01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; enzymes for
scientific and research use; kits for scientific and
research use, namely, kits comprised of enzymes for
molecular biology and cell biology applications; reagents
for scientific and research use in the field of molecular
biology and cell biology applications; enzymes for
scientific and research use in the field of molecular
biology and cell biology applications; reagents for
scientific and research use; reagents for scientific and
research use for use in sequencing nucleic acids; kits for
use in sequencing nucleic acids comprising at least one of
enzymes, buffers, cells and nucleic acids.
2.
FCE MRNA CAPPING ENZYME COMPOSITIONS, METHODS AND KITS
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.
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.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Reagents for scientific purposes; Biochemical reagents used for non-medical purposes; Biochemical preparations for scientific purposes Chemical reagents for medical purposes; Diagnostic reagents for medical use; Enzymes for medical purposes
5.
Polynucleotide Error Recognition Methods and Compositions
The present disclosure relates, according to some embodiments, to systems, apparatus, compositions, kits, workflows, and/or methods that address errors in synthesizing and/or copying polynucleotide sequences. The present disclosure provides, for example, systems, apparatus, compositions, kits, workflows, and methods for detecting, reducing, and/or removing sequence errors including mismatches and/or indels. Enzyme composition may include, in some embodiments, a T4EndoVII endonuclease and a mismatch endonuclease, wherein the composition is cell-free, the composition has a temperature of 30° C. to 45° C., the composition comprises ≥1 unit of T4EndoVII per μL and ≥1 unit of μL of the mismatch endonuclease, the composition comprises ≥0.2 ng T4EndoVII per 20 μL and ≥7 ng mismatch endonuclease per 20 μL, the composition further comprises a buffering agent, and/or the mismatch endonuclease is EndoMS.
The present disclosure relates, according to some embodiments, to systems, apparatus, compositions, kits, workflows, and/or methods that address errors in synthesizing and/or copying polynucleotide sequences. The present disclosure provides, for example, systems, apparatus, compositions, kits, workflows, and methods for detecting, reducing, and/or removing sequence errors including mismatches and/or indels. Enzyme composition may include, in some embodiments, a T4EndoVII endonuclease and a mismatch endonuclease, wherein the composition is cell-free, the composition has a temperature of 30°C to 45°C, the composition comprises ≥ 1 unit of T4EndoVII per μL and ≥ 1 unit of μL of the mismatch endonuclease, the composition comprises ≥ 0.2 ng T4EndoVII per 20 μL and ≥ 7 ng mismatch endonuclease per 20 μL, the composition further comprises a buffering agent, and/or the mismatch endonuclease is EndoMS.
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
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
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.
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
C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
C12Q 1/6816 - Hybridisation assays characterised by the detection means
8.
Target Initiation and Amplification of Long DNA with Nuclease and Replisome Enzymes
Compositions, methods and kits are provided for long range amplification of nucleic acid sequences in vitro. This includes a site-specific or sequence-specific nick in one strand of a duplex to initiate strand displacement linear amplification without the need for primers. Preferably, modified components of a T7 replisome are used for the in vitro linear amplification reaction enabling copying of at least 300 bases and as much as 50 kb of the target nucleic acid.
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.
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.
C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase
C12Q 1/44 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase involving esterase
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Enzymes for scientific and research use; Kits for scientific and research use, namely, kits for molecular biology and cell biology applications comprising enzymes; Enzymes for scientific and research use in the field of molecular biology and cell biology applications
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.
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses 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
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.
Kits and methods are provided that utilize a mesophilic strand displacing polymerase selected from Bsu DNA polymerase (large fragment) and Klenow in Loop mediated amplification (LAMP) at temperatures in the range of 34° C.-52ºC. This contrasts with 60° C.-65° C. required for standard Bst polymerase dependent LAMP. The reduced temperature of the LAMP reaction enables the use of other proteins that are temperature sensitive in a one-step reaction. For example, a Cas protein such as Cas12a may be used with a target nucleic acid specific guide RNA and optionally a reporter oligonucleotide containing a quencher and a fluorophore or lateral flow reagents to determine the presence of pathogens in a sample.
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Kits for scientific and research use, namely, kits for molecular biology and cell biology applications comprising cells and for protein expression; Reagents for scientific and research use in the field of molecular biology and cell biology applications and for protein expression; Cells for scientific and research use, namely, cells for molecular biology and cell biology applications and for protein expression
16.
