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Bioorthogonal chemistry

Junu Bae, Zijian Zhou, Thomas Theis, Warren S Warren, Qiu Wang
Hyperpolarized magnetic resonance (HP-MR) is a powerful, sensitive, and noninvasive approach to visualize molecular structure, function, and dynamics in vitro and in vivo. Current applications of HP-MR mostly rely on hyperpolarization of target compounds in dedicated hyperpolarizers because biomolecules can typically not be hyperpolarized directly in vivo. The injected hyperpolarized probes often undergo multiple metabolic pathways in living systems, and it remains challenging to localize and identify specific targets with high chemical selectivity...
March 2018: Science Advances
Wenshu Zheng, Huiling Li, Wenwen Chen, Jiangjiang Zhang, Nuoxin Wang, Xuefeng Guo, Xingyu Jiang
A fast (1 min), straightforward but efficient, click chemistry-based system that enables the rapid detection of free copper (Cu) ions in either biological fluids or living cells without tedious pretreatment is provided. Cu can quickly induce the conjugation between graphene oxide (GO) and a fluorescent dye via click reaction. On the basis of the high specificity of bioorthogonal reaction and the effective quenching ability of GO, the assay studied in this paper can respond to Cu ions in less than 1 min with excellent selectivity and sensitivity, which is the fastest sensor for Cu as far as it is known...
March 1, 2018: Small
Katja Hartstock, Benedikt Nilges, Anna Ovcharenko, Nicolas Cornelissen, Nikolai Puellen, Sebastian Leidel, Andrea Rentmeister
m6A is the most abundant internal modification in eukaryotic mRNA. It is introduced by METTL3-METTL14 and tunes mRNA metabolism, impacting cell differentiation and development. Precise transcriptome-wide assignment of m6A sites is of utmost importance. However, m6A does not interfere with Watson-Crick base pairing making polymerase-based detection challenging. We developed a chemical-biology approach for the precise mapping of methyltransferase (MTase) target sites based on the introduction of a bioorthogonal propargyl group in vitro and in cells...
February 20, 2018: Angewandte Chemie
Gaochao Lv, Ke Li, Ling Qiu, Ying Peng, Xueyu Zhao, Xi Li, Qingzhu Liu, Shanshan Wang, Jianguo Lin
PURPOSE: Improving the targeting efficiency of imaging agents or anticancer drugs has become essential in the current primary mission to enhance the diagnostic or therapeutic effects. To improve the tumor diagnosis and therapy effect, a promising drug-delivery and targeting strategy was established based on the bioorthogonal chemistry. METHOD: The delivery system was composed of the pre-targeting carrier Biotin-MSNs-DBCO nanoparticles and the azido cargoes. The fluorescence probe 1-(3-azidopropyl) fluorescein (FITC-N 3 ) and ruthenium N-heterocyclic carbene complex N 3 -S-S-NHC-Ru were synthesized and served as the tumor imaging and therapy probes, respectively...
February 14, 2018: Pharmaceutical Research
Clémence Simon, Corentin Spriet, Simon Hawkins, Cedric Lion
Lignin is one of the most prevalent biopolymers on the planet and a major component of lignocellulosic biomass. This phenolic polymer plays a vital structural and protective role in the development and life of higher plants. Although the intricate mechanisms regulating lignification processes in vivo strongly impact the industrial valorization of many plant-derived products, the scientific community still has a long way to go to decipher them. In a simple three-step workflow, the dual labeling protocol presented herein enables bioimaging studies of actively lignifying zones of plant tissues...
January 26, 2018: Journal of Visualized Experiments: JoVE
Selma Eising, Nicole van der Linden, Fleur Kleinpenning, Kimberly M Bonger
Bioorthogonal chemistry can be used for the selective modification of biomolecules without interfering with any other functionality present in the cell. The tetrazine ligation is very suitable as bioorthogonal reaction because of its selectivity and high reaction rates with several alkenes and alkynes. Recently, we described vinylboronic acids (VBAs) as novel hydrophilic bioorthogonal moieties that react efficiently with dipyridyl-s-tetrazines and used them for protein modification in cell lysate. It is not clear, however, whether VBAs are suitable for labeling experiments in living cells because of the possible coordination with, for example, vicinal carbohydrate diols...
