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https://www.readbyqxmd.com/read/29775058/multiple-click-selective-trna-synthetases-expand-mammalian-cell-specific-proteomics
#1
Andrew C Yang, Haley du Bois, Niclas Olsson, David Gate, Benoit Lehallier, Daniela Berdnik, Kyle D Brewer, Carolyn R Bertozzi, Joshua E Elias, Tony Wyss-Coray
Bio-orthogonal tools enable cell-type-specific proteomics, a prerequisite to understanding biological processes in multicellular organisms. Here we report two engineered aminoacyl-tRNA synthetases for mammalian bio-orthogonal labeling: a tyrosyl ( ScTyrY34G ) and a phenylalanyl ( MmPheT412G ) tRNA synthetase that incorporate azide-bearing noncanonical amino acids specifically into the nascent proteomes of host cells. Azide-labeled proteins are chemoselectively tagged via azide-alkyne cycloadditions with fluorophores for imaging or affinity resins for mass spectrometric characterization...
May 18, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29773065/copper-catalyzed-azide-alkyne-cycloaddition-cuaac-mediated-macrocylization-of-peptides-impact-on-conformation-and-biological-activity
#2
Chiara Testa, Anna Maria Papini, Michael Chorev, Paolo Rovero
The long lasting impetus to design novel modes of macrocyclization, and their implementation into a wide range of bioactive peptides, originates from their contributions to the restriction of conformational space and the stabilization of preferential bioactive conformations that support higher efficacy and binding affinity to cognate macromolecular targets, improved specificity and lowering susceptibility to enzymatic degradation processes. Introducing CuI-catalyzed azide-alkyne cycloadditon (CuAAC), a prototypical click reaction, to the field of peptide sciences as a bio-orthogonal reaction that generates a disubstituted-[1,2,3]triazol-1-yl moiety as a pseudopeptidic bond that is peptidomimetic in nature, paved the way to its wide spread application as a new and promising mode of macrocyclization...
May 17, 2018: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29725066/isothermal-folding-of-a-light-up-bio-orthogonal-rna-origami-nanoribbon
#3
Emanuela Torelli, Jerzy Wieslaw Kozyra, Jing-Ying Gu, Ulrich Stimming, Luca Piantanida, Kislon Voïtchovsky, Natalio Krasnogor
RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter...
May 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29692987/synthesis-of-symmetrical-tetrameric-conjugates-of-the-radiolanthanide-chelator-dotpi-for-application-in-endoradiotherapy-by-means-of-click-chemistry
#4
Alexander Wurzer, Adrienn Vágner, Dávid Horváth, Flóra Fellegi, Hans-Jürgen Wester, Ferenc K Kálmán, Johannes Notni
Due to its 4 carbonic acid groups being available for bioconjugation, the cyclen tetraphosphinate chelator DOTPI, 1,4,7,10-tetraazacyclododecane-1,4,7, 10-tetrakis[methylene(2-carboxyethylphosphinic acid)], represents an ideal scaffold for synthesis of tetrameric bioconjugates for labeling with radiolanthanides, to be applied as endoradiotherapeuticals. We optimized a protocol for bio-orthogonal DOTPI conjugation via Cu(I)-catalyzed Huisgen-cycloaddition of terminal azides and alkynes (CuAAC), based on the building block DOTPI(azide)4 ...
2018: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29676153/quantifying-cellular-internalization-with-a-fluorescent-click-sensor
#5
Laura Ina Selby, Luigi Aurelio, Daniel Yuen, Bim Graham, Angus P R Johnston
The ability to determine the amount of material endocytosed by a cell is important for our understanding of cell biology and in the de-sign of effective carriers for drug delivery. To quantify internalization by fluorescence, the signal from material remaining on the cell sur-face must be differentiated from endocytosed material. Sensors for internalization offer advantages over traditional methods for achiev-ing this as they exhibit improved sensitivity, allow for multiple fluorescent markers to be used simultaneously, and are amenable to high throughput analysis...
