Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• . Fluorescence microscopy revealed a cytoplasmic localization of the oligonucleotide without accumulation in the nuclei. This indicated an endocytotic uptake mechanism with (at least partial) retention of the material in the endocytotic vesicles. No unspecific cytotoxic effect of the guanidinylated

• nuclease and serum stability as well as significantly enhanced cellular uptake relative to their native congeners. As for the aforementioned phosphoramidates, fluorescence microscopy indicated a cytoplasmic localization of the tested zwitterionic oligonucleotide without significant accumulation in the

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• -DNA by fluorescence microscopy with preference for A·T-rich sequences [106]. Two positively charged lysine residues are expected to interact with ds-DNA electrostatically. Upon binding to the minor groove of ds-DNA, the conformation of conjugate 43 was changed from an extended to a folded form

Development of novel cyclic NGR peptide–daunomycin conjugates with dual targeting property

• Andrea Angelo Pierluigi Tripodi,
• Szilárd Tóth,
• Kata Nóra Enyedi,
• Gitta Schlosser,
• Gergely Szakács and
• Gábor Mező

Beilstein J. Org. Chem. 2018, 14, 911–918, doi:10.3762/bjoc.14.78

• -side chain cycle). In vitro fluorescence microscopy studies of an Oregon Green (OG) labeled c[KNGRE]-NH2 (OG attached to the side chain of Lys) revealed selective binding to CD13-receptor positive (CD13+) HT-1080 human fibrosarcoma cells and minimal binding to receptor negative (CD13−) MCF-7 human

Synthesis and in vitro biochemical evaluation of oxime bond-linked daunorubicin–GnRH-III conjugates developed for targeted drug delivery

• Sabine Schuster,
• Beáta Biri-Kovács,
• Bálint Szeder,
• Viktor Farkas,
• László Buday,
• Zsuzsanna Szabó,
• Gábor Halmos and
• Gábor Mező

Beilstein J. Org. Chem. 2018, 14, 756–771, doi:10.3762/bjoc.14.64

• microscopy. Hereby, the drug daunorubicin could be visualized in different subcellular compartments by following the localization of the drug in a time-dependent manner. Colocalization studies were carried out to prove the presence of the drug in lysosomes (early stage) and on its site of action (nuclei

• linked to the DNA by formation of a tyrosine phosphodiester [10][11][12]. Moreover, anthracyclines provide a beneficial auto-fluorescence allowing the performance of fluorescence based studies like confocal laser scanning microscopy (CLSM) and fluorescence-activated cell sorting (FACS) to investigate the

• or even higher than the IC50 value of the other compounds 2, 4 and 5. It can be assumed that this effect occurred due to the reduced release of the smallest Dau-containing metabolite. Confocal laser scanning microscopy (CLSM) studies Next to the quantitative analysis of the cellular uptake by flow

Heterogeneous Pd catalysts as emulsifiers in Pickering emulsions for integrated multistep synthesis in flow chemistry

• Katharina Hiebler,
• Georg J. Lichtenegger,
• Manuel C. Maier,
• Eun Sung Park,
• Renie Gonzales-Groom,
• Bernard P. Binks and
• Heidrun Gruber-Woelfler

Beilstein J. Org. Chem. 2018, 14, 648–658, doi:10.3762/bjoc.14.52

• ). The stability of emulsions to gravity-induced creaming or coalescence was assessed by monitoring the position of the water–emulsion or oil–emulsion interfaces respectively. Microscopy images of the emulsions were recorded using an Olympus BX53 microscope with GXCAM-U318 camera attached and GXCapture-T

• initially, it rapidly coalesces until complete phase separation in some cases. At and above 1.0 wt % (lower), emulsions can be re-stabilised to some extent although visible oil drops (mm-sized) develop within the cream. For the stable emulsions at low particle concentrations, optical microscopy reveals the

• in water of 0.03 wt % (upper), 0.30 wt % (middle) and 1.0 wt % (lower) at different times since preparation. A is the aqueous dispersion of particles, B is after addition of oil but before emulsification. Optical microscopy images of cyclohexane-in-water emulsions of Figure 4 after one month for

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

• a polymer electrolyte membrane electrochemical reactor (PEMER). Palladium (Pd) nanoparticles were synthesised and supported on a carbonaceous matrix (Pd/C) with a 28 wt % of Pd with respect to carbon material. Pd/C was characterised by transmission electron microscopy (TEM), and thermogravimetric

• is the Toray paper support. Morphology, size and dispersion of Pd nanoparticles in Pd/C were analysed by a transmission electron microscopy (TEM) using a JEOL JEM-2012 instrument with an accelerating voltage of 300 kV. The TEM was connected with an energy dispersion X-ray (EDX) for the analysis of