February 13, 2018: Bioconjugate Chemistry
Mathis Baalmann, Marcel Best, Richard Wombacher
Here, we describe a two-step protocol for selective protein labeling based on enzyme-mediated peptide labeling utilizing lipoic acid ligase (LplA) and bioorthogonal chemistry. The method can be applied to purified proteins, protein in cell lysates, as well as living cells. In a first step a W37V mutant of the lipoic acid ligase (LplAW37V) from Escherichia coli is utilized to ligate a synthetic chemical handle site-specifically to a lysine residue in a 13 amino acid peptide motif-a short sequence that can be genetically expressed as a fusion with any protein of interest...
2018: Methods in Molecular Biology
Robert J Blizzard, True E Gibson, Ryan A Mehl
Genetic code expansion is commonly used to introduce bioorthogonal reactive functional groups onto proteins for labeling. In recent years, the inverse electron demand Diels-Alder reaction between tetrazines and strained trans-cyclooctenes has increased in popularity as a bioorthogonal ligation for protein labeling due to its fast reaction rate and high in vivo stability. We provide methods for the facile synthesis of a tetrazine containing amino acid, Tet-v2.0, and the site-specific incorporation of Tet-v2...
2018: Methods in Molecular Biology
Robyn M Barfield, David Rabuka
Enzymatic modification of proteins can generate uniquely reactive chemical functionality, enabling site-specific reactions on the protein surface. Formylglycine-generating enzyme (FGE) is one enzyme that can be exploited in this fashion. FGE binds its consensus sequence (CXPXR, known as the "aldehyde-tag") and converts the cysteine to a formylglycine (fGly). fGly-containing proteins contain a bioorthogonal aldehyde on their surface that can be modified selectively in the presence of the 20 canonical amino acids...
2018: Methods in Molecular Biology
Jonathan Carlson, Hannes Mikula, Ralph Weissleder
Recent developments in bond cleavage reactions have expanded the scope of bioorthogonal chemistry beyond click ligation and enabled new strategies for probe activation and therapeutic delivery. These applications, however, remain in their infancy, with further innovations needed to achieve the efficiency required for versatile and broadly useful tools in vivo. Amongst these chemistries, the tetrazine/trans-cyclooctene click-to-release reaction has exemplary kinetics and adaptability but achieves only partial release and is incompletely understood, which has limited its application...
January 31, 2018: Journal of the American Chemical Society
Jan-Philip Meyer, Kathryn M Tully, James Jackson, Thomas R Dilling, Thomas Reiner, Jason S Lewis
Pretargeting strategies have gained popularity for the in vivo imaging and therapy of cancer by combining antibodies with small molecule radioligands. In vivo re-combination of both moieties can be achieved using the bioorthogonal inverse electron demand Diels-Alder (IEDDA) chemistry between tetrazine (Tz) and trans-cyclooctene (TCO). An issue that arises with pretargeting strategies is that while part of the antibody dose accumulates at antigen-expressing tumor tissue, there is a significant portion of the injected antibody that remains in circulation, causing a reduction in target-to-background ratios...
January 30, 2018: Bioconjugate Chemistry
Xudong Shi, Kai Gao, Hao Huang, Ran Gao
Pretargeted immuno-PET imaging based on the bioorthogonal chemistry between 18F-labeled Reppe anhydride derivatives and tetrazine conjugates of the EGFR-specific monoclonal antibodies cetuximab and panitumumab was performed. This pretargeting approach yielded high target-to-nontarget ratios. Furthermore, due to the fast clearance rate of the PET probe, the overall radiation burden to nontarget tissues was also substantially decreased.
January 16, 2018: Bioconjugate Chemistry
Siddharth Sai Matikonda, Jessica M Fairhall, Franziska Fiedler, Suchaya Sanhajariya, Robert A J Tucker, Sarah Hook, Anna L Garden, Allan B Gamble
Bioorthogonal prodrug activation/decaging strategies need to be selective, rapid and release the drug from the masking group upon activation. The rates of the 1,3-dipolar cycloaddition between a trans-cyclooctene (TCO) and a series of fluorine-substituted azido-PABC self-immolative spacers caging two model drugs, and subsequent release from the 1,2,3-triazoline are reported. As the number of fluorine substituents on the PABC linker increases from one to four, the rate of cycloaddition increases by almost one-order of magnitude...
January 12, 2018: Bioconjugate Chemistry
Johannes G Rebelein, Thomas R Ward
Bioorthogonal chemistry largely relies on the use of abiotic metals to catalyze new-to-nature reactions in living systems. Over the past decade, metal complexes and metal-encapsulated systems such as nanoparticles have been developed to unravel the reactivity of transition metals, including ruthenium, palladium, iridium, copper, iron, and gold in biological systems. Thanks to these remarkable achievements, abiotic catalysts are able to fluorescently label cells, uncage or form cytotoxic drugs and activate enzymes in cellulo/vivo...
