Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

• Shahien Shahsavari,
• Dhananjani N. A. M. Eriyagama,
• Bhaskar Halami,
• Vagarshak Begoyan,
• Marina Tanasova,
• Jinsen Chen and
• Shiyue Fang

Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108

• -β-cyanoethyl-dT phosphoramidite were used for incorporating dA, dC, dG and dT nucleotides, respectively. The coupling conditions were standard except that in some cases, coupling was increased from two to three times. Capping failure sequences was achieved using the phosphoramidite 25 with 5

• detected. Before using 25 for capping and a trityl group for 5'-tagging in ODN synthesis using 3a–c and 4, we tried to synthesize ODNs under standard conditions using acetic anhydride for capping and without tagging the 5'-end of ODNs. RP HPLC analyses showed that the peaks of the desired ODNs and branched

• purification as described above. The reason for us to use 25 instead of acetic anhydride for capping was based on two considerations. One was that if a branched sequence failed to react at one or more sites during coupling, capping with a hydrophobic agent would still make the branched sequence more

Homo- and hetero-difunctionalized β-cyclodextrins: Short direct synthesis in gram scale and analysis of regiochemistry

• Gábor Benkovics,
• Mihály Bálint,
• Éva Fenyvesi,
• Erzsébet Varga,
• Szabolcs Béni,
• Konstantina Yannakopoulou and
• Milo Malanga

Beilstein J. Org. Chem. 2019, 15, 710–720, doi:10.3762/bjoc.15.66

• installation of designed disulfonyl capping moieties to the CD core and their subsequent substitution by the desired functional groups or (ii) the indirect difunctionalization based on the regioselective removal of protecting groups from a previously perfunctionalized CD derivative. The first approach was

• developed by Fujita et al. by introducing customized capping reagents for β-CD [10]. Tabushi and co-workers developed a series of capping agents providing 6A,6B-, 6A,6C-, or 6A,6D-selectivity on β-CD (Scheme 1) [11][12]. The cap could be subsequently removed by a suitable nucleophilic substitution to afford

• the homo-disubstituted derivatives, e.g., 6A,6X-diazido-β-CDs can be prepared using sodium azide in N,N-dimethylformamide (DMF) and moderate heating (Scheme 1). Although capping reagents are selective in disubstitution and this methodology revolutionized CD difunctionalization, their application has

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• evade and suppress host immune responses [5][12][13][14][15]. The most prominent of these cell surface glycoconjugates, lipophosphoglycan (LPG), consists of a glycosylphosphatidylinositol (GPI) anchor and variable sugar capping structures (Figure 1) [15][16][17][18][19][20]. The capping sugar tropisms

• vary with Leishmania species (>20 species) and life stage of the pathogen, making it challenging to define how the capping sugars interact and modulate host immune responses [21][22][23][24]. Since these cell-surface glycans are structurally diverse and difficult to isolate in appreciable quantities

• investigated how truncated oligosaccharide capping structures of LPG interact with macrophage pattern recognition receptors (PRRs) to modulate an innate immune response to L. major-induced leishmaniasis in vitro and in vivo [11][40][41][42]. These studies showed that a neutral α-1,2-trimannose capping

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• host proteins and cell types, for example the invariant N-acetyl-D-glucosamine or N-acetyl-D-galactosamine residues that attach N- or O-glycans, respectively, to the peptide side chains, the large variety and possible permutations of “capping” residues (for example D-mannopyranosides, D

• )-branched α-D-arabinofuranoside-containing polymers [52]. LAM can further be peripherally modified, also known as ”capping“, the nature of which differs between mycobacterial species. In pathogenic mycobacteria, such as Mtb, LAM is capped to various degrees with one to three α-D-mannopyranosides [53], while

A tutorial review of stereoretentive olefin metathesis based on ruthenium dithiolate catalysts

• Daniel S. Müller,
• Olivier Baslé and
• Marc Mauduit

Beilstein J. Org. Chem. 2018, 14, 2999–3010, doi:10.3762/bjoc.14.279

• ) [4]. 6 The in situ methylene capping strategy Experimental observations clearly indicate that terminal alkenes are detrimental for stereoretentive metathesis reactions with ruthenium dithiolate catalysts. In 2017 Hoveyda proposed the in situ methylene capping strategy as a solution to this problem

