases are disclosed. The first phase amplification reaction preferably lacks one or more components required for exponential amplification. The lacking component is subsequently provided in a second, third or further phase(s) of amplification, resulting in a rapid exponential amplification reaction. The multiphase protocol results in faster and more sensitive detection and lower variability at low analyte concentrations. Compositions for carrying out the claimed methods are also disclosed.

公开(公告)号：US11773436B2

公开(公告)日：2023-10-03

申请号：US17091639

申请日：2020-11-06

Applicant: Becton, Dickinson and Company

Inventor： Christina Chang ,  Margaret Nakamoto

IPC: C12Q1/6806 ,  C12Q1/6865 ,  C12Q1/6867 ,  C12Q1/6874

CPC classification number: C12Q1/6865 ,  C12Q1/6867 ,  C12Q1/6874 ,  C12Q2521/101 ,  C12Q2521/107 ,  C12Q2565/1025

Abstract: Disclosed herein include systems, methods, compositions, and kits for labeling nucleic acid targets in a sample. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3′ end and are subsequently barcoded on the 5′ end following a template switching reaction and intermolecular and/or intramolecular hybridization and extension. 5′- and/or 3′-barcoded nucleic acid targets can serve as templates for amplification reactions and/or random priming and extension reactions to generate a sequencing library. The method can comprise generating a full-length sequence of the nucleic acid target by aligning a plurality of sequencing reads. Immune repertoire profiling methods are also provided in some embodiments.

公开(公告)号：US20190185911A1

公开(公告)日：2019-06-20

申请号：US16241778

申请日：2019-01-07

Applicant: GEN-PROBE INCORPORATED

Inventor： Norman C. NELSON ,  Lyle J. ARNOLD ,  Lizhong DAI ,  Steven PHELPS ,  Jijumon CHELLISERRY

IPC: C12Q1/6806 ,  C12Q1/6865 ,  C12Q1/6825 ,  C12Q1/6848 ,  C12P19/34 ,  C12Q1/70 ,  C12Q1/68

CPC classification number: C12Q1/6806 ,  C12P19/34 ,  C12Q1/68 ,  C12Q1/6825 ,  C12Q1/6848 ,  C12Q1/6865 ,  C12Q1/70 ,  C12Q2537/101 ,  C12Q2545/10

Abstract: Improved methods for use in nucleic acid amplification, including multiplex amplification, where the amplification is carried out in two or more distinct phases are disclosed. The first phase amplification reaction preferably lacks one or more components required for exponential amplification. The lacking component is subsequently provided in a second, third or further phase(s) of amplification, resulting in a rapid exponential amplification reaction. The multiphase protocol results in faster and more sensitive detection and lower variability at low analyte concentrations. Compositions for carrying out the claimed methods are also disclosed.

公开(公告)号：US20180201967A1

公开(公告)日：2018-07-19

申请号：US15743988

申请日：2016-07-13

Applicant: CureVac AG

Inventor： Fabian Johannes EBER ,  Stefanie SEWING ,  Wenke WAGNER

IPC: C12P19/34 ,  C12N15/52

CPC classification number: C12P19/34 ,  C12N15/52 ,  C12Q1/6865 ,  C12Q2521/119 ,  C12Q2521/337 ,  C12Q2531/125

Abstract: The present invention is concerned with a method of producing a target RNA using a circular DNA, wherein said method does not comprise a step of linearizing said circular DNA. The present invention further relates to a circular DNA comprising an RNA polymerase promoter sequence, followed by a sequence encoding a target RNA, followed by a sequence encoding a self-cleaving ribozyme, followed by an RNA polymerase terminator sequence element, wherein the latter element may comprise several RNA polymerase terminator sequences. Multimeric DNA obtained by rolling circle amplification of said circular DNA is also within the scope of the present invention.

公开(公告)号：US20170342475A1

公开(公告)日：2017-11-30

申请号：US15674468

申请日：2017-08-10

Applicant: Takara Bio USA, Inc.

Inventor： Vladimir L. MAKAROV ,  Emmanuel KAMBEROV ,  Brendan J. TARRIER

IPC: C12Q1/68 ,  C12P19/34 ,  C12N15/10

CPC classification number: C12Q1/6853 ,  C12N15/1068 ,  C12P19/34 ,  C12Q1/6855 ,  C12Q1/686 ,  C12Q1/6865 ,  C12Q2525/301 ,  C12Q2525/119 ,  C12Q2521/301 ,  C12Q2525/191 ,  C12Q2521/501

Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

公开(公告)号：US09777319B2

公开(公告)日：2017-10-03

申请号：US13538955

申请日：2012-06-29

Applicant: John Richard Nelson ,  Robert Scott Duthie ,  Gregory Andrew Grossmann ,  Ryan Charles Heller

Inventor： John Richard Nelson ,  Robert Scott Duthie ,  Gregory Andrew Grossmann ,  Ryan Charles Heller

IPC: C12Q1/68

CPC classification number: C12Q1/6865 ,  C12Q2525/117 ,  C12Q2545/114

Abstract: A method of amplifying RNA template is provided. The method comprises reverse-transcribing a ribonucleic acid (RNA) template to form a cDNA using a first reaction mixture comprising RNA template, at least one primer capable of hybridizing to the RNA template, a reverse transcriptase and deoxynucleoside triphosphates (dNTPs); and amplifying the cDNA to form an amplified product using a second reaction mixture comprising at least one strand displacement DNA polymerase, at least one inosine-containing primer and a nuclease that is capable of nicking DNA 3′ to an inosine residue of the primer. The method is accomplished under an isothermal condition without denaturing the cDNA template. A method of quantifying RNA template in a sample and a method of detecting RNA template in a sample are also provided.