Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• with a 6-thioguanosine cap analogue. Synthesis of biotin-labeled caps was achieved with a 2′-NH2-modified cap analogue which was reacted with an N-hydroxysuccinimide biotin active ester [73]. The biotin-labeled cap analogue could be incorporated into mRNA during IVT and retained binding to eIF4E and

• dyes which could be applied as FRET pair. In this case, labeling was achieved in two bioorthogonal reactions, an iEDDA and a SPAAC reaction. Furthermore, dual modification with an azido and an alkyne function enabled fluorophore/biotin labeling using a combination of SPAAC and CuAAC reaction. Efficient

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• ) [120] rescued L929 fibroblasts from mycolactone-promoted apoptosis while silencing FoxO3 by RNA interference was only partially protective. The latter finding might be explained by the compensating effects of other FoxO proteins. Two synthetic mycolactone-derived probes bearing a biotin tag as a

Recent advances in metathesis-derived polymers containing transition metals in the side chain

• Ileana Dragutan,
• Valerian Dragutan,
• Bogdan C. Simionescu,
• Albert Demonceau and
• Helmut Fischer

Beilstein J. Org. Chem. 2015, 11, 2747–2762, doi:10.3762/bjoc.11.296

• corresponding monomers, appended to Ir bipyridine complexes, oligoethylene glycol and biotin entities, have been examined by fluorescence spectroscopy for their self-assembling behavior and biodetection capability (Scheme 15). In a very interesting work, Blechert, Buchmeiser and coworkers [61] copolymerized

Learning from the unexpected in life and DNA self-assembly

• Jennifer M. Heemstra

Beilstein J. Org. Chem. 2015, 11, 2713–2720, doi:10.3762/bjoc.11.292

• a solution containing the other split aptamer fragment functionalized with a biotin. In the first step of the assay, the concentration of the target molecule is transduced into a dose-dependent ligation of the split aptamer, which then allows for pull-down of a streptavidin-functionalized reporter

Biocatalysis for the application of CO₂ as a chemical feedstock

• Apostolos Alissandratos and
• Christopher J. Easton

Beilstein J. Org. Chem. 2015, 11, 2370–2387, doi:10.3762/bjoc.11.259

• number of carboxylases, phosphoanhydride bonds in ATP are hydrolysed to drive CO2 transformation through various molecular mechanisms. For example, biotin carboxylase catalysed reactions proceed through electrophilic activation of CO2 to carboxyphosphate to facilitate an attack by a nucleophile [28]. In

Engineering Pichia pastoris for improved NADH regeneration: A novel chassis strain for whole-cell catalysis

• Martina Geier,
• Christoph Brandner,
• Gernot A. Strohmeier,
• Mélanie Hall,
• Franz S. Hartner and
• Anton Glieder

Beilstein J. Org. Chem. 2015, 11, 1741–1748, doi:10.3762/bjoc.11.190

• mg/L biotin supplemented either with 2% (w/v) D-glucose (BMD), 1% (w/v) glycerol (BMG) or 0.5% (v/v) methanol (BMM). Growth rates of the generated das knock-out strains were determined by measuring the optical density (OD600) of cultures in biological triplicate during the exponential growth phase

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• DNA can drive the assembly to form extended networks [19]. Although the relationship between the primary and quaternary structures of peptides and proteins are less clear than for DNA, protein-based recognition systems containing antigen–antibody [20], biotin–streptavidin [21], and peptide–peptide [22

Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds

• Michaela Mühlberg,
• Michael G. Hoesl,
• Christian Kuehne,
• Jens Dernedde,
• Nediljko Budisa and
• Christian P. R. Hackenberger

Beilstein J. Org. Chem. 2015, 11, 784–791, doi:10.3762/bjoc.11.88

• (CuAAC) and oxime ligation. This method was applied to the conjugation of biotin and β-linked galactose residues to yield an enzymatically active thermophilic lipase, which revealed specific binding to Erythrina cristagalli lectin by SPR binding studies. Keywords: chemoselectivity; dual protein