• the in situ methylene capping strategy Hoveyda and co-workers first applied the methylene capping strategy to cross-metathesis reactions (Scheme 6a) [21]. Almost 20 examples were isolated in modest to good yields and with excellent stereoisomeric purity. To assure high conversion in cross-metathesis

• styrene 32 the protonation and loss of the catechothiolate ligand by Brønsted acid 34 is a faster process leading to catalyst degradation. It should be noted that stereoretentive CM and RCM with (E)-2-butene (E-25) as capping reagent were also reported, however, these reactions required a significantly

MoO₃ on zeolites MCM-22, MCM-56 and 2D-MFI as catalysts for 1-octene metathesis

• Hynek Balcar,
• Martin Kubů,
• Naděžda Žilková and
• Mariya Shamzhy

Beilstein J. Org. Chem. 2018, 14, 2931–2939, doi:10.3762/bjoc.14.272

• oligomerization in these blank experiments is several times higher than that achieved over metathesis catalysts: it may be due to the partial capping of support acid sites with Mo species catalysts and also due the parallel consumption of 1-octene in metathesis. Figure 5b shows oligomerization of 1-octene, 2

Enhanced single-isomer separation and pseudoenantiomer resolution of new primary rim heterobifunctionalized α-cyclodextrin derivatives

• Iveta Tichá,
• Gábor Benkovics,
• Milo Malanga and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2018, 14, 2829–2837, doi:10.3762/bjoc.14.261

• regioisomers on the primary rim of homobifunctionalized diazido-α-CDs by selective substitution on the primary rim. Specifically, three positional regioisomers 6A,6B-, 6A,6C-, and 6A,6D-diazido-α-CDs were prepared via different intermediates (using sulfonylation with capping agents, bromination and tosylation

• using capping agents. For example, Tabushi et al. [13][14][15] studied regioselectively capped-β-CDs with disulfonyl chlorides. Subsequently, Fujita et al. [16] introduced the disulfonyl groups on the primary rim of α-CDs, albeit using non-capping reagents, mesitylenesulfonyl chloride and observed

• almost no preferential selectivity for AB, AC or AD regioisomers. Breslow et al. [17] used the 1,3-dimethoxy-4,6-benzenedisulfonyl chloride as a capping agent to prepare the AB regioisomer. Subsequently, Fujita et al. [18] selectively capped the primary rim of α-CD using a special, sterically hindered

Synthesis of α-D-GalpN₃-(1-3)-D-GalpN₃: α- and 3-O-selectivity using 3,4-diol acceptors

• Emil Glibstrup and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2018, 14, 2805–2811, doi:10.3762/bjoc.14.258

• and readily available building block. Challenging the α,3-O-selectivity with the different 6-O-protecting group variants. Representative glycosylations with closely related systems [34][44]. Capping the free 4-OH, allowing for easier separation of mixtures obtained during glycosylation

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• (6) ring threaded onto a water-soluble axle [80]. The rotaxane was synthesized in 23% yield by a template/capping strategy where one stopper is attached using copper-catalyzed azide–alkyne click chemistry after the formation of the precursor pseudorotaxane. Due to the hydrophobic effect, the neutral

• . Very recently, our group reported on a crown/ammonium rotaxane 17 in which a TTF unit is implemented in the crown-ether wheel (Figure 15) [82]. The rotaxane was synthesized by a catalyst-free nitrile oxide capping strategy in 67% yield. In the neutral state, the wheel is strongly bound to the ammonium

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• effect, kO/kS, is 2.8 for the hydroxide-ion-catalyzed reaction, 0.2 for the pH-independent cleavage and 8 for the pH-independent isomerization [104]. Models for the cleavage by large ribozymes Transesterification reactions catalyzed by the large ribozymes (group I and II introns, the lariat capping

An alternative to hydrogenation processes. Electrocatalytic hydrogenation of benzophenone

• Cristina Mozo Mulero,
• Alfonso Sáez,
• Jesús Iniesta and
• Vicente Montiel

Beilstein J. Org. Chem. 2018, 14, 537–546, doi:10.3762/bjoc.14.40

• using NaBH4 as reducing agent in a water-in-oil (w/o) microemulsion in the presence of polyethylene glycol hexadecyl ether, Brij@30 as capping agent and n-heptane as organic solvent (water/Brij@30/n-heptane). After precipitation and copiously washing with acetone and water, Pd nanoparticles were

