New England Biolabs, Inc.

Ivan R Correa, Jr

Nan Dai

Nathan Tanner

Yinhua Zhang

Nicole Nichols

Laurence Ettwiller

Clotilde K Carlow

Zhiru Li

Gregory Patton

Guoping Ren

Ira Schildkraut

Eric Hunt

Esta Slayton

Andrew Barry

Catherine B Poole

Harriet M Strimpel

Yu Brian Zheng

Zhenyu Zhu

Shengxi Guan

Aine Quimby

Richard J Roberts

Romualdas Vaisvila

Lana Saleh

George Tzertzinis

Janine Borgaro

Madalee G Wulf

June Pais

Megumu Mabuchi

Thomas C Evans, Jr

Sriharsa Pradhan

Hang-Gyeong Chin

Jurate Bitinaite

Bo Yan

John Buswell

Ece Alpaslan

Erbay Yigit

Sebastian Grünberg

Eric Wolf

Michael Sproviero

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.,, and) 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.

Compositions and analysis of dephosphorylated oligoribonucleotides

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.

Rapid diagnostic test for lamp

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.

Rapid diagnostic test for LAMP

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.

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

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&#x2032;-diphosphorylated or 5&#x2032;-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&#x2032; or 3&#x2032; 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.

Methods for labeling a population of RNA molecules

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&#x2032; end of the population of cDNAs using a terminal transferase, to produce an cDNA library.

Enrichment and sequencing of RNA species

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&#x2032;-diphosphorylated or 5&#x2032;-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.

Methods for enriching for a population of RNA molecules

Methods, compositions and kits for selectively altering and detecting modified cytosine residues are provided.

Mapping cytosine modifications

5-methylpyrimidine oxygenases and their use in the modification of nucleic acids are described.

Compositions and methods for oxygenation of nucleic acids containing 5-methylpyrimidine

Nucleic acids comprising &#x3b2;-glucosaminyloxy-5-methylcytosine; compositions, kits and methods of producing the nucleic acids using a glycosyltransferase; and methods of using the nucleic acids are described.

Compositions and methods for the transfer of a hexosamine to a modified nucleotide in a nucleic acid

Composition and methods of oxygenation of nucleic acids containing 5-methylpyrimidine

Growing community of inventors

Ipswich, MA, United States of America

Ivan R Correa, Jr