New England BioLabs, Inc.

United States of America

Back to Profile

1-100 of 195 for New England BioLabs, Inc. Sort by
Query
Patent
United States - USPTO
Aggregations Reset Report
Date
2024 May 4
2024 (YTD) 4
2023 17
2022 18
2021 21
See more
IPC Class
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids 65
C12N 9/22 - Ribonucleases 51
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA 48
C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7) 46
C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides 46
See more
Status
Pending 33
Registered / In Force 162
Found results for  patents
  1     2        Next Page

1.

Analysis of Chromatin Using a Nicking Enzyme

      
Application Number 18509884
Status Pending
Filing Date 2023-11-15
First Publication Date 2024-05-16
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ponnaluri, Chaithanya
  • Chin, Hang-Gyeong
  • Esteve, Pierre O.
  • Pradhan, Sriharsa

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.

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12Q 1/6841 - In situ hybridisation
  • C12Q 1/6869 - Methods for sequencing

2.

Compositions and Methods for Labeling Modified Nucleotides in Nucleic Acids

      
Application Number 18546896
Status Pending
Filing Date 2022-02-17
First Publication Date 2024-05-16
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ettwiller, Laurence
  • Weigele, Peter R.
  • Yang, Weiwei
  • Lee, Yan-Jiun
  • Correa, Jr., Ivan R.

Abstract

Compositions, methods and kits are provided that describe a novel enzyme family called here a hydroxymethylcytosine carbamoyltransferase that transfers a carbamoyl phosphate substrate onto a hydroxymethylcytosine nucleoside triphosphate or a hydroxymethylcytosine in a nucleic acid. The carbamoyl phosphate substrate may be tagged with a chemically reactive group and optionally a functional group. This enables multiple uses of this enzyme and substrate for detecting nucleic acids with modified nucleotides, enriching for such nucleic acids, sequencing nucleic acids containing modified nucleotides, and for synthesizing oligonucleotides with various labels for various molecular biology applications including stabilizing RNA.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 9/10 - Transferases (2.)

3.

TelA variants, compositions, and methods

      
Application Number 18478512
Grant Number 11981936
Status In Force
Filing Date 2023-09-29
First Publication Date 2024-05-14
Grant Date 2024-05-14
Owner New England Biolabs, Inc. (USA)
Inventor
  • Xu, Shuang-Yong
  • Gardner, Andrew F.
  • Heiter, Daniel
  • Hsieh, Pei-Chung
  • Kucera, Rebecca
  • Pan, Juan

Abstract

The present disclosure relates, according to some embodiments, to telomere resolvases (e.g., TelA variants) having a turnover number over 1.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6844 - Nucleic acid amplification reactions

4.

RNase Inhibitors

      
Application Number 18509899
Status Pending
Filing Date 2023-11-15
First Publication Date 2024-05-09
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Ong, Jennifer
  • Slayton, Esta
  • Maduzia, Lisa L.
  • Russello, Salvatore V.

Abstract

Compositions, methods and kits are provided that include an inhibitory oligonucleotide RNase inhibitor capable of inhibiting one or more types of RNase that coexist with biological samples or are introduced in the laboratory, thereby protecting RNA in the sample from degradation. More than one type of oligonucleotide RNase inhibitor may be combined in a mixture to inhibit a plurality of different RNases. Single oligonucleotides were identified to have inhibitory activity for a plurality of different RNases. The RNase oligonucleotide inhibitor may be immobilized on beads or other surface. It may be stored in a lyophilized form or in solution.

IPC Classes  ?

  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction

5.

Vaccinia Capping Enzyme Compositions and Methods

      
Application Number 18462868
Status Pending
Filing Date 2023-09-07
First Publication Date 2023-12-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vainauskas, Saulius
  • Chan, Siu-Hong
  • Taron, Christopher H.

Abstract

The present disclosure relates, according to some embodiments, to compositions, methods, and/or kits for producing vaccinia capping enzyme. For example, active, heterodimers of vaccinia capping enzyme may be produced as fusions comprising D1 and D12 subunits. Vaccinia capping enzyme fusion proteins may further comprise a linker.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 15/81 - Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts

6.

FCE MRNA CAPPING ENZYME COMPOSITIONS, METHODS AND KITS

      
Application Number 18340083
Status Pending
Filing Date 2023-06-23
First Publication Date 2023-12-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ganatra, Mehul
  • Chan, Siu-Hong
  • Taron, Christopher H.
  • Robb, G. Brett

Abstract

The present disclosure relates to compositions, kits, and methods of making RNA vaccines having an appropriate cap structure. Systems, apparatus, compositions, and/or methods may include and/or use, in some embodiments, non-naturally occurring single-chain RNA capping enzymes. In some embodiments, an RNA capping enzyme may include an FCE variant having (a) an amino acid sequence at least 90% identical to positions 1 to 878 of SEQ ID NO: 1, and/or (b) one or more substitutions relative to SEQ ID NO: 1 at a position selected from positions corresponding to positions 215, 337, 572, 648, and 833 (e.g., a position selected from positions corresponding to position 215, 337, and 572) of SEQ ID NO: 1.

IPC Classes  ?

  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 9/10 - Transferases (2.)
  • A61K 39/245 - Herpetoviridae, e.g. herpes simplex virus
  • C12N 7/00 - Viruses, e.g. bacteriophages; Compositions thereof; Preparation or purification thereof

7.

Rapid Diagnostic Test for LAMP

      
Application Number 18452104
Status Pending
Filing Date 2023-08-18
First Publication Date 2023-12-21
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Hunt, Eric
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Barry, Andrew
  • Nichols, Nicole
  • Poole, Catherine B.
  • Strimpel, Harriet M.
  • Correa, Jr., Ivan R.
  • Carlow, Clotilde
  • Slayton, Esta
  • Evans, Jr., Thomas C.

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.

IPC Classes  ?

  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour

8.

RNase inhibitors

      
Application Number 17207507
Grant Number 11827885
Status In Force
Filing Date 2021-03-19
First Publication Date 2023-11-28
Grant Date 2023-11-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Ong, Jennifer
  • Slayton, Esta
  • Maduzia, Lisa
  • Russello, Salvatore V.

Abstract

Compositions, methods and kits are provided that include an inhibitory oligonucleotide RNase inhibitor capable of inhibiting one or more types of RNase that coexist with biological samples or are introduced in the laboratory, thereby protecting RNA in the sample from degradation. More than one type of oligonucleotide RNase inhibitor may be combined in a mixture to inhibit a plurality of different RNases. Single oligonucleotides were identified to have inhibitory activity for a plurality of different RNases. The RNase oligonucleotide inhibitor may be immobilized on beads or other surface. It may be stored in a lyophilized form or in solution.

IPC Classes  ?

  • C12N 15/11 - DNA or RNA fragments; Modified forms thereof
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
  • C12N 9/58 - Proteinases derived from fungi

9.

Double-Stranded DNA Deaminases and Uses Thereof

      
Application Number 18323143
Status Pending
Filing Date 2023-05-24
First Publication Date 2023-11-09
Owner New England Biolabs, Inc. (USA)
Inventor
  • Sun, Zhiyi
  • Johnson, Sean R.
  • Yan, Bo
  • Chen, Lixin
  • Robb, G. Brett
  • Evans, Jr., Thomas C.
  • Vaisvila, Romualdas

Abstract

Provided herein, among other things, is a method for deaminating a double-stranded nucleic acid. In some embodiments, the method may comprise contacting a double-stranded DNA substrate that comprises cytosines and a double-stranded DNA deaminase having an amino acid sequence that is at least 80% identical to any of SEQ ID NOS: 21, 40, 47, 49, 50, 55, 58, 59, 62, 63, 65, 67, 70, 71, 76, 106, 107, 110, 112, 114, 117, 163 and/or 164 to produce a deamination product that comprises deaminated cytosines. Enzymes and kits for performing the method are also provided.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12N 9/10 - Transferases (2.)
  • C12N 9/78 - Hydrolases (3.) acting on carbon to nitrogen bonds other than peptide bonds (3.5)

10.

Compositions and Analysis of Dephosphorylated Oligoribonucleotides

      
Application Number 18298291
Status Pending
Filing Date 2023-04-10
First Publication Date 2023-09-14
Owner New England Biolabs, Inc. (USA)
Inventor
  • Correa, Jr., Ivan R.
  • Wolf, Eric
  • Dai, Nan
  • Yigit, Erbay
  • Grünberg, Sebastian

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.

IPC Classes  ?

  • C12Q 1/6872 - Methods for sequencing involving mass spectrometry

11.

IMMOBILIZED ENZYME COMPOSITIONS AND METHODS

      
Application Number 18182122
Status Pending
Filing Date 2023-03-10
First Publication Date 2023-09-14
Owner New England Biolabs, Inc. (USA)
Inventor
  • Xu, Ming-Qun
  • García-Marquina, Guillermo
  • Chan, Siu-Hong
  • Correa, Jr., Ivan R.
  • Zhang, Aihua
  • Fang, Yi
  • Sproviero, Michael

Abstract

The present disclosure relates, according to some embodiments, to immobilized enzyme compositions and methods for cleaving polynucleotide molecules including, for example, double-stranded DNA. Immobilized enzymes may comprise, for example, an enzyme (e.g., a type IIS restriction endonuclease, an RNAP, a capping enzyme), a support (e.g., a magnetic bead), and optionally, a linker disposed between the enzyme and the support. In some embodiments, methods may include contacting an immobilized enzyme with a polynucleotide substrate to form reaction products, separating the immobilized enzyme from the reaction products, and optionally reusing the immobilized enzymes in one or more subsequent reactions. preparing a library for sequencing. For example, a method may comprise (a) in a coupled reaction, (i) contacting a population of nucleic acid fragments with a tailing enzyme to produce tailed fragments, and (ii) ligating to the tailed fragments a sequencing adapter with a ligase to produce adapter-tagged fragments; and/or separating adapter-tagged fragments from the tailing enzyme and the ligase to produce separated adapter-tagged fragments and, optionally, separated tailing enzyme and/or separated ligase.

IPC Classes  ?

12.

Double-Stranded DNA Deaminases

      
Application Number 18058115
Status Pending
Filing Date 2022-11-22
First Publication Date 2023-08-17
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Johnson, Sean R.
  • Sun, Zhiyi
  • Evans, Jr., Thomas C.

Abstract

Provided herein, among other things, is a method for deaminating a double-stranded nucleic acid. In some embodiments, the method may comprise contacting a double-stranded DNA substrate that comprises cytosines and a double-stranded DNA deaminase having an amino acid sequence that is at least 80% identical to any of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 19, 24, 26, 27, 28, 33, 40, 49, 50, 63, 95, 96, 97, and/or 99 to produce a deamination product that comprises deaminated cytosines. Enzymes and kits for performing the method are also provided.

