DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• microscopy. Figure 3 shows that FAM-labelled Ts and N+-modified DNAs are concentrated in vesicles (punctate foci in the oligo/FAM panel) that accumulate around the edge of the nucleus. Interestingly, the Ts-modified oligo is also present in the nucleus as indicated by the colocalisation of the ON (Figure 3E

• are shown for each section, along with merge where pseudo-coloured panels are overlaid, nucleus (blue) and oligo (magenta). Scale bar: 40 μm. Representative confocal microscopy section showing the FAM vesicles inside the cell. Mouse NIH 3T3 fibroblasts were incubated with 20 µM of the FAM-labelled 4Ts

• Information Supporting Information File 62: Experimental part. Acknowledgements Manawatu Microscopy and Imaging Centre, NMR and mass spectrometry facilities at Massey University, and the assistance of Mr. Raoul Solomon, Dr. Patrick J. B. Edwards, and Mr. David Lun are gratefully acknowledged. We thank Dr

A new and efficient methodology for olefin epoxidation catalyzed by supported cobalt nanoparticles

• Lucía Rossi-Fernández,
• Viviana Dorn and
• Gabriel Radivoy

Beilstein J. Org. Chem. 2021, 17, 519–526, doi:10.3762/bjoc.17.46

• confirming the heterogeneous nature of the catalytic method. The freshly prepared CoNPs/MgO catalyst was characterized by means of transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDX), inductively coupled plasma atomic emission spectroscopy (ICP-AES), X-ray diffraction (XRD) and

• determined with a Shimadzu GC-14B instrument equipped with a flame-ionisation detector and a 30 m column (HP-5MS, 0.25 mm, 0.25 μm), using nitrogen as carrier gas. Catalyst characterization The freshly prepared catalyst was characterized by transmission electron microscopy (TEM) in a JEOL 100CX2 instrument

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• increase MB half-lives. The microbubbles were prepared by mechanical agitation using a Vialmix shaker and were characterized by optical microscopy immediately after the preparation and over time. The results show that the incorporation of F-lipopeptides 1–3 led to MBs that are somewhat smaller than those

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• their functional architecture. Such an approach typically includes the use of a variety of high-resolution proteomic tools, cryo-electron microscopy and X-ray crystallography to achieve full molecular characterization at the atomic level. However, macromolecules such as DNA/RNA and proteins are not

• ionization and ion mobility), CD spectroscopy and atomic force microscopy, the authors were able to obtain detailed information about the size and secondary structure associated with some of the soluble intermediates. These included: large β-sheet oligomers formed immediately after solubilization (oligomer

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• were used. Atomic force microscopy (AFM) was performed using a NanoWizard 4 from JPK instrument (Berlin, Germany) operated in the tapping-mode with a fixed-spring cantilever holder and a USC-F0.3-k0.3-10 ultrashort cantilever with a force constant of 0.3 Nm−1. The cantilever has been tested and

Tuning the solid-state emission of liquid crystalline nitro-cyanostilbene by halogen bonding

• Subrata Nath,
• Alexander Kappelt,
• Matthias Spengler,
• Bibhisan Roy,
• Jens Voskuhl and
• Michael Giese

Beilstein J. Org. Chem. 2021, 17, 124–131, doi:10.3762/bjoc.17.13

• subsequent drying in vacuo yielded the desired assemblies. The mesomorphic behaviour of the assemblies was investigated by polarised optical microscopy (POM) and differential scanning calorimetry (DSC). It should be noted that the individual building blocks F4St and F4Az as well as NO2-C8 and NO2-C9 do not

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• Research Center of Electron Microscopy, Freie Universität Berlin, Fabeckstr. 34a, 14195 Berlin 10.3762/bjoc.17.10 Abstract The synthesis of a sulfate-modified dendritic peptide amphiphile and its self-assembly into one-dimensional rod-like architectures in aqueous medium is reported. The influence of the