• carbohydrate ligands to the protein barstar [18]. In the current study, we aimed to extend this approach to the dual modification of proteins using a combination of two chemoselective, orthogonal conjugation reactions for the introduction of glycan ligands and biotin to a protein. Our main objective in this

• conjugated with biotin using oxime ligation, by which the protein scaffold was immobilized on a streptavidin gold chip to monitor carbohydrate–protein binding studies by surface plasmon resonance (SPR). This immobilization strategy allowed easy handling and reproducible orientation, which are notable

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• ]. ABPP probes contain two structural units: (1) a reactive group that reacts with the protein target and (2) a reporter unit for detection which could be, e.g., a fluorophore, a MS-tag, biotin or a combination of these [16][17]. For in vivo or in situ applications the alkyne (or azide) modified reactive

Expanding the scope of cyclopropene reporters for the detection of metabolically engineered glycoproteins by Diels–Alder reactions

• Anne-Katrin Späte,
• Verena F. Schart,
• Julia Häfner,
• Andrea Niederwieser,
• Thomas U. Mayer and
• Valentin Wittmann

Beilstein J. Org. Chem. 2014, 10, 2235–2242, doi:10.3762/bjoc.10.232

• ). With the cyclopropene-modified hexosamines in hand we first investigated their metabolic incorporation into cell-surface glycoconjugates of HEK 293T cells. The cells were incubated for 48 h with 1, 2, 3, or solvent control (phosphate buffered saline, PBS) and then reacted with Tz–biotin 10 [19

• ). Cells were harvested, lysed and the lysate was cleared by centrifugation resulting in a mixture of intracellular and membrane proteins. In the cleared lysate we performed a DAinv reaction with Tz–biotin 10. Visualization of glycoproteins was achieved by immunoblotting for biotin, and equal protein

• Modified Eagle’s Medium (DMEM) supplemented with 5% FBS, 100 units mL–1 penicillin and 100 μg mL–1 streptomycin. All cells were incubated in a 5% carbon dioxide, water saturated incubator at 37 °C. Fluorescence microscopy with Tz–biotin 10. HEK 293T cells (22,000 cells/cm2) were seeded in 4-well ibiTreat μ

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

• Nico Rublack and
• Sabine Müller

Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

• a biotin was introduced. Upon periodate oxidation of the 3'-cis diol of the RNA library molecules, the produced dialdehyde is thought to react with the primary amino group of the cytidine derivative allowing immobilization of the resulting modified RNAs onto a solid surface through biotin

• functionalization, protected and suitably activated uridine 3, and a short mono protected diamino linker 4 for the attachment of a biotin moiety 5 in order to immobilize the conjugated RNA molecules onto a streptavidine-coated surface (Figure 1). First, the sugar hydroxy functions of uridine (6) were fully

• -position of 3 in order to attach a biotin unit to the modified nucleoside. Linker 4 was synthesized from 2,2’-(ethylenedioxy)diethylamine (8) with di-tert-butyl dicarbonate (Boc2O) in dioxane [35] (Figure 3). The mono protected diamino linker 4 was purified by chromatography on silica gel and subsequently

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• peptide sequence for analytical investigations (Figure 4). These tools can be spin and radioactive labels, bioactive molecules (such as biotin) or fluorescent dyes. The paramagnetic substance TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) (Figure 5) was manually coupled to NPY

• . Following resin cleavage, radio labeling was performed with NHS-[2,3-3H]propionate (Figure 5) by the Bolton–Hunter reaction. Then, the Nvoc protecting groups could be removed by irradiation with UV light to obtain the fully deprotected, radio-labeled peptide [130]. Biotin and fluorophores such as CF (5(6

Silver and gold-catalyzed multicomponent reactions

• Giorgio Abbiati and
• Elisabetta Rossi

Beilstein J. Org. Chem. 2014, 10, 481–513, doi:10.3762/bjoc.10.46

• ] complex (HC^N = 2-benzylpyridine) in water at 40 °C. The reaction yields ranged from good to excellent, and the method allowed the introduction of alkynes and amines properly functionalized with particular groups,(i.e., dansyl and biotin), or m/p-ethynylbenzenes, suitable for further orthogonal