IPC Classes  ?

  • C12N 9/78 - Hydrolases (3.) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

13.

Fragmentation of DNA

      
Application Number 18305745
Status Pending
Filing Date 2023-04-24
First Publication Date 2023-08-17
Owner New England Biolabs, Inc. (USA)
Inventor
  • Apone, Lynne
  • Sexton, Brittany S.
  • Heider, Margaret
  • Williams, Louise Js
  • Dimalanta, Eileen T.

Abstract

Provided herein is a polymerase-free enzyme mix (FRAG) for fragmenting double-stranded DNA. In some embodiments the enzyme mix may comprise a double-stranded DNA nickase and at least one of a DNA ligase capable of sealing a nick within a DNA, and a single-strand specific DNA nuclease. Methods for fragmenting double-stranded DNA are also provided.

IPC Classes  ?

14.

Isolation of High Molecular Weight DNA Using Beads

      
Application Number 18155975
Status Pending
Filing Date 2023-01-18
First Publication Date 2023-05-18
Owner New England Biolabs, Inc. (USA)
Inventor
  • Koetsier, Paul A.
  • Taron, Barbara W.
  • Cantor, Eric J.

Abstract

Provided herein is a method for isolating high molecular weight (HMW) DNA using beads that are at least 200 μm in diameter that utilizes a device for retaining the beads and where the purified DNA eluant exits the device without shearing the HMW DNA. In some embodiments, the method comprises precipitating the DNA onto the beads, washing the beads in the device, and then eluting the DNA from the beads therein while substantially avoiding shear. Compositions and kits for practicing the method are also provided.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • B01L 9/06 - Test-tube stands; Test-tube holders

15.

Rolling Circle Reverse Transcription of Circular RNA

      
Application Number 17820372
Status Pending
Filing Date 2022-08-17
First Publication Date 2023-05-11
Owner New England Biolabs, Inc. (USA)
Inventor
  • Guan, Shengxi
  • Maguire, Sean
  • Xu, Yan
  • Unlu, Irem

Abstract

Compositions, methods and kits are provided that enable the detection, analysis and/or sequencing of small or large target RNA molecules whether synthetic, purified or within a biological fluid, or in cell lysate that may contain non-target RNA and other contaminating molecules without the need for depletion or purification steps that diminish what might already be low concentrations of the target molecule. The methods, compositions and kits rely on the use of a Group II Intron reverse transcriptase (Intron-RT) that have strand displacing properties and can generate concatemers in cDNA by rolling circle transcription of circRNAs that may be naturally circular or circularized in vitro from linear RNA.

IPC Classes  ?

  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction

16.

Compositions and Methods for Detecting Molecular Targets on Chromosomal DNA

      
Application Number 17907482
Status Pending
Filing Date 2021-06-08
First Publication Date 2023-04-20
Owner New England Biolabs, Inc. (USA)
Inventor
  • Pradhan, Sriharsa
  • Chin, Hang Gyeong
  • Feehery, George R.
  • Xu, Shuang-Yong
  • Udayakumaran Nair Sunitha Kumary, Vishnu
  • Beaulieu, Julie

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.

IPC Classes  ?

17.

Compositions and Methods for Detecting Molecular Targets on Chromosomal DNA

      
Application Number 17933943
Status Pending
Filing Date 2022-09-21
First Publication Date 2023-03-23
Owner New England Biolabs, Inc. (USA)
Inventor
  • Pradhan, Sriharsa
  • Chin, Hang Gyeong
  • Feehery, George R.
  • Xu, Shuang-Yong
  • Udayakumaran Nair Sunitha Kumary, Vishnu
  • Beaulieu, Julie
  • Esteve, Pierre O.

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.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C07K 14/31 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F) from Staphylococcus (G)
  • C12N 9/22 - Ribonucleases

18.

Rapid diagnostic test for lamp

      
Application Number 17936084
Grant Number 11732315
Status In Force
Filing Date 2022-09-28
First Publication Date 2023-02-16
Grant Date 2023-08-22
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Hunt, Eric
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Barry, Andrew
  • Nichols, Nicole
  • Poole, Catherine B.
  • Strimpel, Harriet M.
  • Correa, Jr., Ivan R.
  • Carlow, Clotilde
  • Slayton, Esta
  • Evans, Jr., Thomas C.

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.

IPC Classes  ?

  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour

19.

Methods for Labeling a Population of RNA Molecules

      
Application Number 17932136
Status Pending
Filing Date 2022-09-14
First Publication Date 2023-01-26
Owner New England Biolabs, Inc. (USA)
Inventor
  • Schildkraut, Ira
  • Ettwiller, Laurence
  • Correa, Jr., Ivan R.
  • Tzertzinis, George
  • Buswell, John
  • Wulf, Madalee G.

Abstract

A method of labeling, and optionally enriching, for a population of target RNA molecules in a mixture of RNAs is provided. In some embodiments, the method may comprise (a) adding a label to the 5′ end of 5′-diphosphorylated or 5′-triphosphorylated target RNA molecules in a sample by incubating the sample with labeled GTP and a capping enzyme; and (b) optionally enriching for target RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag. The label may be an oligonucleotide, which may further comprise an affinity group attached either internally or at 5′ or 3′ end of the oligonucleotide where the oligonucleotide label may be added directly, or indirectly via a reaction with a reactive group to the target RNA.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

20.

High Throughput Reaction Assembly

      
Application Number 17936144
Status Pending
Filing Date 2022-09-28
First Publication Date 2023-01-19
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ren, Guoping
  • Xu, Yan
  • Ma, Dong
  • Nichols, Nicole

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.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6816 - Hybridisation assays characterised by the detection means
  • C12Q 1/6851 - Quantitative amplification
  • C12Q 1/686 - Polymerase chain reaction [PCR]
  • C12Q 1/6844 - Nucleic acid amplification reactions

21.

Vitro Cleavage of DNA Using Argonaute

      
Application Number 17930079
Status Pending
Filing Date 2022-09-07
First Publication Date 2023-01-05
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Hunt, Eric

Abstract

Methods, kits and compositions, in some embodiments, may include a thermostable DNA guided Argonaute protein for example TtAgo, a thermostable single-stranded DNA binding protein (SSB) for example, extreme thermostable single-stranded DNA binding protein (ET SSB), and, optionally, a strand-displacing polymerase. A SSB may allow (a) Argonaute/guide DNA complexes to substantially enhance cleavage efficiency of single- and double-stranded DNA substrates; (b) the use of longer guide DNAs (e.g., guide DNAs that are at least 24 nucleotides in length) and/or (c) increases in the sequence specificity of Argonaute-mediated binding and cleavage reactions.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C07K 14/195 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
  • C12N 9/22 - Ribonucleases
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 15/90 - Stable introduction of foreign DNA into chromosome
  • C12N 15/11 - DNA or RNA fragments; Modified forms thereof

22.

Programmable Cleavage of Double-Stranded DNA

      
Application Number 17335500
Status Pending
Filing Date 2021-06-01
First Publication Date 2022-12-01
Owner New England Biolabs, Inc. (USA)
Inventor
  • Bitinaite, Jurate
  • Vaiskunaite, Rita
  • Potapov, Vladimir
  • Tanner, Nathan

Abstract

The present disclosure relates, according to some embodiments, to compositions, methods, systems, and kits for programmable endonucleolytic cleavage of DNA (e.g., ds DNA). For example, the in vitro activity of an Argonaute (e.g., a mesophilic Argonaute CbAgo from Clostridium butyricum) may be synchronized with DNA strand unwinding activity of a helicase (e.g., a nuclease deficient RecBexo-C DNA helicase from E. coli) for a rapid and efficient cleavage of double-stranded DNA targets. Enzymatic properties of CbAgo and different aspects of ds DNA cleavage were thoroughly explored by adapting high-throughput capillary electrophoreses technique for monitoring CbAgo cleavage activity in concurrence with RecBexo-C. The present disclosure shows that in the presence of RecBexo-C, CbAgo can be programmed with guides to cleave any site of interest localized at up to 10 kb distance from the end of linear ds DNA at 37° C. temperature. CbAgo/RecBexo-C can be programmed to generate DNA fragments flanked with unique single-stranded extensions suitable for seamless ligation with compatible DNA fragments. The present disclosure relates further the compositions, methods, systems, and kits for PRC-free assembly of linear DNA molecules by using CbAgo/RecBexo-C programmable DNA endonuclease. The results presented here demonstrate that the combination of CbAgo and RecBexo-C is currently an efficient mesophilic DNA-guided DNA-cleaving programmable endonuclease which can be used to prepare synthetic biology tools that require or benefit from sequence-specific nicking/cleavage of natural DNA at otherwise inaccessible locations.

IPC Classes  ?

  • C12N 9/14 - Hydrolases (3.)
  • C07K 14/195 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
  • C12N 15/11 - DNA or RNA fragments; Modified forms thereof
  • C12N 15/90 - Stable introduction of foreign DNA into chromosome

23.

DNase I variants, compositions, methods, and kits

      
Application Number 17332821
Grant Number 11993792
Status In Force
Filing Date 2021-05-27
First Publication Date 2022-12-01
Grant Date 2024-05-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Crosby, Heidi
  • Ong, Jennifer
  • Luck, Ashley
  • Cantor, Eric J.
  • Potapov, Vladimir

Abstract

The present disclosure relates, according to some embodiments, to systems, apparatus, compositions, methods, and workflows that include DNase I variants with desirable properties including, for example, salt tolerance. A DNase I variant, in some embodiments, may have an amino acid sequence that is at least 85% identical, at least 90% identical, at least 95% identical, and/or at least 98% identical to SEQ ID NO:1 and may be identical to SEQ ID NO:1 at one or more positions selected from the group of positions corresponding to L29, A35, D87, Q88, S94, P103, T108, P121, P132, A135, D145, E161, G172, P190, H208, and A224 of SEQ ID NO:1.

IPC Classes  ?

  • C12N 9/22 - Ribonucleases
  • C07K 14/47 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from humans from vertebrates from mammals

24.

Fragmentation of DNA

      
Application Number 17658485
Grant Number 11667968
Status In Force
Filing Date 2022-04-08
First Publication Date 2022-12-01
Grant Date 2023-06-06
Owner New England Biolabs, Inc. (USA)
Inventor
  • Apone, Lynne
  • Sexton, Brittany S.
  • Heider, Margaret
  • Williams, Louise J S
  • Dimalanta, Eileen T.