• ionic strength on the supramolecular polymerization was probed via circular dichroism spectroscopy and cryogenic transmission electron microscopy. Physiological salt concentrations efficiently screen the charges of the dendritic building block equipped with eight sulfate groups and trigger the formation

• the effect of sulfate modification on the self-assembly properties of the dendritic peptide amphiphiles were performed using circular dichroism (CD) spectroscopy and electron transmission microscopy (TEM) as well as cryogenic TEM. Finally, the binding affinity of the sulfated supramolecular polymers

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• medium. The ONCs have a thin rectangular shape, with an aspect ratio that is controlled by the content of the organic cosolvent (THF). The nanocrystals were characterized in solution by cryogenic transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering. The ONCs retain their structure

• upon drying, as was evidenced by TEM and atom force microscopy. Photophysical studies, including femtosecond transient absorption spectroscopy, revealed a distinct influence of the ONC morphology on their photonic properties (excitation energy transfer was observed only in the high-aspect ONCs

• inversion, red shift, and significant broadening in comparison to the molecularly dissolved system (Figure 1B). This is a typical spectral signature of ordered PDI systems and crystals [38][43][44][45][46][47] having a face-to-face orientation of the π-systems. Cryogenic transmission electron microscopy

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• microscopy (cryo-EM) [14]. Traditionally, X-ray crystallography was the preferred method to solve the protein structure and determine protein–protein interfaces. However, protein crystallography has the limitation that some protein assemblies have a low diffraction quality and are difficult to crystallise

• [15]. In the past few years, advances in the cryo-EM technology attracted the interest of more and more structural biologists. In fact, the number of cryo-EM structures has steadily been increasing over the recent years, with over 12,500 electron density maps being deposited in the Electron Microscopy

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• . Thus, it acts as inhibitor by preventing the substrate to reach the active sites in β-tryptase. Confocal laser scanning microscopy (CLSM) confirms that peptide 9 is mast-cell permeable and exhibits inhibitory activity within cells by suppressing their growth (Figure 8B). Heparin detection Heparin is a

• laser scanning microscopy images of CHMAS cells treated with 10 μM peptide 9 for 30 min. Reproduced from [51], “A fluorescent light-up probe as an inhibitor of intracellular β-tryptase”, © 2014 Wang et al., licensed under a Creative Commons Attribution 3.0 Unported Licence, https://creativecommons.org

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• precipitated from the reaction mixture in crystalline form as depicted by scanning electron microscopy (SEM) analysis. The single crystal X-ray diffraction analysis disclosed the arrangement of the α-(arylamino)acetonitrile molecules in the aggregated crystalline state as a racemic mixture. The mutagenic

• angle of 64.5°. The intermolecular distances are situated in the range 2.3–2.6 Å disclosing the lack of intermolecular interactions in the crystal structure. Scanning electron microscopy (SEM) analysis Besides process intensification leading to a shorter reaction time, another advantage of the

A novel and robust heterogeneous Cu catalyst using modified lignosulfonate as support for the synthesis of nitrogen-containing heterocycles

• Bingbing Lai,
• Meng Ye,
• Ping Liu,
• Minghao Li,
• Rongxian Bai and
• Yanlong Gu

Beilstein J. Org. Chem. 2020, 16, 2888–2902, doi:10.3762/bjoc.16.238

• results indicated that all prepared materials could remain stable in the system when used to catalyze organic reactions. FSEM (field emission scanning electron microscopy) and FTEM (field emission transmission electron microscopy) were used to observe the surface morphologies of different catalysts, and

• ) conditions. ICP-MS data were recorded on ELAN DRC-e device. The morphologies of samples were observed by scanning electron microscopy (SEM, Sirion 200, Holland) equipped with an energy dispersive X-ray (EDX) spectroscopy and transmission electron microscopy (TEM, Talos F200X), respectively. 1H and 13C NMR

Dirhamnolipid ester – formation of reverse wormlike micelles in a binary (primerless) system

• David Liese,
• Hans Henning Wenk,
• Xin Lu,
• Jochen Kleinen and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2020, 16, 2820–2830, doi:10.3762/bjoc.16.232