April 20, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29614859/click-conjugation-of-cloaked-peptide-ligands-to-microbubbles
#6
Connor Slagle, Douglas H Thamm, Elissa K Randall, Mark Andrew Borden
Interest in the use of targeted microbubbles for ultrasound molecular imaging (USMI) has been growing in recent years as a safe and efficacious means of diagnosing tumor angiogenesis and assessing response to therapy. Of particular interest are cloaked microbubbles, which improve specificity by concealing the ligand from blood components until they reach the target vasculature, where the ligand can be transiently revealed for firm receptor-binding by ultrasound acoustic radiation force pulses. Herein, a bio-orthogonal "click" conjugation chemistry is introduced to decorate the surface of cloaked 4-5 μm diameter microbubbles as part of a sterile and reproducible production process...
April 4, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29535294/addendum-application-of-bio-orthogonal-proteome-labeling-to-cell-transplantation-and-heterochronic-parabiosis
#7
Yan Liu, Michael J Conboy, Melod Mehdipour, Yutong Liu, Thanhtra P Tran, Aaron Blotnick, Prasanna Rajan, Thalie Cavalcante Santos, Irina M Conboy
No abstract text is available yet for this article.
March 13, 2018: Nature Communications
https://www.readbyqxmd.com/read/29505240/a-multifunctional-polypeptide-via-ugi-reaction-for-compact-and-biocompatible-quantum-dots-with-efficient-bioconjugation
#8
Hang Zhang, Jinlong Chen, Chunsheng Xiao, Youhua Tao, Xianhong Wang
The growing application of quantum dots (QDs) in biomedical research necessitates, in turn, continuous development of surface functionalizing ligands to optimize their performance for ever more challenging and diverse biological applications. Here, we demonstrate the novel multifunctional polypeptide ligands for compact and biocompatible QDs. The target ligand preparation exploits the efficient, activating agent-free Ugi reaction of four functional components to incorporate lipoic acid, pyridine, zwitterion motifs, and reactive functionalities in a one-pot procedure under mild conditions...
April 18, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29483550/oligonucleotide-conjugated-multi-functional-adeno-associated-viruses
#9
Dhruva Katrekar, Ana M Moreno, Genghao Chen, Atharv Worlikar, Prashant Mali
Recombinant adeno-associated viruses (AAVs) are among the most commonly used vehicles for in vivo gene delivery. However, their tropism is limited, and additionally their efficacy can be negatively affected by prevalence of neutralizing antibodies in sera. Methodologies to systematically engineer AAV capsid properties would thus be of great relevance. In this regard, we develop here multi-functional AAVs by engineering precision tethering of oligonucleotides onto the AAV surface, and thereby enabling a spectrum of nucleic-acid programmable functionalities...
February 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29480717/genetic-code-expansion-of-the-silkworm-bombyx-mori-to-functionalize-silk-fiber
#10
Hidetoshi Teramoto, Yoshimi Amano, Fumie Iraha, Katsura Kojima, Takuhiro Ito, Kensaku Sakamoto
The genetic code in bacteria and animal cells has been expanded to incorporate novel amino acids into proteins. Recent efforts have enabled genetic code expansion in nematodes, flies, and mice, whereas such engineering is rare with industrially useful animals. In the present study, we engineered the silkworm Bombyx mori to synthesize silk fiber functionalized with azidophenylalanine. For this purpose, we developed a bacterial system to screen for B. mori phenylalanyl-tRNA synthetases with altered amino-acid specificity...