Abstract

Provided herein is a polymerase-free enzyme mix (FRAG) for fragmenting double-stranded DNA. In some embodiments the enzyme mix may comprise a double-stranded DNA nickase and at least one of a DNA ligase capable of sealing a nick within a DNA, and a single-strand specific DNA nuclease. Methods for fragmenting double-stranded DNA are also provided.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6855 - Ligating adaptors
  • C12Q 1/686 - Polymerase chain reaction [PCR]
  • C40B 20/04 - Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
  • C40B 50/06 - Biochemical methods, e.g. using enzymes or whole viable microorganisms

25.

Compositions and methods for detecting pyrophosphate products of enzyme reactions using pyridylazoaniline dyes

      
Application Number 17661954
Grant Number 11512342
Status In Force
Filing Date 2022-05-04
First Publication Date 2022-11-29
Grant Date 2022-11-29
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Correa, Jr., Ivan R.
  • Zhang, Yinhua
  • Alpaslan, Ece

Abstract

Provided herein is a composition comprising an enzyme that releases pyrophosphate from a substrate and a dye of Formula 1. A method for detecting pyrophosphate is also provided. A kit comprising a polymerase that releases pyrophosphate by hydrolysis of nucleoside triphosphates during nucleic acid replication, a divalent manganese salt, and the dye are also provided. The present composition, method and kits provide a way to detect and/or quantify substrates or products of enzyme reacted substrates associated with the release pyrophosphate (e.g., nucleic acid amplification reactions and other reactions that hydrolyze ATP) via a distinct color change without substantially affecting the sensitivity and/or specificity of the reaction.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/6816 - Hybridisation assays characterised by the detection means
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes

26.

Compositions and Methods Relating to Synthetic RNA Polynucleotides Created From Synthetic DNA Oligonucleotides

      
Application Number 17846620
Status Pending
Filing Date 2022-06-22
First Publication Date 2022-10-20
Owner New England Biolabs, Inc. (USA)
Inventor
  • Robb, G. B.
  • Meek, Isaac B.
  • Schwarz, Dianne S.
  • Schildkraut, Ezra

Abstract

Compositions and methods are provided for forming a single RNA polynucleotide from a plurality of DNA oligonucleotides in a single reaction chamber using combined reagents in a single step reaction. DNA polymerase, RNA polymerase and single stranded (ss) DNA oligonucleotides are combined where each DNA oligonucleotide has one or more sequence modules, wherein one sequence module in the first ss DNA oligonucleotide is complementary to a sequence module at the 3′ end of the second ss DNA oligonucleotide; and wherein a second module on the first ss DNA oligonucleotide is an RNA polymerase promoter sequence; and forming a single RNA polynucleotide, excluding the RNA promoter sequence, derived from the first and second DNA oligonucleotides

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12N 9/22 - Ribonucleases
  • C12N 9/96 - Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates
  • C12N 15/115 - Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith

27.

Method for Removing and/or Detecting Nucleic Acids Having Mismatched Nucleotides

      
Application Number 17825346
Status Pending
Filing Date 2022-05-26
First Publication Date 2022-09-29
Owner New England Biolabs, Inc. (USA)
Inventor Gardner, Andrew F.

Abstract

Provided herein, among other things, are various in vitro methods that involve cleaving dsDNA molecules that comprise a mismatched nucleotide using EndoMS. In some embodiments, the method may comprise ligating a T-tailed double-stranded adapter to A-tailed double-stranded fragments of nucleic acid to produce ligation products that comprise adapter-ligated fragments and double-stranded adapter dimers that comprise a T:T mismatch at the ligation junction and cleaving both strands of the adapter dimers using EndoMS.

IPC Classes  ?

  • C12Q 1/6855 - Ligating adaptors
  • C12N 9/22 - Ribonucleases
  • C12N 9/00 - Enzymes, e.g. ligases (6.); Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating, or purifying enzymes
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]

28.

Application of Immobilized Enzymes for Nanopore Library Construction

      
Application Number 17828574
Status Pending
Filing Date 2022-05-31
First Publication Date 2022-09-22
Owner New England Biolabs, Inc. (USA)
Inventor
  • Xu, Ming-Qun
  • Fang, Yi
  • Zhang, Aihua
  • Sun, Luo

Abstract

The present disclosure relates, according to some embodiments, to methods for preparing a library for sequencing. For example, a method may comprise (a) in a coupled reaction, (i) contacting a population of nucleic acid fragments with a tailing enzyme to produce tailed fragments, and (ii) ligating to the tailed fragments a sequencing adapter with a ligase to produce adapter-tagged fragments; and/or separating adapter-tagged fragments from the tailing enzyme and the ligase to produce separated adapter-tagged fragments and, optionally, separated tailing enzyme and/or separated ligase. In some embodiments, a tailing enzyme and/or a ligase used in library preparation may be immobilized enzymes.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6869 - Methods for sequencing

29.

Use of Thermostable RNA Polymerases to Produce RNAs Having Reduced Immunogenicity

      
Application Number 17826946
Status Pending
Filing Date 2022-05-27
First Publication Date 2022-09-15
Owner New England Biolabs, Inc. (USA)
Inventor
  • Roy, Bijoyita
  • Robb, G. B.

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.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • A61K 31/713 - Double-stranded nucleic acids or oligonucleotides
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • A61K 31/7105 - Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides

30.

Cleavage of Single Stranded DNA Having a Modified Nucleotide

      
Application Number 17637430
Status Pending
Filing Date 2020-08-21
First Publication Date 2022-09-08
Owner New England Biolabs, Inc. (USA)
Inventor
  • Gardner, Andrew F.
  • Zatopek, Kelly M.

Abstract

Methods are provided that, for example, include (a) combining ssDNA containing a modified nucleotide (e.g., a ssDNA with a modified nucleotide proximate to its 5′ end) with a DNA cleavage enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate a first ssDNA fragment having a 3′OH and a second ssDNA fragment having the modified nucleotide); wherein the ratio of enzyme to DNA substrate is less than 1:1 molar ratio (m/m); and (b) cleaving at least 95% of the ssDNA at the modified nucleotide. In some embodiments, a method may comprise (a) combining (i) a ssDNA comprising a modified nucleotide (e.g., proximate to its 5′ end) with (ii) a DNA cleavage enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate (after cleavage) a first ssDNA fragment having a 3′OH and a second ssDNA fragment comprising the modified nucleotide) wherein the ratio of enzyme to DNA substrate is less than 1:1 molar ratio and cleaving at least 95% of the ssDNA at the modified nucleotide. In some embodiments, methods provided herein may include (a) combining (i) a ssDNA (1) immobilized on a substrate and (2) comprising a modified nucleotide with (ii) a ssDNA cleaving enzyme capable of cleaving the ssDNA at the modified nucleotide (e.g., to generate (after cleavage) a first ssDNA fragment having a 3′OH and a second ssDNA fragment comprising the modified nucleotide) ; and (b) cleaving the immobilized ssDNA to release the second single stranded DNA fragment from the substrate. At least 95% (m/m) of an ssDNA comprising a modified nucleotide may be cleaved in less than 60 minutes.

IPC Classes  ?

  • C12N 9/22 - Ribonucleases
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 9/24 - Hydrolases (3.) acting on glycosyl compounds (3.2)
  • C07K 1/10 - General processes for the preparation of peptides using coupling agents

31.

Thermostable Variants of T7 RNA Polymerase

      
Application Number 17742033
Status Pending
Filing Date 2022-05-11
First Publication Date 2022-09-01
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ong, Jennifer
  • Potapov, Vladimir
  • Hung, Kuo-Chan
  • Asahara, Haruichi
  • Chong, Shaorong
  • Tzertzinis, George

Abstract

A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6858 - Allele-specific amplification

32.

FCE mRNA capping enzyme compositions, methods and kits

      
Application Number 17377797
Grant Number 11725196
Status In Force
Filing Date 2021-07-16
First Publication Date 2022-07-28
Grant Date 2023-08-15
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ganatra, Mehul
  • Chan, Siu-Hong
  • Taron, Christopher H.
  • Robb, G. B.

Abstract

The present disclosure relates to compositions, kits, and methods of making RNA vaccines having an appropriate cap structure. Systems, apparatus, compositions, and/or methods may include and/or use, in some embodiments, non-naturally occurring single-chain RNA capping enzymes. In some embodiments, an RNA capping enzyme may include an FCE variant having (a) an amino acid sequence at least 90% identical to positions 1 to 878 of SEQ ID NO: 1, and/or (b) one or more substitutions relative to SEQ ID NO: 1 at a position selected from positions corresponding to positions 215, 337, 572, 648, and 833 (e.g., a position selected from positions corresponding to position 215, 337, and 572) of SEQ ID NO: 1.

IPC Classes  ?

  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • A61K 39/245 - Herpetoviridae, e.g. herpes simplex virus
  • C12N 7/00 - Viruses, e.g. bacteriophages; Compositions thereof; Preparation or purification thereof
  • C12N 9/10 - Transferases (2.)
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • C07K 14/005 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses

33.

Methods and Enzymatic Compositions for Forming Libraries of Adapter Ligated Nucleic Acid Molecules

      
Application Number 17594534
Status Pending
Filing Date 2020-04-24
First Publication Date 2022-07-07
Owner New England Biolabs, Inc, (USA)
Inventor
  • Guan, Shengxi
  • Maguire, Sean

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.

IPC Classes  ?

  • C12Q 1/6855 - Ligating adaptors
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

34.

Rapid diagnostic test for LAMP

      
Application Number 17699950
Grant Number 11525166
Status In Force
Filing Date 2022-03-21
First Publication Date 2022-07-07
Grant Date 2022-12-13
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Hunt, Eric
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Barry, Andrew
  • Nichols, Nicole
  • Poole, Catherine B.
  • Strimpel, Harriet M.
  • Correa, Jr., Ivan R.
  • Carlow, Clotilde
  • Slayton, Esta

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.

IPC Classes  ?

  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour

35.

Chemical Capping for Template Switching

      
Application Number 17610081
Status Pending
Filing Date 2020-05-06
First Publication Date 2022-06-23
Owner New England Biolabs, Inc. (USA)
Inventor
  • Correa, Jr., Ivan R.
  • Guan, Shengxi
  • Wulf, Madalee G.
  • Dai, Nan
  • Maguire, Sean

Abstract

Provided herein is a method for chemically capping polynucleotides having a 5′ monophosphate. In some embodiments the method may comprise: combining an activated nucleoside 5′ mono- or poly-phosphate with a population of polynucleotides that comprises polynucleotides having a 5′ monophosphate, to produce a reaction mix; and incubating the reaction mix to produce reaction products that comprise a polynucleotide and a 5′ nucleoside cap, linked by a 5′ to 5′ polyphosphate linkage. The chemical capping method described herein can be incorporated into a variety of cDNA synthesis methods.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

36.

