Agilent Technologies, Inc.

University of California

Brian Phillip Smart

Joel Myerson

Robert A Ach

Douglas J Dellinger

James Alexander Apffel, Jr

Carolyn Ruth Bertozzi

Kristin Briana Bernick

Javier E Satulovsky

Mark Alan Breidenbach

Magdalena Anna Ostrowski

Gregory Staples

Brooks Bond-Watts

Mistuni Ghosh

Austin A Pitcher

Krishnan K Palaniappan

Craig Daniel Wenger

Compounds and methods for purifying oligonucleotides such as RNA and DNA. A target oligonucleotide is reacted with an orthoester linker comprising an affinity tag to form an orthoester oligonucleotide-orthoester linker conjugate which is subjected to a purification technique to separate the target oligonucleotide from impurities such as truncated oligonucleotides. The orthoester linker can be then removed under mild conditions to generate the target oligonucleotide in high purity.

Orthoester compositions for affinity purification of oligonucleotides

A method for removing an ionic liquid from an aqueous sample is provided. In some embodiments, the method includes: (a) combining an aqueous sample including an ionic liquid with an ion exchanger composition including an ion exchanger counterion to produce a solution including a fluorous salt of the ionic liquid, where at least one of the ionic liquid and the ion exchanger counterion is fluorinated; (b) contacting the solution with a fluorous affinity material, thereby removing fluorous salt from the solution and producing an aqueous eluate; and (c) collecting the aqueous eluate. In certain embodiments, the method further includes: contacting a cell with an ionic liquid composition to lyse the cell and produce an aqueous sample; and contacting the aqueous sample with a reverse phase substrate, thereby adsorbing proteins and/or lipids of the cell on the substrate. Compositions, kits and systems for practicing the subject methods are also provided.

Fluorous affinity extraction for ionic liquid-based sample preparation

Among other things, this disclosure provides a method of detecting a target nucleic acid. Aspects of the method include: (a) obtaining a labeled nucleic acid probe that is complementary to a target nucleic acid, wherein the probe comprises a capture tag; (b) hybridizing the probe with the target nucleic in a fixed cell, in situ, to produce a duplex; (c) linking the probe in the duplex to a peroxidase conjugate via the capture tag to produce a peroxidase-labeled duplex; and (d) incubating the peroxidase-labeled duplex with a peroxidase substrate, wherein the peroxidase activity of the peroxidase conjugate catalyzes deposition of the substrate in the vicinity of the duplex, thereby producing a detectable signal.

Signal amplification of fluorescence in situ hybridization

Provided herein is a method of sample analysis. In certain embodiments, the method comprises: a) cross-linking protein of a cell using a first compound to produce a first cross-linked product comprising cross-linked protein, and RNA; b) contacting the first cross-linked product and a second compound under conditions by which an oligonucleotide portion of the second compound hybridizes to the RNA; c) activating a reaction the first and second compound, thereby covalently crosslinking the oligonucleotide to the cross-linked protein to produce a second cross-linked product; d) isolating the second cross-linked product using an affinity tag; and e) analyzing the isolated second cross-linked product. Compounds for performing the method are also provided.

Isolation of RNA-protein complexes using cross-linking reagents and oligonucleotides

Aspects of the present disclosure include methods for detecting a low abundance protein and methods for identifying a site of N-glycosylation on a protein. In practicing methods according to certain embodiments, a eukaryotic cell is contacted with an isotopic labeling composition and isotopically labeled N-glycosylated peptides obtained from the eukaryotic cell are assessed by liquid chromatography-tandem mass spectrometry. A predetermined isotopic pattern in the mass spectrum is identified and amino acid sequences of the peptides containing the predetermined isotopic pattern are determined. Systems for identifying a predetermined isotopic pattern in mass spectra and determining amino acid sequences of peptides containing the predetermined isotopic pattern are also described.

Isotopic recoding for targeted tandem mass spectrometry

Compound tags and shifting agents are provided that find use in ion mobility spectrometry (IMS), mass spectrometry (MS), or a combination of IMS and MS, and which can substantially increase separation of multiple components in complex samples and facilitate quantitative and multiplexed analyses. In some cases, the compounds include a linker and a normalizing group, each including a structural unit and separated by a cleaveable group, and a crown ether. Also provided are methods for analyzing peptides in a sample. In some cases, the method includes coupling the compound to peptides which include a terminal guanidinium moiety capable of forming an intra-molecular complex with the crown ether.

Ion mobility mass spectrometry tags for quantitative applications and methods thereof

A microfluidic device for glycan analysis includes a deglycosylation column comprising a glycosidase attached to a solid support; a tagging column comprising a reactive ester for reaction with an amino group, wherein the tagging column is arranged downstream of the deglycosylation column; an analytical column comprising a stationary phase capable of separating a derivatized glycan; and a plurality of inlet/outlet ports configured to connect with channels on a switching element to form flow paths.

Derivatization of PNGase F released glycans on an HPLC chip

Crosslinking reagents and methods for using the same for analysis of protein-protein interactions, are provided. The crosslinking reagents include a trifunctional scaffold that links two protein linking groups to each other and branches to link an affinity tag, where the protein linking groups can be fragmented from the scaffold. The distance between the two protein linking groups can be selected to crosslink two proteins of a protein complex via accessible amino acid residues. Also provided are crosslinked polypeptide compounds and kits that include crosslinking reagents. These reagents and methods find use in a variety of applications in which crosslinking of proteins in desired.

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San Jose, CA, United States of America

Brian Phillip Smart