Compositions and Methods for Analyzing Modified Nucleotides
Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.
The present disclosure relates, according to some embodiments, to enzymes, systems, compositions, methods, apparatus, and workflows for selectively cutting, cleaving, digesting and/or hydrolyzing duplex DNA strands or the DNA strand of a DNA/RNA hybrid.
The present disclosure relates, according to some embodiments, to enzymes, systems, compositions, methods, apparatus, and workflows for selectively cutting, cleaving, digesting and/or hydrolyzing duplex DNA strands or the DNA strand of a DNA/RNA hybrid.
C07K 14/435 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; Enzymes for scientific and research use; Kits for scientific and research use, namely, molecular biology and cell biology applications comprising enzymes; Reagents for scientific and research use in the field of molecular biology and cell biology applications; Enzymes for scientific and research use in the field of molecular biology and cell biology applications; Reagents for scientific and research use for reverse transcribing RNA into DNA; Reagent kits for reverse transcribing RNA into DNA comprising at least one of polymerases, buffers, and nucleic acids; Nucleic acid binding reagents for scientific and research use; Diagnostic reagents for scientific and research use; Diagnostic reagents and preparations, except for medical or veterinary use; Diagnostic reagents for in vitro use in biochemistry, clinical chemistry and microbiology; Diagnostic reagent kits for in vitro use for reverse transcribing RNA into DNA comprising at least one of polymerases, buffers, and nucleic acids
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; Enzymes for scientific and research use; Reagents for molecular biology and/or cell biology for scientific, research, laboratory or in vitro diagnostic use; Enzymes for molecular biology and/or cell biology for scientific, research, laboratory or in vitro diagnostic use; Reagents for diagnostic tests and/or diagnostic devices for scientific, research, laboratory or in vitro diagnostic use; Reagents for genetic research, clinical or medical laboratory use
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.
C07K 14/47 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans from vertebrates from mammals
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.
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
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Reagents for scientific and research use; enzymes for
scientific and research use; kits for scientific and
research use, namely, kits comprised of enzymes for
molecular biology and cell biology applications; reagents
for scientific and research use for molecular biology and
cell biology applications; enzymes for scientific and
research use for molecular biology and cell biology
applications; reagents for scientific and research use for
use in sequencing applications; enzymes for scientific and
research use for use in sequencing applications; kits
comprised of reagents and enzymes for use in sequencing
applications for scientific use; biological and biochemical
reagents and kits comprised of biological and biochemical
reagents for scientific or medical research use. Diagnostic reagents for clinical or medical laboratory use.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
(1) Kits comprising enzymes for scientific and research applications in the field of molecular biology and cell biology; reagents for scientific and research use in the field of molecular biology and cell biology applications; enzymes for scientific and research use in the field of molecular biology and cell biology applications.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
(1) Kits comprising enzymes for scientific and research applications in the field of molecular biology and cell biology; reagents for scientific and research use in the field of molecular biology and cell biology applications; enzymes for scientific and research use in the field of molecular biology and cell biology applications.
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.
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.
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
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.
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.
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
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Reagents for scientific and research use; Enzymes for scientific and research use; Kits for scientific and research use, namely, kits for molecular biology and cell biology applications comprised of enzymes; Reagents for scientific and research use in the field of molecular biology and cell biology applications; Enzymes for scientific and research use in the field of molecular biology and cell biology applications; Nucleic acid products, namely, mRNA and mRNA capping reagents for scientific research Nucleic acid products, namely, mRNA and mRNA capping reagents for pharmaceutical purposes and medical purposes
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; Enzymes for scientific and research use; Kits for scientific and research use, namely, kits for molecular biology and cell biology applications comprised of enzymes; Reagents for scientific and research use for molecular biology and cell biology applications; Enzymes for scientific and research use for molecular biology and cell biology applications; Reagents for scientific and research use for use in sequencing applications; Enzymes for scientific and research use for use in sequencing applications; Kits for use in sequencing applications comprised of reagents and enzymes for scientific use; Chemicals for use in industry and science; DNA polymerase, reagents and reagent kits comprising generic DNA circle, DNA polymerase and buffers for scientific, medical or veterinary research use; DNA polymerase, reagents and reagent kits comprising generic DNA circle, DNA primers, DNA polymerase and buffers for use in the biotechnology field
33.