Compositions and Methods for Improved In Vitro Assembly of Polynucleotides

      
Application Number 17644987
Status Pending
Filing Date 2021-12-17
First Publication Date 2022-06-09
Owner NEW ENGLAND BIOLABS, INC. (USA)
Inventor
  • Lohman, Gregory
  • Potapov, Vladimir
  • Pryor, John M.
  • Kucera, Rebecca
  • Bilotti, Katharina
  • Morgan, Richard D.

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.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6855 - Ligating adaptors

37.

Ordered Assembly of Multiple DNA Fragments

      
Application Number 17644516
Status Pending
Filing Date 2021-12-15
First Publication Date 2022-03-31
Owner NEW ENGLAND BIOLABS, INC. (USA)
Inventor
  • Lohman, Gregory
  • Pryor, John M.
  • Kucera, Rebecca
  • Potapov, Vladimir
  • Bilotti, Katharina
  • Morgan, Richard D.

Abstract

A composition and its uses and additionally a kit are provided. The composition is a synthetic self-complementary oligonucleotide that has a double-stranded region and a loop, wherein the double-stranded region contains a binding sequence for PaqCl. Additionally, the oligonucleotide includes unligatable 3′ and 5′ ends that cannot be cleaved by PaqCl. This oligonucleotide composition has been combined with PaqCl or a variant of PaqCl Type IIS restriction endonuclease in a reaction mixture, where the reaction mixture includes PaqCl or variant that can further be combined with a ligase and optionally a deadenylase, crowding molecule such as PEG and/or a repair enzyme such as Endo MS. The kit includes the oligonucleotide and Type IIS restriction endonuclease in the same or different containers.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6869 - Methods for sequencing

38.

Application of immobilized enzymes for nanopore library construction

      
Application Number 17018862
Grant Number 11377654
Status In Force
Filing Date 2020-09-11
First Publication Date 2022-03-24
Grant Date 2022-07-05
Owner New England Biolabs, Inc. (USA)
Inventor
  • Xu, Ming-Qun
  • Fang, Yi
  • Zhang, Aihua
  • Sun, Luo

Abstract

The present disclosure relates, according to some embodiments, to methods for preparing a library for sequencing. For example, a method may comprise (a) in a coupled reaction, (i) contacting a population of nucleic acid fragments with a tailing enzyme to produce tailed fragments, and (ii) ligating to the tailed fragments a sequencing adapter with a ligase to produce adapter-tagged fragments; and/or separating adapter-tagged fragments from the tailing enzyme and the ligase to produce separated adapter-tagged fragments and, optionally, separated tailing enzyme and/or separated ligase. In some embodiments, a tailing enzyme and/or a ligase used in library preparation may be immobilized enzymes.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6869 - Methods for sequencing

39.

Analysis of chromatin using a nicking enzyme

      
Application Number 17454082
Grant Number 11840741
Status In Force
Filing Date 2021-11-09
First Publication Date 2022-02-24
Grant Date 2023-12-12
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ponnaluri, Chaithanya
  • Chin, Hang-Gyeong
  • Esteve, Pierre O.
  • Pradhan, Sriharsa

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6841 - In situ hybridisation
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism

40.

Rapid diagnostic test for LAMP

      
Application Number 17406959
Grant Number 11345970
Status In Force
Filing Date 2021-08-19
First Publication Date 2021-12-30
Grant Date 2022-05-31
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Hunt, Eric
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Barry, Andrew
  • Nichols, Nicole
  • Poole, Catherine B.
  • Strimpel, Harriet M.
  • Correa, Jr., Ivan R.
  • Carlow, Clotilde
  • Slayton, Esta

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.

IPC Classes  ?

  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour
  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage

41.

Vaccinia capping enzyme compositions and methods

      
Application Number 17348127
Grant Number 11788074
Status In Force
Filing Date 2021-06-15
First Publication Date 2021-12-23
Grant Date 2023-10-17
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vainauskas, Saulius
  • Chan, Siu-Hong
  • Taron, Christopher H.

Abstract

The present disclosure relates, according to some embodiments, to compositions, methods, and/or kits for producing vaccinia capping enzyme. For example, active, heterodimers of vaccinia capping enzyme may be produced as fusions comprising D1 and D12 subunits. Vaccinia capping enzyme fusion proteins may further comprise a linker.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 15/81 - Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts
  • C12R 1/84 - Pichia

42.

Compositions and methods for detecting molecular targets on chromosomal DNA

      
Application Number 17342216
Grant Number 11492667
Status In Force
Filing Date 2021-06-08
First Publication Date 2021-12-16
Grant Date 2022-11-08
Owner New England Biolabs, Inc. (USA)
Inventor
  • Pradhan, Sriharsa
  • Chin, Hang Gyeong
  • Feehery, George R.
  • Xu, Shuang-Yong
  • Udayakumaran Nair Sunitha Kumary, Vishnu
  • Beaulieu, Julie
  • Esteve, Pierre O.

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.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C07K 14/31 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F) from Staphylococcus (G)
  • C12N 9/22 - Ribonucleases

43.

Improved Ordered Assembly of Multiple DNA Fragments

      
Application Number 17286066
Status Pending
Filing Date 2019-10-17
First Publication Date 2021-12-09
Owner New England Biolabs, Inc. (USA)
Inventor
  • Lohman, Gregory
  • Potapov, Vladimir
  • Pryor, John M.
  • Kucera, Rebecca

Abstract

Methods and compositions are provided for optimizing ordered assembly of a plurality of polynucleotide fragments. The optimization involves providing sets of overhang sequences with preferred experimental conditions for high fidelity ordered assembly of polynucleotide fragments by ligation under selected experimental conditions. The methods and compositions provide the use of a computer system with inputs having a plurality of menus and outputs that include a variety of media interfaces. The computer system has access to a ligation frequency database to provide sets of overhang sequences for efficient joining of multiple fragments into the target nucleic acid. In-puts include one or more of the following: numbers and sizes of fragments, optionally a desired target polynucleotide sequence from a database, in which case one output are the recommended polynucleotide fragments for ordered assembly, and selected experimental conditions selected from any or all of ligation protocols and ligation temperature with reaction times, salt concentration in the ligation buffer, choice of ligase and restriction endonuclease and the use of DNA repair enzymes.

IPC Classes  ?

  • G16B 30/20 - Sequence assembly
  • C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
  • G16B 50/30 - Data warehousing; Computing architectures

44.

Method for fragmenting DNA by nick translation

      
Application Number 17243707
Grant Number 11802304
Status In Force
Filing Date 2021-04-29
First Publication Date 2021-09-23
Grant Date 2023-10-31
Owner New England Biolabs, Inc. (USA)
Inventor
  • Guan, Chudi
  • Yan, Bo

Abstract

Providing herein, among other things, are kits, compositions and methods that relate to DNA fragmentation. An embodiment of a composition provides combining: one or more enzymes capable of nick translating activity, a dNTP mix comprising at least one dNTP having a modified base, and at least one modification-sensitive nicking endonuclease that is prevented from nicking DNA if its recognition site contains the modified base. When the composition is added to a sample comprising a double-stranded DNA template that comprises recognition sites for the modification-sensitive nicking endonuclease, a reaction mix was produced which could be incubated for any time period in excess of about 5 minutes to produce fragments of a desired size of the double-stranded DNA template. In this method, the fragments produced include the modified base and, as such, are not re-nicked by the nicking endonuclease.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6855 - Ligating adaptors
  • C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
  • C12N 9/22 - Ribonucleases

45.

Rapid diagnostic test using colorimetric lamp

      
Application Number 17178395
Grant Number 11492673
Status In Force
Filing Date 2021-02-18
First Publication Date 2021-09-16
Grant Date 2022-11-08
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Nichols, Nicole

Abstract

Kits and methods are provided for performing multiplex LAMP reactions. These kits and methods are directed to specific and sensitive methods of target nucleic acid detection and more specifically pathogen diagnostics such as detection of Coronavirus. The kits and methods utilize a plurality of sets of oligonucleotide primers for targeting the viral nucleic acid target.

IPC Classes  ?

  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour
  • C12Q 1/6844 - Nucleic acid amplification reactions

46.

Rapid diagnostic test using colorimetric LAMP

      
Application Number 17221451
Grant Number 11155887
Status In Force
Filing Date 2021-04-02
First Publication Date 2021-09-16
Grant Date 2021-10-26
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Nichols, Nicole

Abstract

Kits and methods are provided for performing multiplex Loop-Mediated Isothermal Amplification (LAMP) reactions. These kits and methods are directed to specific and sensitive methods of target nucleic acid detection and more specifically pathogen diagnostics such as detection of Coronavirus. The kits and methods utilize a plurality of sets of oligonucleotide primers for targeting the viral nucleic acid target.

IPC Classes  ?

  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour
  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage

47.

FCE mRNA capping enzyme compositions, methods and kits

      
Application Number 17246454
Grant Number 11098295
Status In Force
Filing Date 2021-04-30
First Publication Date 2021-08-24
Grant Date 2021-08-24
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ganatra, Mehul
  • Chan, Siu-Hong
  • Taron, Christopher H.
  • Robb, G. B.

Abstract

The present disclosure relates to compositions, kits, and methods of making RNA vaccines having an appropriate cap structure. Systems, apparatus, compositions, and/or methods may include and/or use, in some embodiments, non-naturally occurring single-chain RNA capping enzymes. In some embodiments, an RNA capping enzyme may include an FCE variant having (a) an amino acid sequence at least 90% identical to positions 1 to 878 of SEQ ID NO: 1, and/or (b) one or more substitutions relative to SEQ ID NO: 1 at a position selected from positions corresponding to positions 215, 337, 572, 648, and 833 (e.g., a position selected from positions corresponding to position 215, 337, and 572) of SEQ ID NO: 1.

IPC Classes  ?

  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 7/00 - Viruses, e.g. bacteriophages; Compositions thereof; Preparation or purification thereof
  • C12N 9/10 - Transferases (2.)
  • A61K 39/245 - Herpetoviridae, e.g. herpes simplex virus
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies

48.

High Fidelity Restriction Endonucleases

      
Application Number 17226693
Status Pending
Filing Date 2021-04-09
First Publication Date 2021-08-05
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zhu, Zhenyu
  • Quimby, Aine
  • Guan, Shengxi
  • Sun, Dapeng
  • Huang, Yishu
  • Lai, Xuhui
  • Chan, Siu-Hong
  • Li, Xianghui
  • Xu, Shuang-Yong
  • Zhang, Chunhua

Abstract

Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer.

IPC Classes  ?