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• determine exact concentrations. Also, short oligonucleotides can fail in representing a biologically significant structural model, because of heterogeneous binding sites due to the “capping” effect, whereby a ligand can bind similarly to the end base pairs and to a binding site along the helix [19

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

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

• ; enzymatic capping; methyltransferase; RNA; Introduction The 5′-cap is a hallmark of eukaryotic mRNA and involved in numerous interactions required for cellular functions. Chemically, the 5′-cap consists of an inverted 7-methylguanosine connected to the rest of the eukaryotic mRNA via a 5′–5′ triphosphate

• ], NAD-capped RNAs [23][24], 3'-dephospho-CoA linked RNA [25] or methylphosphate capping [26][27] we refer to the indicated articles. Review Enzymatic preparation of capped mRNA Enzymatic preparation of capped mRNA is based on in vitro transcription (IVT) of a DNA template. While RNA synthesized via

• -transcriptional capping In post-transcriptional capping, the RNA from IVT is subjected to a dedicated enzymatic capping reaction. The enzymes used in vitro originate from capping apparatuses of different eukaryotic organisms or DNA viruses and can be produced recombinantly in E. coli [28][29]. Enzymatic formation

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• their potential applications in various fields. Linear or branched polyethyleneimine (PEI) polymers [1][2][3][4][5], as well as polypropyleneimine (PPI) [6][7][8] and polyamidoamine (PAMAM) [7][8][9][10][11][12][13][14][15][16] dendrimers, have been used as proton sponges, capping agents for the

• modelled as a mixture of independent virtual weak bases. We already have employed these products as capping agents for the preparation of silver nanocomposites [37], which in turn have been tested as catalysts for nitroarene reduction and as antimicrobial agents in synergism with classical antibiotics [40

Structure–property relationships and third-order nonlinearities in diketopyrrolopyrrole based D–π–A–π–D molecules

• Jan Podlesný,
• Lenka Dokládalová,
• Oldřich Pytela,
• Adam Urbanec,
• Milan Klikar,
• Numan Almonasy,
• Tomáš Mikysek,
• Jaroslav Jedryka,
• Iwan V. Kityk and
• Filip Bureš

Beilstein J. Org. Chem. 2017, 13, 2374–2384, doi:10.3762/bjoc.13.235

• °C, respectively. The 2,5-thienylene linker decreased the melting point approximately by 40 °C (e.g., 2a/4a with Tm = 244/200 °C). End-capping the DPP derivative with a ferrocene donor brings improved thermal stability (e.g., compound 5b with the second highest Tm and Td values within the series b

Mechanochemical synthesis of small organic molecules

• Tapas Kumar Achar,
• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2017, 13, 1907–1931, doi:10.3762/bjoc.13.186

• ]. Jang and co-workers reported a mechanochemical synthesis of benzimidazoles [143][144], benzoxazole [145] and benzothiazole derivatives in presence of ZnO nano particles as catalyst [146]. Using 0.5 mol % of ZnO nano particles which were grown on aromatic imine D as capping agent, resulted in the best

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• pyridine and 2,6-lutidine using 1-(mesitylene-2-sulfonyl)-3-nitro-1,2,4-triazole (MSNT; 6 equiv) as an activator and N-methylimidazole (NMI; 10 equiv) as a nucleophilic catalyst. Each coupling was followed by precipitation/recrystallization from EtOH, capping with Ac2O in pyridine and precipitation from

• , capping and oxidation (Scheme 4). The building blocks were base-moiety protected 5´-O-DMTr-nucleoside 3´-(2-cyanoethyl-N,N-diisopropylphosphoramidites), i.e., the ones used in standard solid-supported synthesis. Phosphite triesters were oxidized to phosphate triesters after each coupling with tert-butyl

• fully protected 10-mer, d(5´-O-DMTr-GibuABzCBzGibuGibuCBzCBzABzGibuT)3-support, the average yield of an entire coupling cycle was 87% and the overall yield 33%. Conventional ammonolysis was used for the release from the support. Since no capping reaction had been carried out in any coupling cycle, the n

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• capping gold surface with eleven different carbohydrate ligands [78]. To achieve their goal, the authors treated GAuNPs with lectins and used the linear discriminant analysis (LDA) to analyze the LSPR shifts and recognize the lectins in a complex sample. A similar approach, based on LDA, has been employed

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• substrate hindrance affects catalyst activity, even if not directly related to continuous flow operation conditions. It was proposed that ligand-modified surfaces, such as Pd(HHDMA)@C, are three-dimensional catalytic ensembles whose organic capping layer cannot be penetrated with ease by larger alkynes