March 16, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29458213/selective-targeting-and-degradation-of-doxorubicin-loaded-folate-functionalized-dna-nanocages
#11
Sofia Raniolo, Giulia Vindigni, Alessio Ottaviani, Valeria Unida, Federico Iacovelli, Antonio Manetto, Mariangela Figini, Lorenzo Stella, Alessandro Desideri, Silvia Biocca
Selective targeting is a crucial property of nanocarriers used for drug delivery in cancer therapy. We generated biotinylated octahedral DNA nanocages functionalized with folic acid through bio-orthogonal conjugation chemistry. Molecular modelling indicated that a distance of about 2.5 nm between folic acid and DNA nanocage avoids steric hindrance with the folate receptor. HeLa cells, a folate receptor positive tumour cell line, internalize folate-DNA nanocages with efficiency greater than 40 times compared to cells not expressing the folate receptors...
February 17, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/29412139/role-of-the-visual-experience-dependent-nascent-proteome-in-neuronal-plasticity
#12
Han-Hsuan Liu, Daniel B McClatchy, Lucio Schiapparelli, Wanhua Shen, John R Yates, Hollis T Cline
Experience-dependent synaptic plasticity refines brain circuits during development. To identify novel protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we conducted a quantitative proteomic screen of the nascent proteome in response to visual experience in Xenopus optic tectum using bio-orthogonal metabolic labeling (BONCAT). We identified 83 differentially synthesized candidate plasticity proteins (CPPs). The CPPs form strongly interconnected networks and are annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling...
February 7, 2018: ELife
https://www.readbyqxmd.com/read/29361211/bespoke-pretargeted-nanoradioimmunotherapy-for-the-treatment-of-non-hodgkin-lymphoma
#13
Kin Man Au, Ashutosh Tripathy, Carolina Pe-I Lin, Kyle Wagner, Seungpyo Hong, Andrew Z Wang, Steven I Park
Non-Hodgkin lymphoma (NHL) is one of the most common types of hematologic malignancies. Pretargeted radioimmunotherapy (PRIT), the sequential administration of a bispecific antibody-based primary tumor-targeting component followed by a radionucleotide-labeled treatment effector, has been developed to improve the treatment efficacy and to reduce the side effects of conventional RIT. Despite the preclinical success of PRIT, clinical trials revealed that the immunogenicity of the bispecific antibody as well as the presence of competing endogenous effector molecules often compromised the treatment...
February 27, 2018: ACS Nano
https://www.readbyqxmd.com/read/29244484/charge-switchable-nanozymes-for-bioorthogonal-imaging-of-biofilm-associated-infections
#14
Akash Gupta, Riddha Das, Gulen Yesilbag Tonga, Tsukasa Mizuhara, Vincent M Rotello
Early detection of biofilms is crucial for limiting infection-based damage. Imaging these biofilms is challenging: conventional imaging agents are unable to penetrate the dense matrix of the biofilm, and many imaging agents are susceptible to false positive/negative responses due to phenotypical mutations of the constituent microbes. We report the creation of pH-responsive nanoparticles with embedded transition metal catalysts (nanozymes) that effectively target the acidic microenvironment of biofilms. These pH-switchable nanozymes generate imaging agents through bioorthogonal activation of profluorophores inside biofilms...
January 23, 2018: ACS Nano
https://www.readbyqxmd.com/read/29224069/clickseq-replacing-fragmentation-and-enzymatic-ligation-with-click-chemistry-to-prevent-sequence-chimeras
#15
Elizabeth Jaworski, Andrew Routh
We recently reported a fragmentation-free method for the synthesis of Next-Generation Sequencing libraries called "ClickSeq" that uses biorthogonal click-chemistry in place of enzymes for the ligation of sequencing adaptors. We found that this approach dramatically reduces artifactual chimera formation, allowing the study of rare recombination events that include viral replication intermediates and defective-interfering viral RNAs. ClickSeq illustrates how robust, bio-orthogonal chemistry can be harnessed in vitro to capture and dissect complex biological processes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29188996/a-factor-analogues-containing-alkyne-and-azide-functionalized-isoprenoids-are-efficiently-enzymatically-processed-and-retain-wild-type-bioactivity
#16
Veronica Diaz-Rodriguez, Erh-Ting Hsu, Elena Ganusova, Elena R Werst, Jeffrey M Becker, Christine A Hrycyna, Mark D Distefano
Protein prenylation is a post-translational modification that involves the addition of one or two isoprenoid groups to the C-terminus of selected proteins using either farnesyl diphosphate or geranylgeranyl diphosphate. Three crucial enzymatic steps are involved in the processing of prenylated proteins to yield the final mature product. The farnesylated dodecapeptide, a-factor, is particularly useful for studies of protein prenylation because it requires the identical three-step process to generate the same C-terminal farnesylated cysteine methyl ester substructure present in larger farnesylated proteins...