  • C12N 9/22 - Ribonucleases
  • C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/44 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving esterase

49.

High Fidelity Restriction Endonucleases

      
Application Number 17227799
Status Pending
Filing Date 2021-04-12
First Publication Date 2021-07-29
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zhu, Zhenyu
  • Quimby, Aine
  • Xu, Shuang-Yong
  • Guan, Shengxi
  • Wei, Hua
  • Zhang, Penghua
  • Sun, Dapeng
  • Chan, Siu-Hong

Abstract

Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/22 - Ribonucleases
  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)

50.

Compositions and methods for analyzing modified nucleotides

      
Application Number 17181351
Grant Number 11939628
Status In Force
Filing Date 2021-02-22
First Publication Date 2021-07-08
Grant Date 2024-03-26
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Davis, Theodore B.
  • Guan, Shengxi
  • Sun, Zhiyi
  • Ettwiller, Laurence
  • Saleh, Lana

Abstract

5hmC in a DNA.

IPC Classes  ?

  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12N 9/78 - Hydrolases (3.) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

51.

FCE mRNA capping enzyme compositions, methods and kits

      
Application Number 17160256
Grant Number 11028379
Status In Force
Filing Date 2021-01-27
First Publication Date 2021-06-08
Grant Date 2021-06-08
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ganatra, Mehul
  • Chan, Siu-Hong
  • Taron, Christopher H.
  • Robb, G. B.

Abstract

The present disclosure relates to compositions, kits, and methods of making RNA vaccines having an appropriate cap structure. Systems, apparatus, compositions, and/or methods may include and/or use, in some embodiments, non-naturally occurring single-chain RNA capping enzymes. In some embodiments, an RNA capping enzyme may include an FCE variant having (a) an amino acid sequence at least 90% identical to positions 1 to 878 of SEQ ID NO: 1, and/or (b) one or more substitutions relative to SEQ ID NO: 1 at a position selected from positions corresponding to positions 215, 337, 572, 648, and 833 (e.g., a position selected from positions corresponding to position 215, 337, and 572) of SEQ ID NO: 1.

IPC Classes  ?

  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • C12N 7/00 - Viruses, e.g. bacteriophages; Compositions thereof; Preparation or purification thereof
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 9/10 - Transferases (2.)
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61K 39/245 - Herpetoviridae, e.g. herpes simplex virus

52.

Method for removing and/or detecting nucleic acids having mismatched nucleotides

      
Application Number 16616631
Grant Number 11371088
Status In Force
Filing Date 2018-06-11
First Publication Date 2021-06-03
Grant Date 2022-06-28
Owner New England Biolabs, Inc. (USA)
Inventor Gardner, Andrew F.

Abstract

Provided herein, among other things, are various in vitro methods that involve cleaving dsDNA molecules that comprise a mismatched nucleotide using EndoMS. In some embodiments, the method may comprise ligating a T-tailed double-stranded adapter to A-tailed double-stranded fragments of nucleic acid to produce ligation products that comprise adapter-ligated fragments and double-stranded adapter dimers that comprise a T:T mismatch at the ligation junction and cleaving both strands of the adapter dimers using EndoMS.

IPC Classes  ?

  • C12Q 1/6855 - Ligating adaptors
  • C12N 9/22 - Ribonucleases
  • C12N 9/00 - Enzymes, e.g. ligases (6.); Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating, or purifying enzymes
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]

53.

Variant DNA polymerases having improved properties and method for improved isothermal amplification of a target DNA

      
Application Number 17156704
Grant Number 11371028
Status In Force
Filing Date 2021-01-25
First Publication Date 2021-05-27
Grant Date 2022-06-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ong, Jennifer
  • Tanner, Nathan
  • Zhang, Yinhua
  • Bei, Yanxia
  • Potapov, Vladimir

Abstract

Variants of the bacteriophage B103 DNA polymerase are described herein. The variant has improved properties, that include when compared to wild-type Phi29 DNA polymerase, at least one of the following: increased thermostability, improved reaction rate for DNA amplification, reduced background and a reduction of bias. Methods of using the DNA polymerase variant are also described herein.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 7/00 - Viruses, e.g. bacteriophages; Compositions thereof; Preparation or purification thereof

54.

Use of thermostable RNA polymerases to produce RNAs having reduced immunogenicity

      
Application Number 16616734
Grant Number 11376338
Status In Force
Filing Date 2018-06-12
First Publication Date 2021-05-20
Grant Date 2022-07-05
Owner New England Biolabs, Inc. (USA)
Inventor
  • Roy, Bijoyita
  • Robb, G. B.

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.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • A61K 31/713 - Double-stranded nucleic acids or oligonucleotides
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • A61K 31/7105 - Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides

55.

Rapid diagnostic test using colorimetric LAMP

      
Application Number 17122979
Grant Number 11008629
Status In Force
Filing Date 2020-12-15
First Publication Date 2021-05-18
Grant Date 2021-05-18
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Nichols, Nicole

Abstract

Kits and methods are provided for performing multiplex LAMP reactions. These kits and methods are directed to specific and sensitive methods of target nucleic acid detection and more specifically pathogen diagnostics such as detection of Coronavirus. The kits and methods utilize a plurality of sets of oligonucleotide primers for targeting the viral nucleic acid target.

IPC Classes  ?

  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour
  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage

56.

Proteinases with improved properties

      
Application Number 17129112
Grant Number 11390862
Status In Force
Filing Date 2020-12-21
First Publication Date 2021-04-22
Grant Date 2022-07-19
Owner New England Biolabs, Inc. (USA)
Inventor
  • Chen, Minyong
  • Samuelson, James C.
  • Xu, Ming-Qun
  • Zhang, Aihua
  • Heider, Margaret
  • Liu, Pingfang

Abstract

Provided herein is a thermolabile proteinase and methods of using the same. In some embodiments, the thermolabile proteinase may comprise an amino acid sequence that is at least 90% identical to any of SEQ ID NOs:1-11 and at least one amino acid substitution in helix 3. The thermolabile proteinase is active at a temperature in the range of 4° C.-40° C. and is inactivated by raising the temperature to above 50° C., where the proteinase is substantially inactive at 65° C.

IPC Classes  ?

  • C12N 9/64 - Proteinases derived from animal tissue, e.g. rennin
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

57.

Rapid diagnostic test using colorimetric LAMP

      
Application Number 16938575
Grant Number 10968493
Status In Force
Filing Date 2020-07-24
First Publication Date 2021-04-06
Grant Date 2021-04-06
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Zhang, Yinhua
  • Patton, Gregory
  • Ren, Guoping
  • Li, Zhiru
  • Nichols, Nicole

Abstract

Kits and methods are provided for performing multiplex LAMP reactions. These kits and methods are directed to specific and sensitive methods of target nucleic acid detection and more specifically pathogen diagnostics such as detection of Coronavirus. The kits and methods utilize a plurality of sets of oligonucleotide primers for targeting different template sequences in a single nucleic acid target. The kits and methods also include guanidium salts that enhance the sensitivity of the assay.

IPC Classes  ?

  • G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
  • G16B 25/20 - Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
  • C12Q 1/686 - Polymerase chain reaction [PCR]

58.

Variant DNA polymerases having improved properties and method for improved isothermal amplification of a target DNA

      
Application Number 16598554
Grant Number 10934533
Status In Force
Filing Date 2019-10-10
First Publication Date 2021-03-02
Grant Date 2021-03-02
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ong, Jennifer
  • Tanner, Nathan
  • Zhang, Yinhua
  • Bei, Yanxia
  • Potapov, Vladimir

Abstract

Variants of the bacteriophage B103 DNA polymerase are described herein. The variant has improved properties, that include when compared to wild-type Phi29 DNA polymerase, at least one of the following: increased thermostability, improved reaction rate for DNA amplification, reduced background and a reduction of bias. Methods of using the DNA polymerase variant are also described herein.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 7/00 - Viruses, e.g. bacteriophages; Compositions thereof; Preparation or purification thereof

59.

Enzymatic RNA Capping Method

      
Application Number 17001236
Status Pending
Filing Date 2020-08-24
First Publication Date 2021-02-25
Owner NEW ENGLAND BIOLABS, INC. (USA)
Inventor
  • Robb, G. Brett
  • Chan, Siu-Hong
  • Roy, Bijoyita

Abstract

Provided herein is a method for efficiently capping RNA in vitro. In some embodiments the capping reaction may be done at high temperature using Vaccinia capping enzyme or a variant thereof. In other embodiments, the capping reactions may comprise a capping enzyme from a large virus of amoeba, e.g., Faustovirus, mimivirus or moumouvirus, or a variant thereof. Compositions and kits for practicing the method are also provided.

IPC Classes  ?

  • C07H 19/20 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical

60.

Isolation of high molecular weight DNA using beads

      
Application Number 16547844
Grant Number 11591591
Status In Force
Filing Date 2019-08-22
First Publication Date 2021-02-25
Grant Date 2023-02-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Koetsier, Paul A.
  • Taron, Barbara W.
  • Cantor, Eric J.

Abstract

Provided herein is a method for isolating high molecular weight (HMW) DNA using beads that are at least 200 μm in diameter that utilizes a device for retaining the beads and where the purified DNA eluant exits the device without shearing the HMW DNA. In some embodiments, the method comprises precipitating the DNA onto the beads, washing the beads in the device, and then eluting the DNA from the beads therein while substantially avoiding shear. Compositions and kits for practicing the method are also provided.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • B01L 9/06 - Test-tube stands; Test-tube holders

61.

DNA ligase variants

      
Application Number 16227533
Grant Number 10837009
Status In Force
Filing Date 2018-12-20
First Publication Date 2020-11-17
Grant Date 2020-11-17
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ong, Jennifer
  • Lohman, Gregory
  • Quimby, Aine
  • Potapov, Vladimir
  • Pryor, John M.

Abstract

Mutant bacteriophage DNA ligases that have increased tolerance to salt and/or heat is provided. Methods, compositions and kits that employ the same are also provided.

IPC Classes  ?

  • C12N 9/10 - Transferases (2.)
  • C12N 9/00 - Enzymes, e.g. ligases (6.); Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating, or purifying enzymes
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

62.

Polynucleotide adapter design for reduced bias

      
Application Number 16796113
Grant Number 11390915
Status In Force
Filing Date 2020-02-20
First Publication Date 2020-10-29
Grant Date 2022-07-19
Owner New England Biolabs, Inc. (USA)
Inventor
  • Guan, Shengxi
  • Maguire, Sean

Abstract

Compositions are provided for 3′ adapters and methods of use are provided that include methods requiring a plurality of ligation steps involving a single-stranded target polynucleotide and 3′ and 5′ adapters. Embodiments of the 3′ adapters comprise 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.