• is typical for wormlike micelle systems, the normalized Cole–Cole plot of G''/G''max against G'/G''max was obtained as a semicircle centered at G'/G''max = 1. The formation of network structures was also verified by polarized light microscopy. The sample was birefringent at ambient temperature and

• supported by rheological measurements [42] and finally validated by transmission electron microscopy at cryogenic temperature (cryo-TEM) [43]. Temperature-dependent rheology Next, the temperature dependence of the rheology for the RWLM will be described. Oscillatory-shear experiments were performed for the

• due to the intramicellar branches and/or the inverse character of the micelles, as Equation 9 and Equation 10 are defined for normal linear micelles. The behavior of G0 varying with the temperature for inverse micelles was also found by other authors [53][54]. Microscopy Polarized optical microscopy

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• derivatives in aqueous buffer (5 mM tris-HCl, 10 mM NaCl, water/DMSO 99.5:0.5, pH 7.4) were investigated using a combination of absorption and emission spectral studies, dynamic light scattering (DLS) and field emission scanning electron microscopy (FESEM). In a “good solvent” such as DMSO, in which all

Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides

• Dongsik Yang,
• Hongjian He and
• Bing Xu

Beilstein J. Org. Chem. 2020, 16, 2709–2718, doi:10.3762/bjoc.16.221

• nanofibers in the HeLa cells. Then, we used confocal laser scanning microscopy (CLSM) to examine whether these compounds deliver RPE into HeLa cells. After mixing R-phycoerythrin (RPE) [49], a red fluorescent protein, with 1 or 2 at different concentrations, we incubated the mixtures with HeLa cells for 2 h

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• )–dipicolylamine complexes beyond 25% had a negative impact on the limit of detection and the optical response. Transmission electron microscopy provided evidence that the changes of the nanoparticle properties observed in the presence of the phosphates were due to a nanoparticle crosslinking, consistent with the

• signals of the immobilized ligand molecules but no sharp signals, showing that the nanoparticles were not contaminated with unbound ligands or residual citrate. According to transmission electron microscopy (TEM), NPrac-1 had an average diameter of 9.1 ± 2.4 nm and a maximum of the SPR band in the UV–vis

Particle size effect in the mechanically assisted synthesis of β-cyclodextrin mesitylene sulfonate

• Stéphane Menuel,
• Sébastien Saitzek,
• Eric Monflier and
• Frédéric Hapiot

Beilstein J. Org. Chem. 2020, 16, 2598–2606, doi:10.3762/bjoc.16.211

• highlighting the advantages of the mechanically assisted synthesis. Results and Discussion Analysis of ground CDs Scanning electron microscopy (SEM) SEM enables particle size evolution upon grinding to be monitored. The SEM images in Figure 1 show the surface topography changes of polycrystalline β-CD for six

• speed of 0.4°/min) using the Bragg–Brentano configuration. Scanning electron microscopy Scanning electron microscopy (SEM) images were recorded on a SEM JEOL JSM-7800F LV instrument at 3.0 kV. The powder was deposited on a carbon-coated copper grid. The particle size distributions were determined from

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• hydrophobic effect and to host–guest π–π interactions. Hydrophobic surface simulations showed that TBTQ-(OG)6 and C60 forms an amphiphilic supramolecular host–guest complex, which further assembles to microspheres with diameters of 0.3–3.5 μm, as determined by scanning electron microscopy. Keywords

• of this host with C60 and C70-fullerene was investigated in co-organic solvents and in aqueous solution. The hydrophobic surface simulation of this host indicated the formation of a supra-amphiphilic system, which, as shown by scanning electron microscopy, further self-assembles into microspheres in

• -(OG)6, and TBTQ-(OG)6 C60 were investigated by scanning electron microscopy (SEM). As shown in Figure 7a and 7b, respectively, the SEM image of C60-fullerene displays cylindrical nanotubes and that of TBTQ-(OG)6 does not indicate any definite shape. However, well-dispersed microspheres with diameters

