[
{
"id": "authors:q3dw5-ebv06",
"collection": "authors",
"collection_id": "q3dw5-ebv06",
"cite_using_url": "https://authors.library.caltech.edu/records/q3dw5-ebv06",
"type": "article",
"title": "A system for in vitro selection of fully 2\u2032-modified RNA aptamers",
"author": [
{
"family_name": "Ziperman",
"given_name": "Emily D.",
"orcid": "0000-0002-2180-0854",
"clpid": "Ziperman-Emily-D"
},
{
"family_name": "Fitzpatrick",
"given_name": "Kate B.",
"orcid": "0009-0002-4389-1969",
"clpid": "Fitzpatrick-Kate-B"
},
{
"family_name": "Nair",
"given_name": "Malavika A.",
"clpid": "Nair-Malavika-A"
},
{
"family_name": "Sorum",
"given_name": "Alexander W.",
"orcid": "0000-0003-2526-1445",
"clpid": "Sorum-Alexander-W"
},
{
"family_name": "Hsieh-Wilson",
"given_name": "Linda C.",
"orcid": "0000-0001-5661-1714",
"clpid": "Hsieh-Wilson-L-C"
},
{
"family_name": "Krauss",
"given_name": "Isaac J.",
"orcid": "0000-0003-0984-4085",
"clpid": "Krauss-Isaac-J"
}
],
"abstract": "SFM4-3, KOD DGLNK, and Therminator polymerase are investigated for their compatibility with SELection with Modified Aptamers (SELMA), an aptamer discovery method that enables incorporation of large nucleobase modifications such as glycans. We demonstrated that with suitable modifications to the primer design and protocol, these enzymes are compatible with SELMA, enabling 2′-fluoro or 2′-methoxy ribose modifications at all positions. In the case of 2′-fluoro modifications, Therminator exhibits cleaner incorporation of an alkyne-modified nucleobase for click chemistry.
",
"doi": "10.1039/d4ob01505c",
"issn": "1477-0520",
"publisher": "Royal Society of Chemistry",
"publication": "Organic & Biomolecular Chemistry",
"publication_date": "2025"
},
{
"id": "authors:y4e15-az991",
"collection": "authors",
"collection_id": "y4e15-az991",
"cite_using_url": "https://authors.library.caltech.edu/records/y4e15-az991",
"type": "article",
"title": "Chemoenzymatic Labeling, Detection and Profiling of Core Fucosylation in Live Cells",
"author": [
{
"family_name": "Zhu",
"given_name": "Qiang"
},
{
"family_name": "Chaubard",
"given_name": "Jean-Luc"
},
{
"family_name": "Geng",
"given_name": "Didi"
},
{
"family_name": "Shen",
"given_name": "Jiechen",
"orcid": "0000-0002-3722-3991"
},
{
"family_name": "Ban",
"given_name": "Lan"
},
{
"family_name": "Cheung",
"given_name": "Sheldon T."