IPC Classes  ?

  • C12Q 1/6855 - Ligating adaptors
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

63.

Mapping the location, type and strand of damaged and/or mismatched nucleotides in double-stranded DNA

      
Application Number 16758190
Grant Number 11713484
Status In Force
Filing Date 2018-08-21
First Publication Date 2020-10-15
Grant Date 2023-08-01
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zatopek, Kelly M.
  • Potapov, Vladimir
  • Ong, Jennifer
  • Ettwiller, Laurence
  • Chen, Lixin
  • Evans, Jr., Thomas C.
  • Gardner, Andrew F.

Abstract

Providing herein, among other things, is a method comprising incubating a double-stranded nucleic acid having a nick with a nick translating activity, a ligase, and a nucleotide mix comprising at least one modified nucleotide, to generate a product comprising a patch of a newly synthesized strand of a duplex nucleic acid containing a plurality of modified nucleoside monophosphates that are at or adjacent to the site of the nick. In some embodiments, the method may be used to map damaged nucleoside monophosphates in a nucleic acid. Compositions and kits for use in performing the method are also provided.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

64.

Target enrichment

      
Application Number 16721395
Grant Number 11555185
Status In Force
Filing Date 2019-12-19
First Publication Date 2020-06-25
Grant Date 2023-01-17
Owner New England Biolabs, Inc. (USA)
Inventor
  • Hendrickson, Cynthia
  • Bowman, Sarah
  • Emerman, Amy
  • Patel, Kruti

Abstract

The present disclosure provides, among other things, a way to amplify and sequence target sequences in a low-input sample. In some embodiments, the method comprises ligating a double-stranded adaptor onto a population of fragments to produce tagged fragments, and linearly amplifying the tagged fragments.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C40B 50/16 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support involving encoding steps
  • C40B 50/18 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support using a particular method of attachment to the solid support
  • C40B 70/00 - Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or barcodes

65.

β-lactamase targeted photosensitizer for pesticide and pest detection

      
Application Number 16013333
Grant Number 10874107
Status In Force
Filing Date 2018-06-20
First Publication Date 2020-05-21
Grant Date 2020-12-29
Owner
  • The General Hospital Corporation (USA)
  • New England Biolabs (USA)
Inventor
  • Hasan, Tayyaba
  • Sallum, Ulysses W.
  • Slatko, Barton
  • Foster, Jeremy

Abstract

Photoactivatable pesticide compounds and methods for the use thereof in the elimination and detection of pests are provided.

IPC Classes  ?

  • A01N 43/90 - Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds having two or more relevant hetero rings, condensed among themselves or with a common carbocyclic ring system
  • A01N 25/00 - Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests
  • C07D 501/16 - Compounds having a nitrogen atom directly attached in position 7 with a double bond between positions 2 and 3
  • G01N 21/64 - Fluorescence; Phosphorescence

66.

Proteinases with improved properties

      
Application Number 16719097
Grant Number 10633644
Status In Force
Filing Date 2019-12-18
First Publication Date 2020-04-28
Grant Date 2020-04-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Chen, Minyong
  • Samuelson, James C.
  • Xu, Ming-Qun
  • Zhang, Aihua
  • Heider, Margaret
  • Liu, Pingfang

Abstract

Provided herein is a thermolabile proteinase and methods of using the same. In some embodiments, the thermolabile proteinase may comprise an amino acid sequence that is at least 90% identical to any of SEQ ID NOs:1-11 and at least one amino acid substitution in helix 3. The thermolabile proteinase is active at a temperature in the range of 4° C.-40° C. and is inactivated by raising the temperature to above 50° C., where the proteinase is substantially inactive at 65° C.

IPC Classes  ?

  • C12N 9/64 - Proteinases derived from animal tissue, e.g. rennin
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

67.

Thermostable variants of T7 RNA polymerase

      
Application Number 16680014
Grant Number 11359184
Status In Force
Filing Date 2019-11-11
First Publication Date 2020-04-23
Grant Date 2022-06-14
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ong, Jennifer
  • Potapov, Vladimir
  • Hung, Kuo-Chan
  • Asahara, Haruichi
  • Chong, Shaorong
  • Tzertzinis, George

Abstract

A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6858 - Allele-specific amplification

68.

Methods and compositions for increasing capping efficiency of transcribed RNA

      
Application Number 16151908
Grant Number 11072808
Status In Force
Filing Date 2018-10-04
First Publication Date 2020-04-09
Grant Date 2021-07-27
Owner New England Biolabs, Inc. (USA)
Inventor
  • Roy, Bijoyita
  • Ong, Jennifer

Abstract

Methods and compositions for capping RNA in an in vitro transcription mixture are provided that include a thermostable RNA polymerase variant and a cap analog such that when a DNA template is added to the mixture, and the mixture is then incubated under conditions for in vitro transcription, capped RNA is produced.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

69.

Stabilizing 5′-flap endonuclease activity

      
Application Number 15466996
Grant Number 10487317
Status In Force
Filing Date 2017-03-23
First Publication Date 2019-11-26
Grant Date 2019-11-26
Owner New England Biolabs, Inc. (USA)
Inventor
  • Nichols, Nicole
  • Patton, Gregory
  • Graham, Janine

Abstract

A probe qPCR master mix is provided. In some embodiments, the master mix comprises nucleotides, an enzyme comprising a polymerase activity and a flap endonuclease activity, a chelating agent at a concentration greater than 5 μM, and a divalent cation. The relatively high concentration of chelating agent stabilizes the flap endonuclease activity during storage. As such, the polymerase and flap endonuclease activities may be substantially the same before and after storing the master mix for 7 days at 37° C.

IPC Classes  ?

  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
  • C12Q 1/686 - Polymerase chain reaction [PCR]
  • C12N 15/00 - Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor

70.

High fidelity restriction endonucleases

      
Application Number 16355464
Grant Number 11001818
Status In Force
Filing Date 2019-03-15
First Publication Date 2019-09-12
Grant Date 2021-05-11
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zhu, Zhenyu
  • Quimby, Aine
  • Guan, Shengxi
  • Sun, Dapeng
  • Huang, Yishu
  • Lai, Xuhui
  • Chan, Siu-Hong
  • Li, Xianghui
  • Xu, Shuang-Yong
  • Zhang, Chunhua

Abstract

Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer.

IPC Classes  ?

  • C12N 9/22 - Ribonucleases
  • C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/44 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving esterase

71.

Compositions and methods relating to synthetic RNA polynucleotides created from synthetic DNA oligonucleotides

      
Application Number 16375107
Grant Number 11396652
Status In Force
Filing Date 2019-04-04
First Publication Date 2019-07-25
Grant Date 2022-07-26
Owner New England Biolabs, Inc. (USA)
Inventor
  • Robb, G. B.
  • Meek, Isaac B.
  • Schwarz, Dianne S.
  • Schildkraut, Ezra

Abstract

Compositions and methods are provided for forming a single RNA polynucleotide from a plurality of DNA oligonucleotides in a single reaction chamber using combined reagents in a single step reaction. DNA polymerase, RNA polymerase and single stranded (ss) DNA oligonucleotides are combined where each DNA oligonucleotide has one or more sequence modules, wherein one sequence module in the first ss DNA oligonucleotide is complementary to a sequence module at the 3′ end of the second ss DNA oligonucleotide; and wherein a second module on the first ss DNA oligonucleotide is an RNA polymerase promoter sequence; and forming a single RNA polynucleotide, excluding the RNA promoter sequence, derived from the first and second DNA oligonucleotides.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/22 - Ribonucleases
  • C12N 9/96 - Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates
  • C12N 15/115 - Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

72.

Analysis of chromatin using a nicking enzyme

      
Application Number 16327698
Grant Number 11198910
Status In Force
Filing Date 2017-08-31
First Publication Date 2019-07-11
Grant Date 2021-12-14
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ponnaluri, Chaithanya
  • Chin, Hang-Gyeong
  • Esteve, Pierre O.
  • Pradhan, Sriharsa

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6841 - In situ hybridisation
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism

73.

Compositions and methods for analyzing modified nucleotides

      
Application Number 16287604
Grant Number 11001876
Status In Force
Filing Date 2019-02-27
First Publication Date 2019-06-20
Grant Date 2021-05-11
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Davis, Theodore B.
  • Guan, Shengxi
  • Sun, Zhiyi
  • Ettwiller, Laurence
  • Saleh, Lana

Abstract

5hmC in a DNA.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12N 9/78 - Hydrolases (3.) acting on carbon to nitrogen bonds other than peptide bonds (3.5)

74.

Detection of an amplification product using pH-sensitive dye

      
Application Number 16306319
Grant Number 11162133
Status In Force
Filing Date 2017-05-12
First Publication Date 2019-06-06
Grant Date 2021-11-02
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zhang, Yinhua
  • Tanner, Nathan
  • Evans, Jr., Thomas C.

Abstract

Methods are provided for a rapid, low cost approach to monitoring an amplification reaction. This includes monitoring the progress of isothermal or PCR amplification reactions to completion using pH-sensitive dyes that are either colored or fluorescent. Compositions are described that include a mixture of a DNA polymerase, deoxyribonucleotide triphosphate and Tris buffer in the range of 1.5 mM Tris to 5 mM Tris or equivalent.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/6816 - Hybridisation assays characterised by the detection means
  • C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • G01N 33/52 - Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper

75.

Peptide inhibitors of phosphoglycerate mutase and methods of use

      
Application Number 16324424
Grant Number 10808010
Status In Force
Filing Date 2017-08-10
First Publication Date 2019-06-06
Grant Date 2020-10-20
Owner
  • The United States of America, as represented by the Secretary, Department of Health and Human Services (USA)
  • The University of Tokyo (Japan)
  • New England Biolabs, Inc. (USA)
Inventor
  • Inglese, James
  • Dranchak, Patricia
  • Macarthur, Ryan
  • Suga, Hiroaki
  • Yu, Hao
  • Carlow, Clotilde
  • Li, Zhiru

Abstract

Disclosed herein are isolated peptides inhibit activity of a cofactor-independent phosphoglycerate mutase. In some examples, the isolated peptide is 6-20 amino acids long and includes the amino acid sequence of any one of SEQ ID NOs: 1-22 or 54, an analog or derivative thereof, or a pharmaceutically acceptable salt or ester thereof. In some examples, the peptide is a cyclic peptide with an N-terminal ring of 6-15 amino acids (for example, 6-10 amino acids) and a C-terminal linear portion of 1-9 amino acids (for example, 3-8 amino acids. Also disclosed h are methods of treating or inhibiting an infection in a subject, including administering to the subject an effective amount of a composition including one of more of the disclosed peptides, or analogs or derivative thereof, or pharmaceutically acceptable salts or esters thereof.