Physalin H from Solanum nigrum as an Hh signaling inhibitor blocks GLI1–DNA-complex formation

• Midori A. Arai,
• Kyoko Uchida,
• Samir K. Sadhu,
• Firoj Ahmed and
• Masami Ishibashi

Beilstein J. Org. Chem. 2014, 10, 134–140, doi:10.3762/bjoc.10.10

• assay (EMSA) for the detection of the GLI1–DNA complex. The assay uses a slightly modified biotin-tagged DNA and modified amino acids sequences of GLI1 compared to those reported in literature [30][31][32]. In a similar manner as described in [22], GLI1 protein was expressed in Escherichia coli as a 171

• –515 amino chain, including the five Zn finger regions. Horseradish peroxidase (HRP)-conjugated streptavidin detected free “biotin-labeled GLI1-BS” (DNA containing GLI1 binding site; biotin-AGCTACCTGGGTGGTCTCTTCGA; the underlined 9 bps are a consensus sequence [30]; Figure 5, lane 1). After mixing with

• annealing of single strand (ss) DNA; for biotin-labeled GLI1–BS, 5’-biotin-AGCTACCTGGGTGGTCTCTTCGA-3’ and 5’-biotin-TCGAAGAGACCACCCAGGTAGCT-3’. 10 μL of the ssDNA (100 pmol/μL in TE buffer (NIPPON GENE, Tokyo, Japan)) were mixed and annealed by PCR Thermal Cycler Dice (Takara, Kyoto, Japan) (95 °C, 30 s; 72

The myxocoumarins A and B from Stigmatella aurantiaca strain MYX-030

• Tobias A. M. Gulder,
• Snežana Neff,
• Traugott Schüz,
• Tammo Winkler,
• René Gees and
• Bettina Böhlendorf

Beilstein J. Org. Chem. 2013, 9, 2579–2585, doi:10.3762/bjoc.9.293

• CaCl2, 1 mL mineral solution (consisting of 0.1 g H3BO3, 5 g FeSO4·7H2O, 0.05 g KI, 2 g CoCl2·6H2O, 0.2 g CuSO4·5H2O, 2 g MnCl2·4H2O, 4 g ZnSO4·7H2O, 1 g 95% H2SO4 for 1 L solution), 10 mL vitamin solution (consisting of 10 mg folic acid, 6 mg biotin, 0.2 g p-aminobenzoic acid, 1 g thiamin·HCl, 1.2 g

Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway

• Jessica L. Bell,
• Andrew J. Haak,
• Susan M. Wade,
• Yihan Sun,
• Richard R. Neubig and
• Scott D. Larsen

Beilstein J. Org. Chem. 2013, 9, 966–973, doi:10.3762/bjoc.9.111

• current hypothesis regarding the mechanism of action of 1 (redistribution of MKL primarily into the cytosol), which may require an intact actin cytoskeleton or nucleus. We thus elected to design photoaffinity probes that were tag-free, i.e., lacking either a biotin or fluorescent tag [17]. There are a

• isolation and/or visualization (e.g., biotin or fluorophore) via click chemistry. This technology has been highly successful in profiling enzyme activity in living cells and even in whole organisms [21]. In ABPP, covalent linkage by the reactive functionality is usually dependent upon a particular enzymatic

• . Following exposure to UV light, the cells would be lysed, releasing the labeled proteins bound covalently to the probe (B). Click chemistry would then be applied to covalently attach a biotin or fluorescent tag for visualization and/or isolation (C). Any isolated proteins would be digested and identified by

End-labeled amino terminated monotelechelic glycopolymers generated by ROMP and Cu(I)-catalyzed azide–alkyne cycloaddition

• Ronald Okoth and
• Amit Basu

Beilstein J. Org. Chem. 2013, 9, 608–612, doi:10.3762/bjoc.9.66

• acid at the polymer terminus [6], a cis-alkene pentafluorophenol ester based terminating agent that introduces an amine-reactive capping agent [13], and cis-olefin terminating agents that directly introduce biotin and fluorescein at the polymer terminus [14]. A recent report describes the use of a cis