},
{
"family_name": "Wei",
"given_name": "Fangyu"
},
{
"family_name": "Liu",
"given_name": "Yating"
},
{
"family_name": "Sun",
"given_name": "Haofan",
"orcid": "0000-0002-4335-7371"
},
{
"family_name": "Calderon",
"given_name": "Angie"
},
{
"family_name": "Dong",
"given_name": "Wenbo",
"orcid": "0000-0002-0589-7027"
},
{
"family_name": "Qin",
"given_name": "Weijie",
"orcid": "0000-0002-7633-9786"
},
{
"family_name": "Li",
"given_name": "Tiehai",
"orcid": "0000-0002-3600-1828"
},
{
"family_name": "Wen",
"given_name": "Liuqing",
"orcid": "0000-0001-9187-7999"
},
{
"family_name": "Wang",
"given_name": "Peng George"
},
{
"family_name": "Sun",
"given_name": "Shisheng",
"orcid": "0000-0002-7242-7164"
},
{
"family_name": "Yi",
"given_name": "Wen",
"orcid": "0000-0002-4257-3355"
},
{
"family_name": "Hsieh-Wilson",
"given_name": "Linda C.",
"orcid": "0000-0001-5661-1714",
"clpid": "Hsieh-Wilson-L-C"
}
],
"abstract": "Core fucosylation, the attachment of an α-1,6-linked-fucose to the N-glycan core pentasaccharide, is an abundant protein modification that plays critical roles in various biological processes such as cell signaling, B cell development, antibody-dependent cellular cytotoxicity, and oncogenesis. However, the tools currently used to detect core fucosylation suffer from poor specificity, exhibiting cross-reactivity against all types of fucosylation. Herein we report the development of a new chemoenzymatic strategy for the rapid and selective detection of core fucosylated glycans. This approach employs a galactosyltransferase enzyme identified fromCaenorhabditis elegansthat specifically transfers an azido-appended galactose residue onto core fucose via a β-1,4 glycosidic linkage. We demonstrate that the approach exhibits superior specificity toward core fucose on a variety of complex N-glycans. The method enables detection of core fucosylated glycoproteins from complex cell lysates, as well as on live cell surfaces, and it can be integrated into a diagnostic platform to profile protein-specific core fucosylation levels. This chemoenzymatic labeling approach offers a new strategy for the identification of disease biomarkers and will allow researchers to further characterize the fundamental role of this important glycan in normal and disease physiology.
",
"doi": "10.1021/jacs.4c09303",
"issn": "0002-7863",
"publisher": "American Chemical Society",
"publication": "Journal of the American Chemical Society",
"publication_date": "2024-09-16"
},
{
"id": "authors:apbnj-j0165",
"collection": "authors",
"collection_id": "apbnj-j0165",
"cite_using_url": "https://authors.library.caltech.edu/records/apbnj-j0165",
"type": "article",
"title": "Recent advances in the synthesis of extensive libraries of heparan sulfate oligosaccharides for structure\u2013activity relationship studies",
"author": [
{
"family_name": "Ramadan",
"given_name": "Sherif",
"orcid": "0000-0002-8639-4105",
"clpid": "Ramadan-Sherif"
},
{
"family_name": "Mayieka",
"given_name": "Morgan",
"clpid": "Mayieka-Morgan"
},
{
"family_name": "Pohl",
"given_name": "Nicola L. B.",
"orcid": "0000-0001-7747-8983",
"clpid": "Pohl-Nicola-L-B"
},
{
"family_name": "Liu",
"given_name": "Jian",
"clpid": "Liu-Jian"
},
{
"family_name": "Hsieh-Wilson",
"given_name": "Linda C.",
"orcid": "0000-0001-5661-1714",
"clpid": "Hsieh-Wilson-L-C"
},
{
"family_name": "Huang",
"given_name": "Xuefei",
"orcid": "0000-0002-6468-5526",
"clpid": "Huang-Xuefei"
}
],
"abstract": "\n
\n
Heparan sulfate (HS) is a linear, sulfated and highly negatively-charged polysaccharide that plays important roles in many biological events. As a member of the glycosaminoglycan (GAG) family, HS is commonly found on mammalian cell surfaces and within the extracellular matrix. The structural complexities of natural HS polysaccharides have hampered the comprehension of their biological functions and structure–activity relationships (SARs). Although the sulfation patterns and backbone structures of HS can be major determinants of their biological activities, obtaining significant amounts of pure HS from natural sources for comprehensive SAR studies is challenging. Chemical and enzyme-based synthesis can aid in the production of structurally well-defined HS oligosaccharides. In this review, we discuss recent innovations enabling the syntheses of large libraries of HS and how these libraries can provide insights into the structural preferences of various HS binding proteins.
\n
\n
\n
The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describe Networking of Interactors and SubstratEs (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.
\n