IPC Classes  ?

  • C07K 7/64 - Cyclic peptides containing only normal peptide links
  • C07K 7/08 - Linear peptides containing only normal peptide links having 12 to 20 amino acids
  • C07K 7/06 - Linear peptides containing only normal peptide links having 5 to 11 amino acids
  • C07K 7/56 - Cyclic peptides containing at least one abnormal peptide link with at least one abnormal peptide link in the ring the cyclisation not occurring through 2,4-diamino-butanoic acid
  • C07K 14/00 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • A61P 33/10 - Anthelmintics
  • A61K 38/12 - Cyclic peptides
  • A61K 45/06 - Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
  • A61K 38/00 - Medicinal preparations containing peptides

76.

Method for fragmenting DNA by nick translation

      
Application Number 16194552
Grant Number 11021701
Status In Force
Filing Date 2018-11-19
First Publication Date 2019-05-23
Grant Date 2021-06-01
Owner New England Biolabs, Inc. (USA)
Inventor
  • Guan, Chudi
  • Yan, Bo

Abstract

Providing herein, among other things, are kits, compositions and methods that relate to DNA fragmentation. An embodiment of a composition provides combining: one or more enzymes capable of nick translating activity, a dNTP mix comprising at least one dNTP having a modified base, and at least one modification-sensitive nicking endonuclease that is prevented from nicking DNA if its recognition site contains the modified base. When the composition is added to a sample comprising a double-stranded DNA template that comprises recognition sites for the modification-sensitive nicking endonuclease, a reaction mix was produced which could be incubated for any time period in excess of about 5 minutes to produce fragments of a desired size of the double-stranded DNA template. In this method, the fragments produced include the modified base and, as such, are not re-nicked by the nicking endonuclease.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6855 - Ligating adaptors
  • C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
  • C12N 9/22 - Ribonucleases

77.

Compositions and methods for analyzing modified nucleotides

      
Application Number 16217819
Grant Number 11124825
Status In Force
Filing Date 2018-12-12
First Publication Date 2019-04-04
Grant Date 2021-09-21
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Sun, Zhiyi
  • Guan, Shengxi
  • Saleh, Lana
  • Ettwiller, Laurence
  • Davis, Theodore B.

Abstract

A method for identifying any of the presence, location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.

IPC Classes  ?

  • C12Q 1/6858 - Allele-specific amplification
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6872 - Methods for sequencing involving mass spectrometry

78.

Compositions and methods for labeling target nucleic acid molecules

      
Application Number 15051064
Grant Number 10246702
Status In Force
Filing Date 2016-02-23
First Publication Date 2019-04-02
Grant Date 2019-04-02
Owner New England Biolabs, Inc. (USA)
Inventor
  • Richard, Cynthia L.
  • Galvin, Brendan

Abstract

Provided herein are methods and compositions for labeling target nucleic acid molecules with molecular barcodes.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

79.

Universal N-glycan binding reagent

      
Application Number 16105027
Grant Number 10507233
Status In Force
Filing Date 2018-08-20
First Publication Date 2019-01-10
Grant Date 2019-12-17
Owner New England Biolabs, Inc. (USA)
Inventor
  • Chen, Minyong
  • Shi, Xiaofeng
  • Samuelson, James C.
  • Taron, Christopher H.

Abstract

Methods of capturing N-glycan linked glycomolecules including N-glycans, N-glycopeptides and N-glycoproteins are described. The methods provide substantially unbiased capture of charged and uncharged N-glycans and/or N-glycan linked glycomoleules. Binding reagents for substantially unbiased binding of N-glycans and/or N-glycan linked glycomolecules are also described.

IPC Classes  ?

  • C12N 9/96 - Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates
  • C12N 9/00 - Enzymes, e.g. ligases (6.); Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating, or purifying enzymes
  • A61K 38/53 - Ligases (6)
  • C12N 9/04 - Oxidoreductases (1.), e.g. luciferase acting on CHOH groups as donors, e.g. glucose oxidase, lactate dehydrogenase (1.1)
  • C12N 9/10 - Transferases (2.)
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical

80.

In vitro cleavage of DNA using argonaute

      
Application Number 16018806
Grant Number 11466264
Status In Force
Filing Date 2018-06-26
First Publication Date 2019-01-03
Grant Date 2022-10-11
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Hunt, Eric

Abstract

Methods, kits and compositions, in some embodiments, may include a thermostable DNA guided Argonaute protein for example TtAgo, a thermostable single-stranded DNA binding protein (SSB) for example, ET SSB, and, optionally, a strand-displacing polymerase. A SSB may allow (a) Argonaute/guide DNA complexes to substantially enhance cleavage efficiency of single- and double-stranded DNA substrates; (b) the use of longer guide DNAs (e.g., guide DNAs that are at least 24 nucleotides in length) and/or (c) increases in the sequence specificity of Argonaute-mediated binding and cleavage reactions.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C07K 14/195 - Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
  • C12N 9/22 - Ribonucleases
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 15/11 - DNA or RNA fragments; Modified forms thereof
  • C12N 15/90 - Stable introduction of foreign DNA into chromosome

81.

Method for performing multiple enzyme reactions in a single tube

      
Application Number 15623756
Grant Number 10155939
Status In Force
Filing Date 2017-06-15
First Publication Date 2018-12-18
Grant Date 2018-12-18
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Higgins, Lauren
  • Luck, Ashley

Abstract

Among other things, a method for performing multiple enzyme reactions in a single tube is provided. In some embodiments, the method may comprise producing a reaction mix comprising a thermolabile UDG, an AP lyase and DNA fragments that comprise one or more uracil residues, incubating the reaction mix at a relatively low temperature to cleave fragments at the one or more uracil residues, raising the temperature of the reaction mix to a relatively high temperature to inactivate the thermolabile UDG; and deaminating the fragments, thereby converting any cytosine in the fragments of DNA to uracil.

IPC Classes  ?

  • C12N 9/88 - Lyases (4.)
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C07H 19/073 - Pyrimidine radicals with 2-deoxyribosyl as the saccharide radical
  • C12N 9/22 - Ribonucleases
  • C12N 15/09 - Recombinant DNA-technology
  • C11D 3/12 - Water-insoluble compounds
  • C12N 9/00 - Enzymes, e.g. ligases (6.); Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating, or purifying enzymes
  • C12Q 1/52 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase involving transaminase

82.

Fusion polymerase and method for using the same

      
Application Number 16105502
Grant Number 11639498
Status In Force
Filing Date 2018-08-20
First Publication Date 2018-12-13
Grant Date 2023-05-02
Owner New England Biolabs, Inc. (USA)
Inventor
  • Hsieh, Pei-Chung
  • Sun, Luo
  • Evans, Jr., Thomas C.
  • Davis, Theodore B.
  • Gardner, Andrew F.

Abstract

This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 15/64 - General methods for preparing the vector, for introducing it into the cell or for selecting the vector-containing host
  • C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
  • C12N 9/22 - Ribonucleases
  • C12N 9/96 - Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates
  • C12N 9/20 - Triglyceride splitting, e.g. by means of lipase

83.

Compositions and methods for analyzing modified nucleotides

      
Application Number 15771275
Grant Number 10619200
Status In Force
Filing Date 2016-10-28
First Publication Date 2018-11-01
Grant Date 2020-04-14
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Sun, Zhiyi
  • Guan, Shengxi
  • Saleh, Lana
  • Ettwiller, Laurence
  • Davis, Theodore B.

Abstract

A method for identifying the location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and optionally reacting a second portion of the sample with a dioxygenase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase that is more efficient at converting methylcytosine to carboxymethylcytosine is also provided.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12Q 1/6858 - Allele-specific amplification
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6872 - Methods for sequencing involving mass spectrometry

84.

Cleavage of fucose in N-glycans

      
Application Number 15894252
Grant Number 10260056
Status In Force
Filing Date 2018-02-12
First Publication Date 2018-09-20
Grant Date 2019-04-16
Owner New England Biolabs, Inc. (USA)
Inventor
  • Taron, Christopher H.
  • Vainauskas, Saulius
  • Shi, Xiaofeng

Abstract

Provided herein is an α-fucosidase that can cleave a conjugate comprising an N-glycan and a label where the label is added by amine reactive chemistry. The α-fucosidase also has an accelerated reaction time using Schiff base labeled N-glycans compared with bovine kidney fucosidase. A reaction mix, enzyme mix and kit comprising the α-fucosidase are provided, as well as a method for analyzing glycoproteins. The α-fucosidase finds particular use in analyzing the N-glycans of therapeutic glycoproteins.

IPC Classes  ?

  • C12N 9/26 - Hydrolases (3.) acting on glycosyl compounds (3.2) acting on alpha-1, 4-glucosidic bonds, e.g. hyaluronidase, invertase, amylase
  • C07H 5/06 - Aminosugars
  • C12N 9/24 - Hydrolases (3.) acting on glycosyl compounds (3.2)
  • C07K 1/13 - Labelling of peptides
  • C12P 21/00 - Preparation of peptides or proteins

85.

Methods and compositions for preventing concatemerization during template-switching

      
Application Number 15947971
Grant Number 10246706
Status In Force
Filing Date 2018-04-09
First Publication Date 2018-08-09
Grant Date 2019-04-02
Owner New England Biolabs, Inc. (USA)
Inventor
  • Guan, Shengxi
  • Evans, Jr., Thomas C.
  • Nichols, Nicole
  • Bei, Yanxia

Abstract

Compositions and methods for performing a template-switching reaction are provided that may include reducing or eliminating concatemerization of the template-switching oligonucleotide (TSO). In some embodiments, the composition may comprise: a reverse transcriptase; a TSO that includes a recognition sequence for a site-specific double strand nucleic acid cleaving enzyme, wherein the TSO has at its 3′ end at least one nucleotide capable of hybridizing to at least one or more non-templated nucleotides added to a templated cDNA strand by the reverse transcriptase; and a site-specific double strand nucleic acid cleaving enzyme that cleaves the TSO at the recognition sequence.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction

86.

Use of thermostable RNA polymerases to produce RNAs having reduced immunogenicity

      
Application Number 15820656
Grant Number 10034951
Status In Force
Filing Date 2017-11-22
First Publication Date 2018-07-31
Grant Date 2018-07-31
Owner New England Biolabs, Inc. (USA)
Inventor
  • Roy, Bijoyita
  • Robb, G. B.

Abstract

Provided herein, among other things, is a method for producing an RNA product that has reduced immunogenicity without requiring removal of any dsRNA from the RNA product. In some embodiments, the method involves transcribing a template DNA with a thermostable RNA polymerase at a temperature of greater than 44° C.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • A61K 45/06 - Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

87.