Versatile synthesis of end-reactive polyrotaxanes applicable to fabrication of supramolecular biomaterials

• Atsushi Tamura,
• Asato Tonegawa,
• Yoshinori Arisaka and
• Nobuhiko Yui

Beilstein J. Org. Chem. 2016, 12, 2883–2892, doi:10.3762/bjoc.12.287

• an axle polymer and commercially available 4-substituted benzoic acids as capping reagents. The terminal 2-amino-3-phenylpropyl groups of PEG-Ph-NH2 block the dethreading of the α-CDs after capping with 4-substituted benzoic acids. By this method, two series of azide group-terminated polyrotaxanes

• introduction of reactive functional groups during the preparation of PRXs is both simple and convenient. However, although the capping of pseudopolyrotaxanes via click reactions between azide (or alkyne)-terminated axle polymers and bulky stoppers containing alkyne (or azide) groups is employed broadly [15][16

• ][17][18][19][20][21], few have reported on the synthesis of PRXs bearing terminal azides or alkynes [22][23]. This is probably because of the difficulties in synthesizing sufficient amounts of bulky stopper molecules containing azide or alkynyl groups for the capping reaction. Herein, we describe a

Nucleic acids through condensation of nucleosides and phosphorous acid in the presence of sulfur

• Tuomas Lönnberg

Beilstein J. Org. Chem. 2016, 12, 670–673, doi:10.3762/bjoc.12.67

• higher than the parent oligonucleotide. Similar derivatives of monomeric thymidine were also detected in the fastest eluting fractions. The 80 Da difference in molecular weight could arise from capping of a free hydroxy function by a phosphate or an H-phosphonothioate group and distinguishing between

• these two alternatives on the basis of MS alone is challenging. To verify the structure of the capping groups, a sample of the most abundant product, comprising two thymidines and two phosphorus atoms, was analyzed by 31P NMR. Phosphorothioate and H-phosphonothioate signals accounted for approximately

Size-controlled and redox-responsive supramolecular nanoparticles

• Raquel Mejia-Ariza,
• Gavin A. Kronig and
• Jurriaan Huskens

Beilstein J. Org. Chem. 2015, 11, 2388–2399, doi:10.3762/bjoc.11.260

• most stable particles were formed when using Ad-PEG as the stabilizer. Larger particles were observed for Fc-PEG than for Ad-PEG, but these also appeared stable (sizes after 20 min and 4 h are similar). The shorter Ad-TEG was less efficient in capping and stabilizing the SNPs compared to polymeric Ad

Convenient preparation of high molecular weight poly(dimethylsiloxane) using thermally latent NHC-catalysis: a structure-activity correlation

• Stefan Naumann,
• Johannes Klein,
• Dongren Wang and
• Michael R. Buchmeiser

Beilstein J. Org. Chem. 2015, 11, 2261–2266, doi:10.3762/bjoc.11.246

• end-capping with TMS-Cl. Discussed mechanisms proposed to operate in NHC-mediated polymerization of D4 in presence/absence of BnOH. Polymerization of D4 in bulk using different protected NHCs (80 °C, 16 h). Supporting Information Supporting Information File 512: Details on the synthesis of NHC-CO2

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• available N-hydroxysuccinimide (NHS)-carboxy-dT phosphoramidite 5 (Scheme 3). This method allows the sequential introduction of any amine-functionalized glycan during DNA synthesis and was shown to be compatible with more complex glycans such as Lewis X trisaccharide. The capping step in DNA synthesis

• panel of seven different lectins (ConA, Bc2LA, BambL, BSL, LecA , StxB and MAL) showed a distinct binding selectivity in each case for a conjugate of two glycans (relative to control with a single glycan) with a unique linker and capping group combination thus establishing the synergy of interaction

Automated solid-phase synthesis of oligosaccharides containing sialic acids

• Chian-Hui Lai,
• Heung Sik Hahm,
• Chien-Fu Liang and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2015, 11, 617–621, doi:10.3762/bjoc.11.69

• min with a solvent ratio of CH2Cl2 and dioxane of 3:2, mainly the desired α-anomer was obtained (2:1). A double coupling of building block 8 to install the α-galactosamine linker was followed by a capping step. Incorporation of building block 4, cleavage from the resin and purification by HPLC yielded