• the Pd nanoparticles. Thermogravimetric analysis (TGA) was performed using a Mettler Toledo model TGA/SDTA851 and /SF/1100 using a heating slope of 10 K min−1 from 298 K to 1023 K under a N2:O2 (4:1) atmosphere. For the characterisation of the Pdx/C/T scanning electron microscopy (SEM) micrographs

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• . Moreover, confocal microscopy studies showed that the positively charged oligoT escaped endosomal vesicles and migrated to the nucleus of Vero or GC-2 cells. This observation may support the correlation between cellular uptake and the activity of thermosensitive DNA prodrugs. Supplementary experiments with

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• chips have been used as the solid support for the PNA–CPP based DNA assay. Using this assay format, a combination of long-wavelength emissive CPP and PNA allowed detection of as low as 150 attomol of unlabeled DNA, or 300 copies (0.5 zeptomol) of Cy5-labeled DNA targets by confocal microscopy [127]. A

Halogen-containing thiazole orange analogues – new fluorogenic DNA stains

• Aleksey A. Vasilev,
• Meglena I. Kandinska,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• David Sucunza,
• Juan J. Vaquero,
• Obis D. Castaño,
• Stanislav Baluschev and
• Silvia E. Angelova

Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283

• [12][13], DNA fragment sizing [14][15], as reporter groups in hybridization probes [16][17][18][19][20][21][22][23], single DNA molecule fluorescence microscopy [24][25], gel staining [26], in real-time PCR analysis [27][28]) because of their excellent staining properties. Unsymmetrical cyanines have

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• . Confocal microscopy confirmed that 5 predominantly stains mitochondria but it also accumulates in the nucleoli of the cells. Keywords: confocal microscopy; luminescence; nucleobases; oligonucleotide binding; pyrene; X-ray; Introduction Pyrene is a planar, polycyclic aromatic hydrocarbon which shows well

• synthesis, DFT calculations, photophysical characterization, oligonucleotide binding studies, and confocal microscopy studies of the novel pyrene–nucleobase conjugates 2–5 (nucleobase = thymine (2 and 4), and adenine (3 and 5)). Our compounds represent a simple bifunctional design combining the fluorescent

• better to single-stranded T10 and double-stranded (dA)10-T10. Confocal microscopy Over the past years, there has been an increased interest in the development of luminescent probes for bioimaging. In that respect, both metal-containing [35] as well as organic [36] luminophores were examined. We found

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• light scattering (DLS) [18][19][20][21] and cryo-transmission electron microscopy (Cryo-TEM) [22][23][24]. Results and Discussion Synthesis We present two approaches for the synthesis of naphthylallyl (NA) derivatives. The first approach is a cross-metathesis of peracetylated allyl derivatives of γ-CD

• nm and 300 nm. The 2-O-sample did not show any temperature dependence. Transmission cryo-electron microscopy (Cryo-TEM) The supramolecular properties of the individual regioisomers (2-O-, 3-O-, 6-O-) of NA-γ-CD 2a–c and the dependence of the formation of the self-assembled structures on their

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

• utilized in two-photon excited fluorescence microscopy and bioimaging [13][14], most often upon their further structural tuning towards higher polar character and solubility in water [20][21][22]. Their linking to porphyrins proved to be a useful strategy for two-photon photodynamic therapy [23][24][25

New bio-nanocomposites based on iron oxides and polysaccharides applied to oxidation and alkylation reactions

• Daily Rodríguez-Padrón,
• Alina M. Balu,
• Antonio A. Romero and
• Rafael Luque

Beilstein J. Org. Chem. 2017, 13, 1982–1993, doi:10.3762/bjoc.13.194

• three materials (Table 1). The materials exhibited, in general, satisfying surface areas and pore volumes, particularly taking into account their preparation methodology. Electron microscopy The morphology of the nanomaterials was determined by scanning electron microscopy (SEM) and transmission

• electron microscopy (TEM). The micrographs show a homogeneous distribution of iron oxide nanoparticles for the three catalysts (Figure 3A,C,E). The analysis of the SEM images reveals the tendency of the constituent particles of the magnetic material to form agglomerates due to their nanometer size (Figure

• obtained from the N2 desorption branch. Electron microscopy SEM images and the elemental composition were recorder using the JEOL JSM-6490 LV microscope. The samples were Au/Pd-coated on a high-resolution sputter SC7640 at a sputtering rate of 1.5 kV per minute, up to 7 nm thickness. TEM micrographs were