METHODS FOR CHARACTERIZING AN IMMUNE RESPONSE REPERTOIRE
This disclosure provides synthetic nucleic acid oligonucleotides and related methods for analysis of immune repertoires. A disclosed synthetic oligonucleotide contains (a) one or more tags with a sequence that is not contained in a eukaryotic immune repertoire, wherein at least one tag is positioned between a region corresponding to a diversity and joining region (( D)J) and a constant region (C) of an immunoglobulin (IG) or T cell receptor, thereby distinguishing the synthetic oligonucleotide from naturally occurring sequences in the eukaryotic immune repertoire; and wherein the V(D)J region has a predetermined V(D)J clonotype, the synthetic oligonucleotide optionally further comprising a tag proximate to a region corresponding to a eukaryotic variable region (V); and optionally wherein C further comprises one or more priming sites for nucleic acid amplification.
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
34.
MONARCH DNA & RNA PURIFICATION NEW ENGLAND BIOLABS MONARCH DNA & RNA PURIFICATION
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Kits comprising biological and biochemical reagents for scientific research use; Kits comprising biological and biochemical reagents for medical research use; Diagnostic reagents for clinical laboratory use; Diagnostic reagents for medical laboratory use; Chemical products for commercial and scientific purposes, namely, chemicals for the isolation and purification of nucleic acids for scientific purposes and for use in polymerase chain reaction
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
(1) Reagents for scientific and research use; enzymes for scientific and research use; kits for scientific and research use, namely, kits comprised of enzymes for molecular biology and cell biology applications; reagents for scientific and research use for molecular biology and cell biology applications; enzymes for scientific and research use for molecular biology and cell biology applications; reagents for scientific and research use for use in sequencing applications; enzymes for scientific and research use for use in sequencing applications; kits comprised of reagents and enzymes for use in sequencing applications for scientific use; biological and biochemical reagents and kits comprised of biological and biochemical reagents for scientific or medical research use.
(2) Diagnostic reagents for clinical or medical laboratory use.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific research use; reagents for molecular
biology and/or cell biology for scientific, research,
laboratory or in vitro diagnostic use; reagents for
diagnostic tests and/or diagnostic devices for scientific,
research, laboratory or in vitro diagnostic use; reagents
for genetic research, clinical or medical laboratory use;
enzyme reagents for scientific, research, laboratory or in
vitro diagnostic use; enzymes for scientific and/or research
use; enzymes for molecular biology research and/or cell
biology scientific and research applications.
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.
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.
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.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses 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
40.
METHODS AND COMPOSITIONS FOR THE SIMULTANEOUS IDENTIFICATION AND MAPPING OF DNA METHYLATION
Provided herein is a method for generating a strand of DNA. In some embodiments, this method may comprise: (a) ligating a hairpin adaptor to a double-stranded fragment of DNA to produce a ligation product; (b) enzymatically generating a free 3' end in a double-stranded region of the hairpin adaptor in the ligation product; and (c) extending the free 3' end in a dCTP-free reaction mix that comprises a strand-displacing or nick-translating polymerase, dGTP, dATP, dTTP and modified dCTP to generate a hairpin product that has an original strand and a neosynthesized strand that contains modified Cs.
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.
C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
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.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
(1) Reagents for scientific research use; reagents for molecular biology and/or cell biology for scientific, research, laboratory or in vitro diagnostic use; reagents for diagnostic tests and/or diagnostic devices for scientific, research, laboratory or in vitro diagnostic use; reagents for genetic research, clinical or medical laboratory use; enzyme reagents for scientific, research, laboratory or in vitro diagnostic use; enzymes for scientific and/or research use; enzymes for molecular biology research and/or cell biology scientific and research applications.
Homo sapiens, Escherichia coli, Aspergillus oryzae, Momordica charanlia. Pyrococcus furiosus, Cucumis sativusSus scrojdSus scrojd) 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.
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.
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.