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it

Palladium nanoparticles supported on chitin-based nanomaterials as heterogeneous catalysts for the Heck coupling reaction

• Tony Jin,
• Malickah Hicks,
• Davis Kurdyla,
• Sabahudin Hrapovic,
• Edmond Lam and
• Audrey Moores

Beilstein J. Org. Chem. 2020, 16, 2477–2483, doi:10.3762/bjoc.16.201

• Information File 1) [16]. ChNCs were treated with ammonium persulfate (APS) for 16 h to form disperse ChNCs after washing. ChsNCs were made by deacetylating ChNCs in the presence of concentrated NaOH as well as a small amount of NaBH4 (Scheme 1). As seen through transmission electron microscopy (TEM) in

• Information File 498: Experimental part. Acknowledgements We thank the Facility for Electron Microscopy Research of McGill University for help in data collection. We thank the MC2 facility at McGill University for help in acquiring the FTIR spectra. Specifically, we thank Dr. Hatem Titi from the MC2 facility

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• by means of UV–vis spectroscopy, Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), and transmission electron microscopy (TEM) analysis (see Supporting Information File 1). Concerning the chemical structure of the conjugate, the data reported in the literature were

• ° scattering angle with temperature controlled at 25 °C in 1 mL polystyrene cuvettes. Dex-1b was characterized in terms of size. Short time measurements were carried out for a total of 15 min, with three consecutive measurements for each sample. Transmission electron microscopy images were aquired by a JEOL

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• fractal-like morphologies, as verified by circular dichroism (CD), Fourier-transform infrared (FTIR) spectroscopy, thioflavin T (ThT) fluorescence spectroscopy assay, and atomic force microscopy (AFM). Upon changing the pH value (using pH 5.5 and 13.0), PEP-1 forms different types of secondary structures

• . PEP-1 self-assembles to produce β-sheet-rich structures at physiological pH 7.4, as confirmed by CD, FTIR spectroscopy, and ThT assay. Microscopy studies revealed the hierarchical formation of fractal-like structures from nanobelts. The target peptide PEP-1 appeared to be highly sensitive towards pH

• two hours, the fluorescence spectra were registered using an excitation wavelength of 440 nm on a JASCO Spectrofluorometer FP-8500 within a wavelength range between 450 and 700 nm and 5 nm slits. AFM studies For microscopy studies, peptide solutions at a concentration of 5 × 10−4 M were prepared at

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• high-content (HC) microscopy can satisfy this need. The automated imaging of thousands of cells per condition in multiwell plates allows us to obtain quantitative data on not only the fluorescence intensity but also on the localization in a very short time. Quantitative and statistically relevant

• automated HT format with image-based information. To summarize briefly what has been outlined previously in more detail [56], HCS requires automated high-speed microscopy, including robotic liquid handlers and plate washers, automated data analysis tools, and large data storage systems for the terabits of

• employed to generate dose–response curves and to calculate the CP50 value of the transporters, described as the half-maximal cell penetration. In a CAPA, the final fluorescence response is usually recorded by flow cytometry [55][62]. In a HC CAPA, flow cytometry is replaced by HC automated microscopy

Natural dolomitic limestone-catalyzed synthesis of benzimidazoles, dihydropyrimidinones, and highly substituted pyridines under ultrasound irradiation

• Kumar Godugu,
• Venkata Divya Sri Yadala,
• Mohammad Khaja Mohinuddin Pinjari,
• Trivikram Reddy Gundala,
• Lakshmi Reddy Sanapareddy and
• Chinna Gangi Reddy Nallagondu

Beilstein J. Org. Chem. 2020, 16, 1881–1900, doi:10.3762/bjoc.16.156

• positions might be due to the presence of trace metal contents and impurities. The morphology of the NDL catalyst was analyzed by scanning electron microscopy (Figure 5). The SEM images revealed that the morphology of the NDL catalyst consists of irregular shapes and sizes with a random dispersion. Further

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125