Methods for labeling a population of RNA molecules

      
Application Number 15908522
Grant Number 11479766
Status In Force
Filing Date 2018-02-28
First Publication Date 2018-07-12
Grant Date 2022-10-25
Owner New England Biolabs, Inc. (USA)
Inventor
  • Schildkraut, Ira
  • Ettwiller, Laurence
  • Correa, Jr., Ivan R.
  • Tzertzinis, George
  • Buswell, John
  • Wulf, Madalee G.

Abstract

A method of labeling, and optionally enriching, for a population of target RNA molecules in a mixture of RNAs is provided. In some embodiments, the method may comprise (a) adding a label to the 5′ end of 5′-diphosphorylated or 5′-triphosphorylated target RNA molecules in a sample by incubating the sample with labeled GTP and a capping enzyme; and (b) optionally enriching for target RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag. The label may be an oligonucleotide, which may further comprise an affinity group attached either internally or at 5′ or 3′ end of the oligonucleotide where the oligonucleotide label may be added directly, or indirectly via a reaction with a reactive group to the target RNA.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical

88.

High fidelity restriction endonucleases

      
Application Number 15882603
Grant Number 10450559
Status In Force
Filing Date 2018-01-29
First Publication Date 2018-06-21
Grant Date 2019-10-22
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zhu, Zhenyu
  • Quimby, Aine
  • Xu, Shuang-Yong
  • Guan, Shengxi
  • Wei, Hua
  • Zhang, Penghua
  • Sun, Dapeng
  • Chan, Siu-Hong

Abstract

Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

IPC Classes  ?

  • C12N 9/22 - Ribonucleases
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)

89.

Helicase suppression of non-template amplification

      
Application Number 15888437
Grant Number 10301673
Status In Force
Filing Date 2018-02-05
First Publication Date 2018-06-21
Grant Date 2019-05-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Tanner, Nathan
  • Evans, Jr., Thomas C.

Abstract

Provided herein is a method for reducing amplification of non-template molecules in a nucleic acid sample. In certain embodiments, the method involves adding a helicase to a reaction mixture for non-helicase-dependent amplification of target nucleic acid.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6853 - Nucleic acid amplification reactions using modified primers or templates
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction

90.

Compositions and methods for analyzing modified nucleotides

      
Application Number 15893373
Grant Number 10260088
Status In Force
Filing Date 2018-02-09
First Publication Date 2018-06-21
Grant Date 2019-04-16
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Davis, Theodore B.
  • Guan, Shengxi
  • Sun, Zhiyi
  • Ettwiller, Laurence
  • Saleh, Lana

Abstract

5hmC in a DNA.

IPC Classes  ?

  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12N 9/78 - Hydrolases (3.) acting on carbon to nitrogen bonds other than peptide bonds (3.5)

91.

High fidelity BbsI

      
Application Number 15337597
Grant Number 09988614
Status In Force
Filing Date 2016-10-28
First Publication Date 2018-06-05
Grant Date 2018-06-05
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zhu, Zhenyu
  • Quimby, Aine

Abstract

A composition comprising a variant BbsI restriction endonuclease having reduced star activity is provided, as well as kits and methods employing the same.

IPC Classes  ?

  • C12N 9/22 - Ribonucleases
  • C12N 9/00 - Enzymes, e.g. ligases (6.); Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating, or purifying enzymes
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

92.

High fidelity restriction endonucleases

      
Application Number 15824413
Grant Number 10294464
Status In Force
Filing Date 2017-11-28
First Publication Date 2018-05-31
Grant Date 2019-05-21
Owner New England Biolabs, Inc. (USA)
Inventor
  • Zhu, Zhenyu
  • Quimby, Aine
  • Guan, Shengxi
  • Sun, Dapeng
  • Huang, Yishu
  • Lai, Xuhui
  • Chan, Siu-Hong
  • Li, Xianghui
  • Xu, Shuang-Yong
  • Zhang, Chunhua

Abstract

Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer.

IPC Classes  ?

  • C12N 9/22 - Ribonucleases
  • C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
  • C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/44 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving esterase

93.

Mutant reverse transcriptase

      
Application Number 15406160
Grant Number 09932567
Status In Force
Filing Date 2017-01-13
First Publication Date 2018-03-29
Grant Date 2018-04-03
Owner New England Biolabs, Inc. (USA)
Inventor
  • Xu, Yan
  • Ong, Jennifer
  • Guan, Shengxi
  • Nichols, Nicole

Abstract

A mutant MMLV reverse transcriptase that may have an improvement in one or more properties is provided. For example, the present reverse transcriptase is believed to be more efficient relative to other commercially available MMLV reverse transcriptase variants, particularly for templates with a higher GC content.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/686 - Polymerase chain reaction [PCR]
  • C12N 9/22 - Ribonucleases
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

94.

Methods and compositions for preventing concatemerization during template-switching

      
Application Number 15240166
Grant Number 10240148
Status In Force
Filing Date 2016-08-18
First Publication Date 2018-02-08
Grant Date 2019-03-26
Owner New England Biolabs, Inc. (USA)
Inventor
  • Guan, Shengxi
  • Evans, Jr., Thomas C.
  • Nichols, Nicole
  • Bei, Yanxia

Abstract

Compositions and methods for performing a template-switching reaction are provided that may include reducing or eliminating concatemerization of the template-switching oligonucleotide (TSO). In some embodiments, the composition may comprise: a reverse transcriptase; a TSO that includes a recognition sequence for a site-specific double strand nucleic acid cleaving enzyme, wherein the TSO has at its 3′ end at least one nucleotide capable of hybridizing to at least one or more non-templated nucleotides added to a templated cDNA strand by the reverse transcriptase; and a site-specific double strand nucleic acid cleaving enzyme that cleaves the TSO at the recognition sequence.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical

95.

Enrichment and sequencing of RNA species

      
Application Number 15786020
Grant Number 11225658
Status In Force
Filing Date 2017-10-17
First Publication Date 2018-02-01
Grant Date 2022-01-18
Owner New England Biolabs, Inc. (USA)
Inventor
  • Yan, Bo
  • Ettwiller, Laurence
  • Schildkraut, Ira
  • Tzertzinis, George
  • Correa, Jr., Ivan R.
  • Dai, Nan
  • Wulf, Madalee G.

Abstract

Provided herein is a method for making an cDNA library, comprising adding an affinity tag-labeled GMP to the 5′ end of targeted RNA species in a sample by optionally decapping followed by incubating the sample with an affinity tag-labeled GTP and a capping enzyme, enriching for RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag, reverse transcribing the enriched RNA to produce a population of cDNAs, and adding a tail to the 3′ end of the population of cDNAs using a terminal transferase, to produce an cDNA library.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6869 - Methods for sequencing
  • C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

96.

Compositions and methods relating to synthetic RNA polynucleotides created from synthetic DNA oligonucleotides

      
Application Number 15469681
Grant Number 10301619
Status In Force
Filing Date 2017-03-27
First Publication Date 2017-10-05
Grant Date 2019-05-28
Owner New England Biolabs, Inc. (USA)
Inventor
  • Robb, G. B.
  • Meek, Isaac B.
  • Schwarz, Dianne S.
  • Schildkraut, Ezra

Abstract

Compositions and methods are provided for forming a single RNA polynucleotide from a plurality of DNA oligonucleotides in a single reaction chamber using combined reagents in a single step reaction. DNA polymerase, RNA polymerase and single stranded (ss) DNA oligonucleotides are combined where each DNA oligonucleotide has one or more sequence modules, wherein one sequence module in the first ss DNA oligonucleotide is complementary to a sequence module at the 3′ end of the second ss DNA oligonucleotide; and wherein a second module on the first ss DNA oligonucleotide is an RNA polymerase promoter sequence; and forming a single RNA polynucleotide, excluding the RNA promoter sequence, derived from the first and second DNA oligonucleotides.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 9/22 - Ribonucleases
  • C12N 9/96 - Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates
  • C12N 15/115 - Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

97.

Methods for enriching for a population of RNA molecules

      
Application Number 15137394
Grant Number 10428368
Status In Force
Filing Date 2016-04-25
First Publication Date 2017-09-07
Grant Date 2019-10-01
Owner New England Biolabs, Inc. (USA)
Inventor
  • Schildkraut, Ira
  • Ettwiller, Laurence
  • Correa, Jr., Ivan R.
  • Sproviero, Michael

Abstract

A method of enriching for a population of RNA molecules in a mixture of RNAs is provided. In some embodiments, the method may comprise (a) adding an affinity tag to the 5′ end of 5′-diphosphorylated or 5′-triphosphorylated RNA molecules in a sample by incubating the sample with an affinity tag-labeled GTP and a capping enzyme; and (b) enriching for RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6869 - Methods for sequencing

98.

Thermostable variants of T7 RNA polymerase

      
Application Number 15594090
Grant Number 10519431
Status In Force
Filing Date 2017-05-12
First Publication Date 2017-08-31
Grant Date 2019-12-31
Owner New England Biolabs, Inc. (USA)
Inventor
  • Ong, Jennifer
  • Potapov, Vladimir
  • Hung, Kuo-Chan
  • Asahara, Haruichi
  • Chong, Shaorong
  • Tzertzinis, George

Abstract

A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6858 - Allele-specific amplification

99.

Compositions and methods for extending storage time of competent cells at -20° C

      
Application Number 15321319
Grant Number 09963672
Status In Force
Filing Date 2015-07-15
First Publication Date 2017-07-13
Grant Date 2018-05-08
Owner New England Biolabs, Inc. (USA)
Inventor An, Lixin

Abstract

Compositions and methods are provided for storing prokaryotic cells including competent prokaryotic cells at −20° C. in a buffer so that the cells are suitable for transformation at 0° C. with a foreign molecule.

IPC Classes  ?

  • C12N 1/04 - Preserving or maintaining viable microorganisms
  • C12N 1/20 - Bacteria; Culture media therefor

100.

Compositions and methods for analyzing modified nucleotides

      
Application Number 15441431
Grant Number 10227646
Status In Force
Filing Date 2017-02-24
First Publication Date 2017-07-13
Grant Date 2019-03-12
Owner New England Biolabs, Inc. (USA)
Inventor
  • Vaisvila, Romualdas
  • Sun, Zhiyi
  • Guan, Shengxi
  • Saleh, Lana
  • Ettwiller, Laurence
  • Davis, Theodore B.

Abstract

A method for identifying any of the presence, location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • C12Q 1/6872 - Methods for sequencing involving mass spectrometry
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12Q 1/6869 - Methods for sequencing
  1     2        Next Page