February 21, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29136199/site-specific-dual-color-labeling-of-long-rnas-for-single-molecule-spectroscopy
#17
Meng Zhao, Fabio D Steffen, Richard Börner, Michelle F Schaffer, Roland K O Sigel, Eva Freisinger
Labeling of long RNA molecules in a site-specific yet generally applicable manner is integral to many spectroscopic applications. Here we present a novel covalent labeling approach that is site-specific and scalable to long intricately folded RNAs. In this approach, a custom-designed DNA strand that hybridizes to the RNA guides a reactive group to target a preselected adenine residue. The functionalized nucleotide along with the concomitantly oxidized 3'-terminus can subsequently be conjugated to two different fluorophores via bio-orthogonal chemistry...
February 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29128539/injectable-nanocomposite-cryogels-for-versatile-protein-drug-delivery
#18
Sandeep T Koshy, David K Y Zhang, Joshua M Grolman, Alexander G Stafford, David J Mooney
Sustained, localized protein delivery can enhance the safety and activity of protein drugs in diverse disease settings. While hydrogel systems are widely studied as vehicles for protein delivery, they often suffer from rapid release of encapsulated cargo, leading to a narrow duration of therapy, and protein cargo can be denatured by incompatibility with the hydrogel crosslinking chemistry. In this work, we describe injectable nanocomposite hydrogels that are capable of sustained, bioactive, release of a variety of encapsulated proteins...
January 2018: Acta Biomaterialia
https://www.readbyqxmd.com/read/29066549/selective-proteomic-analysis-of-antibiotic-tolerant-cellular-subpopulations-in-pseudomonas-aeruginosa-biofilms
#19
Brett M Babin, Lydia Atangcho, Mark B van Eldijk, Michael J Sweredoski, Annie Moradian, Sonja Hess, Tim Tolker-Nielsen, Dianne K Newman, David A Tirrell
Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and their responses to antibiotics. Here, we describe the use of the bio-orthogonal noncanonical amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance to antibiotics...
October 24, 2017: MBio
https://www.readbyqxmd.com/read/29043774/augmenting-influenza-specific-t-cell-memory-generation-with-a-natural-killer-t-cell-dependent-glycolipid-peptide-vaccine
#20
Regan J Anderson, Jasmine Li, Lukasz Kedzierski, Benjamin J Compton, Colin M Hayman, Taryn L Osmond, Ching-Wen Tang, Kathryn J Farrand, Hui-Fern Koay, Catarina Filipa Dos Santos Sa E Almeida, Lauren R Holz, Geoffrey M Williams, Margaret A Brimble, Zhongfang Wang, Marios Koutsakos, Katherine Kedzierska, Dale I Godfrey, Ian F Hermans, Stephen J Turner, Gavin F Painter
The development of a universal vaccine for influenza A virus (IAV) that does not require seasonal modification is a long-standing health goal, particularly in the context of the increasing threat of new global pandemics. Vaccines that specifically induce T cell responses are of considerable interest because they can target viral proteins that are more likely to be shared between different virus strains and subtypes and hence provide effective cross-reactive IAV immunity. From a practical perspective, such vaccines should induce T cell responses with long-lasting memory, while also being simple to manufacture and cost-effective...
November 17, 2017: ACS Chemical Biology
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