The present disclosure relates, according to some embodiments, to methods and compositions for preparing polynucleotide libraries enriched for a target sequence from source materials (e.g., samples comprising or constituting biological fluids, tissues, and/or specimens). Methods and compositions may provide efficient enrichment of the targeted polynucleotide. Enrichment may include increasing the relative abundance of the target from the source materials (where it may be present in low abundance) to the produced libraries (where it may be present in higher abundance). In some embodiments, methods include attaching (e.g., ligating, joining or otherwise fusing) an adapter to fragments of interest, nick translation, amplification (e.g., linear amplification), and target sequence selection using, for example, affinity tagging.
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.
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.
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.
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.
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.
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.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
Goods & Services
Biological and biochemical reagents for scientific or medical research use; Biological and biochemical kits comprising enzymes and reagents for scientific or medical research use; Diagnostic reagents for clinical or medical laboratory use; Chemical products for commercial and scientific purposes, namely, chemicals or biochemicals for the stabilization, preservation, purification, modification, and manipulation of nucleic acids for scientific purposes and for use in polymerase chain reaction; Reagents for scientific and research use, for the stabilization, preservation, purification, modification, and manipulation of biologic samples, namely, nucleic acids (RNA and DNA); Reagents for scientific and research use, for the inactivation of infectious agents, namely, virus, bacteria, and parasites; Reagents for sample preparation, stabilization, preservation, purification, lysis, modification, and manipulation of cells and tissues Reagents for medical use in the stabilization of biologic samples, namely, nucleic acids (RNA and DNA); Reagents for medical use for the inactivation of infectious agents, namely, virus, bacteria, and parasites; Reagents for medical use for preparation, stabilization, preservation, purification, lysis, modification, and manipulation of cells and tissues Devices, namely, sample collection tubes for scientific and research use for the inactivation of infectious agents, namely, virus, bacteria, and parasites; Devices, namely, sample collection tubes for scientific and research use for the preparation, stabilization, preservation, purification, lysis, modification, and manipulation of cells and tissues; Devices, namely, sample collection tubes for scientific and research use, for the stabilization, preservation, purification, modification, and manipulation of biologic samples, namely, nucleic acids (RNA and DNA)
56.
Rolling Circle Reverse Transcription of Circular RNA
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.
C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
57.
COMPOSITIONS AND METHODS FOR DETECTING PYROPHOSPHATE PRODUCTS OF ENZYME REACTIONS USING PYRIDYLAZOANILINE DYES
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.
C09B 29/036 - Monoazo dyes prepared by diazotising and coupling characterised by the diazo component from diazotised amines containing a heterocyclic ring the heterocyclic ring containing only nitrogen as hetero atoms
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
G01N 33/52 - Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper
G01N 33/84 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving inorganic compounds or pH
58.
COMPOSITIONS AND METHODS FOR DETECTING PYROPHOSPHATE PRODUCTS OF ENZYME REACTIONS USING PYRIDYLAZOANILINE DYES
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.
G01N 33/52 - Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C09B 29/036 - Monoazo dyes prepared by diazotising and coupling characterised by the diazo component from diazotised amines containing a heterocyclic ring the heterocyclic ring containing only nitrogen as hetero atoms
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.
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.
C07K 14/31 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from bacteria from Micrococcaceae (F) from Staphylococcus (G)
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; enzymes for
scientific and research use; reagents for scientific and
research use in the field of molecular biology; enzymes for
scientific and research use in the field of molecular
biology; kits comprising enzymes for scientific and research
applications in the field of molecular biology.
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.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses 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
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
(1) Reagents for scientific and research use; enzymes for scientific and research use; reagents for scientific and research use in the field of molecular biology; enzymes for scientific and research use in the field of molecular biology; kits comprising enzymes for scientific and research applications in the field of molecular biology.
64.
Methods for Labeling a Population of RNA Molecules
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.
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
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; Enzymes for scientific and research use; Kits for scientific and research use, namely, molecular biology and cell biology applications comprising enzymes; Reagents for scientific and research use in the field of molecular biology and cell biology applications; Enzymes for scientific and research use in the field of molecular biology and cell biology applications; Reagents for scientific and research use for genetic research, clinical or medical laboratory use; Kits for genetic research, nucleic acid sequencing, clinical or medical laboratory use comprising at least one of enzymes, buffers, cells and nucleic acids; Reagents for scientific and research use for use in sequencing nucleic acids; Kits for use in sequencing nucleic acids comprising at least one of enzymes, buffers, cells and nucleic acids
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.
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C12Q 1/6816 - Hybridisation assays characterised by the detection means
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.