January 4, 2018: Current Opinion in Biotechnology
Young Kim, Zhe Zhang, Jae-Hyuck Shim, Tae Sup Lee, Ching-Hsuan Tung
Cell therapies are promising up-and-coming therapeutic strategies for many diseases. For maximal therapeutic benefits, injected cells have to navigate their way to a designated area, including organ and tissue; unfortunately, the majority of therapeutic cells are currently administered without a guide or homing device. To improve this serious shortcoming, a functionalization method was developed to equip cells with a homing signal. Its application was demonstrated by applying an Azadibenzocyclooctyne-bisphosphonate (ADIBO-BP) and azide paired bioorthogonal chemistry on cells for bone specific homing...
December 26, 2017: Bioorganic & Medicinal Chemistry
Ainara Leizeaga, Margarita Estrany, Irene Forn, Marta Sebastián
A major challenge in microbial ecology is linking diversity and function to determine which microbes are actively contributing to processes occurring in situ. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising technique for detecting and quantifying translationally active bacteria in the environment. This technique consists of incubating a bacterial sample with an analog of methionine and using click-chemistry to identify the cells that have incorporated the substrate. Here, we established an optimized protocol for the visualization of protein-synthesizing cells in oligotrophic waters that can be coupled with taxonomic identification using Catalyzed Reporter Deposition Fluorescent in Situ Hybridization...
2017: Frontiers in Microbiology
Yujia Qing, Gökçe Su Pulcu, Nicholas A W Bell, Hagan Bayley
Tetrazine- and sydnone-based click reactions have emerged as important bioconjugation strategies with fast kinetics and N2 or CO2 as the only byproduct. Mechanistic studies of these reactions have focused on the initial rate-determining cycloaddition steps. The subsequent N2 or CO2 release from the bicyclic intermediates has been approached mainly through computational studies, which have predicted lifetimes of femtoseconds. In the present study, bioorthogonal cycloadditions involving N2 or CO2 extrusion have been examined experimentally at the single-molecule level by using a protein nanoreactor...
January 26, 2018: Angewandte Chemie
Kazuya Matsuo, Yuki Nishikawa, Marie Masuda, Itaru Hamachi
The development of bioorthogonal approaches for labeling of endogenous proteins under the multimolecular crowding conditions of live cells is highly desirable for the analysis and engineering of proteins without using genetic manipulation. N-Sulfonyl pyridone (SP) is reported as a new reactive group for protein sulfonylation. The ligand-directed SP chemistry was able to modify not only purified proteins in vitro, but also endogenous ones on the surface of and inside live cells selectively and rapidly, which allowed to convert endogenous proteins to FRET-based biosensors in situ...
January 15, 2018: Angewandte Chemie
Man Kyu Shim, Hong Yeol Yoon, Sangmin Lee, Mun Kyeong Jo, Jooho Park, Jong-Ho Kim, Seo Young Jeong, Ick Chan Kwon, Kwangmeyung Kim
Apoptosis is one of the most important intracellular events in living cell, which is a programmed cell death interrelated with caspase enzyme activity for maintaining homeostasis in multicellular organisms. Therefore, direct apoptosis imaging of living cells can provide enormous advantages for diagnosis, drug discovery, and therapeutic monitoring in various diseases. However, a method of direct apoptosis imaging has not been fully validated, especially for live cells in in vitro and in vivo. Herein, we developed a new apoptosis imaging technology via a direct visualization of active caspase-3/-7 activity in living cells...
November 30, 2017: Scientific Reports
Robert Serfling, Christian Lorenz, Maja Etzel, Gerda Schicht, Thore Böttke, Mario Mörl, Irene Coin
The pyrrolysyl-tRNA synthetase/tRNAPyl pair is the most versatile and widespread system for the incorporation of non-canonical amino acids (ncAAs) into proteins in mammalian cells. However, low yields of ncAA incorporation severely limit its applicability to relevant biological targets. Here, we generate two tRNAPyl variants that significantly boost the performance of the pyrrolysine system. Compared to the original tRNAPyl, the engineered tRNAs feature a canonical hinge between D- and T-loop, show higher intracellular concentrations and bear partially distinct post-transcriptional modifications...
January 9, 2018: Nucleic Acids Research
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