公开(公告)号：US12188011B2

公开(公告)日：2025-01-07

申请号：US17644987

申请日：2021-12-17

Applicant: New England Biolabs, Inc.

Inventor： Gregory Lohman ,  Vladimir Potapov ,  John M. Pryor ,  Rebecca Kucera ,  Katharina Bilotti ,  Richard D. Morgan

IPC: C12N15/10 ,  C12P19/34 ,  C12Q1/6855

Abstract: Ordered assembly of large numbers of fragments into a single large DNA have been improved in both frequency and fidelity of the assembled product. This has been achieved by novel compositions and methods that are utilized in a computer system that integrates comprehensive ligation data from multiple sources to provide optimized synthetic overhangs or overhangs from restriction endonuclease cleavage on DNA fragments for assembly by ligation. Intragenic cut sites are avoided by the use of a novel restriction endonuclease which recognizes 7 nucleotides (bases) and cuts DNA to create 4-base overhangs with the help of a synthetic activator oligonucleotide. Variations in ligation preferences by different ligases provide extra precision in assembly reactions. The use of the improved methods are exemplified by the successful assembly from 52 fragments of a viral genome and also a 52 fragment ordered assembly of a bacteria operon.

公开(公告)号：US12173368B2

公开(公告)日：2024-12-24

申请号：US18298291

申请日：2023-04-10

Applicant: New England Biolabs, Inc.

Inventor： Ivan R. Correa, Jr. ,  Eric Wolf ,  Nan Dai ,  Erbay Yigit ,  Sebastian Grünberg

IPC: C12Q1/6806 ,  C12Q1/6872

Abstract: The present disclosure relates, according to some embodiments, to compositions and analysis of RNA (e.g., dephosphorylated oligoribonucleotides) including, for example, natural and/or synthetic RNAs. A composition may comprise, for example, an endoribonuclease having an amino acid sequence that (i) corresponds to an amino acid sequence of a first species (e.g., Homo sapiens, Escherichia coli, Aspergillus oryzae, Momordica charantia, Pyrococcus furiosus, Cucumis sativus, and Sus scrofa) or (ii) is a non-naturally occurring sequence; and/or an RNA end repair enzyme having an amino acid sequence that (i) corresponds to an amino acid sequence of a species other than the first species (e.g., a bacterial species or a bacteriophage species) or (ii) is a non-naturally occurring sequence.

公开(公告)号：US20240271189A1

公开(公告)日：2024-08-15

申请号：US18615301

申请日：2024-03-25

Applicant: New England Biolabs, Inc.

Inventor： Romualdas Vaisvila ,  Theodore B. Davis ,  Shengxi Guan ,  Zhiyi Sun ,  Laurence Ettwiller ,  Lana Saleh

IPC: C12Q1/6827 ,  C12N9/02 ,  C12N9/78 ,  C12Q1/6806

CPC classification number: C12Q1/6827 ,  C12N9/0071 ,  C12N9/78 ,  C12Q1/6806 ,  C12Y114/11 ,  C12Y305/04005

Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.

公开(公告)号：US20240158870A1

公开(公告)日：2024-05-16

申请号：US18509884

申请日：2023-11-15

Applicant: New England Biolabs, Inc.

Inventor： Chaithanya Ponnaluri ,  Hang-Gyeong Chin ,  Pierre O. Esteve ,  Sriharsa Pradhan

IPC: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6841 ,  C12Q1/6869

CPC classification number: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q2521/301 ,  C12Q2521/331 ,  C12Q2525/117 ,  C12Q2527/156 ,  C12Q2531/119 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/131 ,  C12Q2565/133 ,  C12Q2600/154

Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.

公开(公告)号：US11732315B2

公开(公告)日：2023-08-22

申请号：US17936084

申请日：2022-09-28

Applicant: New England Biolabs, Inc.

Inventor： Nathan Tanner ,  Yinhua Zhang ,  Eric Hunt ,  Gregory Patton ,  Guoping Ren ,  Zhiru Li ,  Andrew Barry ,  Nicole Nichols ,  Catherine B. Poole ,  Harriet M. Strimpel ,  Ivan R. Correa, Jr. ,  Clotilde Carlow ,  Esta Slayton ,  Thomas C. Evans, Jr.