Synthesis and evaluation of cell-permeable biotinylated PU-H71 derivatives as tumor Hsp90 probes

• Tony Taldone,
• Anna Rodina,
• Erica M. DaGama Gomes,
• Matthew Riolo,
• Hardik J. Patel,
• Raul Alonso-Sabadell,
• Danuta Zatorska,
• Maulik R. Patel,
• Sarah Kishinevsky and
• Gabriela Chiosis

Beilstein J. Org. Chem. 2013, 9, 544–556, doi:10.3762/bjoc.9.60

• Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA Department of Pharmacology, Weill Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10065, USA 10.3762/bjoc.9.60 Abstract The attachment of biotin to a small molecule provides a powerful tool in

• and, as we show, represents a unique and useful tool to probe tumor Hsp90 biology in live cells by affinity capture, flow cytometry and confocal microscopy. To our knowledge, 2g is the only reported biotinylated Hsp90 probe to have such combined characteristics. Keywords: affinity capture; biotin

• ., PU-H71 nonbinding) complexes. The attachment of biotin to a small molecule provides a powerful tool in biology. As research tools, biotin-labeled chemical tools have the potential to extend the study of single targets to a particular class of molecules or even to an entire proteome. In addition, the

An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates

• Hao Xu,
• Hairat Sabit,
• Gordon L. Amidon and
• H. D. Hollis Showalter

Beilstein J. Org. Chem. 2013, 9, 89–96, doi:10.3762/bjoc.9.12

• Michigan, Ann Arbor, MI 48109-1065, USA 10.3762/bjoc.9.12 Abstract The fluorophosphonate (FP) moiety attached to a biotin tag is a prototype chemical probe used to quantitatively analyze and enrich active serine hydrolases in complex proteomes in an approach called activity-based protein profiling (ABPP

• ). In this study we have designed a novel synthetic route to a known FP probe linked by polyethylene glycol to a biotin tag (FP–PEG–biotin). Our route markedly increases the efficiency of the probe synthesis and overcomes several problems of a prior synthesis. As a proof of principle, FP–PEG–biotin was

• evaluated against isolated protein mixtures and different rat-tissue homogenates, showing its ability to specifically target serine hydrolases. We also assessed the ability of FP–PEG–biotin to compete with substrates that have high enzyme turnover rates. The reduced protein-band intensities resulting in

Chemical–biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target

• Jonathan W. Choy,
• Clifford Bryant,
• Claudia M. Calvet,
• Patricia S. Doyle,
• Shamila S. Gunatilleke,
• Siegfried S. F. Leung,
• Kenny K. H. Ang,
• Steven Chen,
• Jiri Gut,
• Juan A. Oses-Prieto,
• Jonathan B. Johnston,
• Michelle R. Arkin,
• Alma L. Burlingame,
• Jack Taunton,
• Matthew P. Jacobson,
• James M. McKerrow,
• Larissa M. Podust and
• Adam R. Renslo

Beilstein J. Org. Chem. 2013, 9, 15–25, doi:10.3762/bjoc.9.3

• test compounds in T. cruzi parasites. To do this, we designed and synthesized the “clickable” activity-based probe 9 in which a propargyl group (replacing methyl in 1) serves as a chemical handle for conjugation to TAMRA- or biotin-containing reagents (10 and 11, respectively, Figure 5). Probe 9 was

• was an apparent target of the electrophilic inhibitors described above. To enrich for this protein, C2C12 cells were labeled with 9 as before and then reacted with the biotin azide reagent 11, followed by biotin capture onto streptavidin beads. A base-cleavable ester function was introduced in the

The Amadori rearrangement as glycoconjugation method: Synthesis of non-natural C-glycosyl type glycoconjugates

• Katharina Gallas,
• Gerit Pototschnig,
• Florian Adanitsch,
• Arnold E. Stütz and
• Tanja M. Wrodnigg