Kits and methods are provided that utilize a mesophilic strand displacing polymerase selected from Bsu DNA polymerase (large fragment) and Klenow in Loop mediated amplification (LAMP) at temperatures in the range of 34°C-52°C. This contrasts with 60°C -65°C required for standard Bst polymerase dependent LAMP. The reduced temperature of the LAMP reaction enables the use of other proteins that are temperature sensitive in a one-step reaction. For example, a Cas protein such as Cas12a may be used with a target nucleic acid specific guide RNA and optionally a reporter oligonucleotide containing a quencher and a fluorophore or lateral flow reagents to determine the presence of pathogens in a sample.
Clostridium butyricumClostridium butyricum) may be synchronized with DNA strand unwinding activity of a helicase (e.g., a nuclease deficient RecBexo- E.coli 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 Cb Ago/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.
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.
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.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; enzymes for
scientific and research use; kits comprising enzymes for
scientific and research applications in the field of
molecular biology or cell biology; reagents for scientific
and research use in the field of molecular biology or cell
biology applications; enzymes for scientific and research
use in the field of molecular biology or cell biology
applications; reagents for in vitro transcription for
scientific and research use.
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.
C07K 14/47 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans from vertebrates from mammals
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.
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
76.
Compositions and methods for detecting pyrophosphate products of enzyme reactions using pyridylazoaniline dyes
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.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
(1) Reagents for scientific and research use; enzymes for scientific and research use; kits comprising enzymes for scientific and research applications in the field of molecular biology or cell biology; reagents for scientific and research use in the field of molecular biology or cell biology applications; enzymes for scientific and research use in the field of molecular biology or cell biology applications; reagents for in vitro transcription for scientific and research use.
78.
Compositions and Methods Relating to Synthetic RNA Polynucleotides Created From Synthetic DNA Oligonucleotides
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
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.
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.
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.
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
82.
Cleavage of Single Stranded DNA Having a Modified Nucleotide
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.
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.
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.
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
85.
FAUSTOVIRUS CAPPING ENZYME, MRNA CAPPING ENZYME COMPOSITIONS, METHODS AND KITS
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.
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.
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.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses 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
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; Enzymes for scientific and research use; Kits for scientific and research use, namely, kits comprised of enzymes for molecular biology and cell biology applications; Reagents for scientific and research use for molecular biology and cell biology applications; Enzymes for scientific and research use for molecular biology and cell biology applications; Reagents for scientific and research use for use in sequencing applications; Enzymes for scientific and research use for use in sequencing applications; Kits comprised of reagents and enzymes for use in sequencing applications for scientific use; Diagnostic reagents for clinical or medical laboratory use; Biological and biochemical reagents and kits comprised of biological and biochemical reagents for scientific or medical research use
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.
Ordered assembly of large numbers of fragments into a single large DN A 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 DIMA 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.
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.
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.
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.
41 - Education, entertainment, sporting and cultural services
Goods & Services
On-line journals, namely, blogs featuring topics on science, art, lab tips, environmental sustainability, career advice and social responsibility; Providing a website featuring blogs and non-downloadable publications in the nature of articles in the field(s) of life sciences
96.
APPLICATION OF IMMOBILIZED ENZYMES FOR NANOPORE LIBRARY CONSTRUCTION
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.
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.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses 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
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.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagents for scientific and research use; Enzymes for scientific and research use; Kits for scientific and research use, namely, molecular biology and cell biology applications comprising enzymes; Reagents for scientific and research use in the field of molecular biology and cell biology applications; Enzymes for scientific and research use in the field of molecular biology and cell biology applications; Reagents for scientific and research use for genetic research, clinical or medical laboratory use; Kits for genetic research, nucleic acid sequencing, clinical or medical laboratory use comprising at least one of enzymes, buffers, cells and nucleic acids; Reagents for scientific and research use for use in sequencing nucleic acids; Kits for use in sequencing nucleic acids comprising at least one of enzymes, buffers, cells and nucleic acids
42 - Scientific, technological and industrial services, research and design
Goods & Services
Providing a website featuring on-line non-downloadable software tools for use in molecular biology and diagnostic experimental design, namely, software for designing, analyzing, and visualizing polynucleotide assembly components, polynucleotide assemblies, and assembly ligation fidelity