IPC: C12Q1/70 ,  G01N21/78

CPC classification number: C12Q1/701 ,  G01N21/78

Abstract: Compositions and methods are described that are directed to specific and sensitive methods of target nucleic acid detection and more specifically detecting target nucleic acids directly from biological samples. The compositions and methods were developed to be easy to use involving a minimum number of steps and giving rapid and consistent results either at point of care or in high throughput situations. The compositions and methods are directed to labelled probes and their uses in Loop-Mediated Isothermal Amplification (LAMP) diagnostic tests to detect target DNA from the environment or from an individual and also to detect specific variants of the target DNA, both with similar sensitivity. The compositions and methods may use any single improvement or combination of improvements selected from thermolabile enzyme variants, poloxamers, various salts, indicators and one or more LAMP primer sets for detecting single and/or multiple targets, probes for detecting variants of the targets including SARS-CoV-2 variants and lateral flow devices.

公开(公告)号：US20230013384A1

公开(公告)日：2023-01-19

申请号：US17936144

申请日：2022-09-28

Applicant: New England Biolabs, Inc.

Inventor： Guoping Ren ,  Yan Xu ,  Dong Ma ,  Nicole Nichols

IPC: C12N9/12 ,  C12Q1/48 ,  C12Q1/6806 ,  C12Q1/6816 ,  C12Q1/6851 ,  C12Q1/686 ,  C12Q1/6844

Abstract: Provided herein is a reverse transcriptase mixture comprising a reverse transcriptase and a colored dye at a concentration in the range of 0.003%-1% (v/w). The colored dye may be visually observed during transfer of the mix from one vessel to another and addition of the mix to another mix can be confirmed by eye by observing the colored dye.

公开(公告)号：US11525166B2

公开(公告)日：2022-12-13

申请号：US17699950

申请日：2022-03-21

Applicant: New England Biolabs, Inc.

Inventor： Nathan Tanner ,  Yinhua Zhang ,  Eric Hunt ,  Gregory Patton ,  Guoping Ren ,  Zhiru Li ,  Andrew Barry ,  Nicole Nichols ,  Catherine B. Poole ,  Harriet M. Strimpel ,  Ivan R. Correa, Jr. ,  Clotilde Carlow ,  Esta Slayton

IPC: C12Q1/70 ,  G01N21/78

Abstract: Kits and methods are described that are directed to specific and sensitive methods of target nucleic acid detection and more specifically detecting target nucleic acids directly from biological samples. The kits and methods were developed to be easy to use involving a minimum number of steps and giving rapid and consistent results either at point of care or in high throughput situations. The kits and methods utilize in various combinations, reversible inhibitors of kit components, thermolabile enzymes, poloxamers, various salts, indicators and one or more Loop-Mediated Isothermal Amplification (LAMP) primer sets for detecting single and/or multiple targets and variants of the targets including SARS-CoV-2 targets and variants thereof in a single reaction. The kits and methods permit detection of the target nucleic with similar sensitivity regardless of the presence of undefined mutations that may enhance the virulence of cells or viruses containing the undefined mutations.

公开(公告)号：US11492667B2

公开(公告)日：2022-11-08

申请号：US17342216

申请日：2021-06-08

Applicant: New England Biolabs, Inc.

Inventor： Sriharsa Pradhan ,  Hang Gyeong Chin ,  George R. Feehery ,  Shuang-Yong Xu ,  Vishnu Udayakumaran Nair Sunitha Kumary ,  Julie Beaulieu ,  Pierre O. Esteve

IPC: C12Q1/6869 ,  C07K14/31 ,  C12N9/22

Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.

公开(公告)号：US20220213539A1

公开(公告)日：2022-07-07

申请号：US17594534

申请日：2020-04-24

Applicant: New England Biolabs, Inc,

Inventor： Shengxi Guan ,  Sean Maguire

IPC: C12Q1/6855 ,  C12N15/10

Abstract: Compositions and methods of use are provided that among other things, allow for efficient adapter ligation to small RNAs. Embodiments of the compositions include partially double stranded polynucleotides for use as 3′ adapters that contain a cleavable linker positioned between a single-stranded region and a double-stranded region. Upon ligating the 3′ adapters, the single-stranded region is released by cleaving the cleavable linker.

公开(公告)号：US11376338B2

公开(公告)日：2022-07-05

申请号：US16616734

申请日：2018-06-12

Applicant: New England Biolabs, Inc.

Inventor： Bijoyita Roy ,  G. B. Robb

IPC: A61K48/00 ,  C12P19/34 ,  A61K31/713 ,  C12N9/12 ,  A61K31/7105 ,  C12N15/113

Abstract: Provided herein, among other things, is a method for producing an RNA product that has reduced immunogenicity. In some embodiments, the method involves transcribing a template DNA with a thermostable RNA polymerase at a temperature of greater than 44° C.