Beilstein J. Org. Chem. 2012, 8, 1619–1629, doi:10.3762/bjoc.8.185

• surfaces (glycosylated surfaces, e.g., “glyco-chips”, gold, polystyrene plates, glass, nanoparticles), or labelling and imaging of carbohydrates (fluorescence markers, biotin, photolabelling) [27][28]. Herein we describe the application of the Amadori rearrangement as a key step for the synthesis of non

Automated synthesis of sialylated oligosaccharides

• Davide Esposito,
• Mattan Hurevich,
• Bastien Castagner,
• Cheng-Chung Wang and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2012, 8, 1601–1609, doi:10.3762/bjoc.8.183

• antigens in antibody selection by phage-display methods [31]. Thus, trisaccharide 16 (Scheme 7) was reacted with biotin derivative 31 in PBS buffer to afford compound 32 in 80% yield after gel filtration. Conclusion The synthesis of sialosides is important to create tools for glycobiology. The work

An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells

• Grazia Marano,
• Claas Gronewold,
• Martin Frank,
• Anette Merling,
• Christian Kliem,
• Sandra Sauer,
• Manfred Wiessler,
• Eva Frei and
• Reinhard Schwartz-Albiez

Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89

• of the carbohydrate moieties unaffected [15]. With biotin-labeled Diels–Alder products of branched saccharide mimetics, discrete staining patterns were observed on surfaces of human epithelial tumor cells, but not on immortalized normal fibroblasts. Screening of the library to find members with anti

Chemo-enzymatic modification of poly-N-acetyllactosamine (LacNAc) oligomers and N,N-diacetyllactosamine (LacDiNAc) based on galactose oxidase treatment

• Christiane E. Kupper,
• Ruben R. Rosencrantz,
• Birgit Henßen,
• Helena Pelantová,
• Stephan Thönes,
• Anna Drozdová,
• Vladimir Křen and
• Lothar Elling

Beilstein J. Org. Chem. 2012, 8, 712–725, doi:10.3762/bjoc.8.80

• -aldo product. Further modification of the aldehyde containing glycans, either by chemical conversion or enzymatic elongation, was established. Base-catalysed β-elimination, coupling of biotin–hydrazide with subsequent reduction to the corresponding hydrazine linkage, and coupling by reductive amination

• galactose residues for further chemical conversions. As an example, the 6-aldehydes of poly-LacNAc oligomers were converted with (+)-biotinamidohexanoic acid hydrazide (BACH), resulting in biotin-labelled poly-LacNAc glycans (Scheme 3). Moreover, the amine group obtained after deprotection of the NH2-linker

• moieties. Labelling of 6-aldehydes of poly-LacNAc oligomers The 6-aldehyde products of poly-LacNAc oligomers 3a–c were further reacted with BACH (12) to incorporate a site-specific biotin label for subsequent detection of immobilised glycans. Conversion with 12 and subsequent reduction were performed

En route to photoaffinity labeling of the bacterial lectin FimH

• Thisbe K. Lindhorst,
• Michaela Märten,
• Andreas Fuchs and
• Stefan D. Knight

Beilstein J. Org. Chem. 2010, 6, 810–822, doi:10.3762/bjoc.6.91

• appropriate methodology in this endeavour and hence biotin-labeled photoactive mannosides were designed and synthesized for photoaffinity labeling of FimH. So far, the photo-crosslinking properties of the new photoactive mannosides could be detailed with the peptide angiotensin II and labeling of FimH was

• biotin-labeled photophore 5, which is well suited for the streptavidine-based photoaffinity labeling, relying on the extraordinary high affinity of the protein streptavidine for biotin (Figure 2b) [16]. Results and Discussion In order to learn more about the ligand properties of the previously prepared

• photoaffinity-labeling of FimH. Our earlier work suggested that diazirines are more useful photoactive groups than aryl azides and benzophenones [15]. Therefore, the synthesis of a biotin-labeled daizirine-functionalized mannoside was our next target. In this synthesis, aspartic acid was utilized as the