An effective Pd nanocatalyst in aqueous media: stilbene synthesis by Mizoroki–Heck coupling reaction under microwave irradiation

• Carolina S. García,
• Paula M. Uberman and
• Sandra E. Martín

Beilstein J. Org. Chem. 2017, 13, 1717–1727, doi:10.3762/bjoc.13.166

• QP 5050 spectrometer equipped with a VF-5 ms, 30 m × 0.25 mm × 0.25 μm column. Melting points were determined with an electrical instrument. MW-induced reactions were performed in a CEM Focused Microwave TM Synthesis System, Model Discover single mode instrument. Transmission electron microscopy was

Block copolymers from ionic liquids for the preparation of thin carbonaceous shells

• Sadaf Hanif,
• Bernd Oschmann,
• Dmitri Spetter,
• Muhammad Nawaz Tahir,
• Wolfgang Tremel and
• Rudolf Zentel

Beilstein J. Org. Chem. 2017, 13, 1693–1701, doi:10.3762/bjoc.13.163

• 10% for the carbon coated particles (Figure 4a). The resulting particles were also characterized by transmission electron microscopy (TEM), and corresponding images are shown in Figure 6a and 6b. The average particle diameter is ≈8 nm. Figure 6b shows nanoparticles sheathed and connected through

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

• bands. The method has been validated for a mouse footpad model of M. ulcerans infection [69] and for skin tissue samples from Buruli ulcer patients [70]. With a detection rate of 73%, TLC proved superior to microscopy (30–60%) or culture (35–60%) and comparable to histology (82%), but inferior to PCR

New electroactive asymmetrical chalcones and therefrom derived 2-amino- / 2-(1H-pyrrol-1-yl)pyrimidines, containing an N-[ω-(4-methoxyphenoxy)alkyl]carbazole fragment: synthesis, optical and electrochemical properties

• Daria G. Selivanova,
• Alexei A. Gorbunov,
• Olga A. Mayorova,
• Alexander N. Vasyanin,
• Igor V. Lunegov,
• Elena V. Shklyaeva and
• Georgii G. Abashev

Beilstein J. Org. Chem. 2017, 13, 1583–1595, doi:10.3762/bjoc.13.158

• scanning tunneling microscopy. Results and Discussion Synthetic toolbox The objective of the presented work involves the design and further synthesis of 4,6-diaryl-substituted 2-(pyrrol-1-yl)pyrimidines, embedding 9-[ω-(4-methoxyphenoxy)alkyl]carbazole moieties as substituents, one of which is directly

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• to regain their 3D structure [33][46]. Using MPD is not only beneficial for the polymerization process, but also enables the use of characterization techniques such as transmission electron microscopy and atomic force microscopy. Polymeric detergents are effective protein-stabilizing agents mainly at

Mechanochemical synthesis of graphene oxide-supported transition metal catalysts for the oxidation of isoeugenol to vanillin

• Ana Franco,
• Sudipta De,
• Alina M. Balu,
• Araceli Garcia and
• Rafael Luque

Beilstein J. Org. Chem. 2017, 13, 1439–1445, doi:10.3762/bjoc.13.141

• diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFT). N2 adsorption measurements were performed at 77 K by using a Micromeritics ASAP 2000 volumetric adsorption analyzer. The samples were degassed

Mechanochemistry-assisted synthesis of hierarchical porous carbons applied as supercapacitors

• Desirée Leistenschneider,
• Nicolas Jäckel,
• Felix Hippauf,
• Volker Presser and
• Lars Borchardt

Beilstein J. Org. Chem. 2017, 13, 1332–1341, doi:10.3762/bjoc.13.130

• voltage of 20 kV. Transmission electron microscopy (TEM) was executed with a TEM Libra 200 system from Carl Zeiss Microscopy GmbH with an acceleration voltage of 200 kV. For the TEM, the sample powder was sonicated in acetone for 5 s. A lacey-carbon film on copper net (300 mesh) from Plano was used as TEM

BODIPY-based fluorescent liposomes with sesquiterpene lactone trilobolide

• Ludmila Škorpilová,
• Silvie Rimpelová,
• Michal Jurášek,
• Miloš Buděšínský,
• Jana Lokajová,
• Roman Effenberg,
• Petr Slepička,
• Tomáš Ruml,
• Eva Kmoníčková,
• Pavel B. Drašar and
• Zdeněk Wimmer

Beilstein J. Org. Chem. 2017, 13, 1316–1324, doi:10.3762/bjoc.13.128

• create construct 6. The liposomes were composed of dipalmitoyl-3-trimethylammoniumpropane and phosphatidylethanolamine. The whole system was characterized by atomic force microscopy, the average size of the liposomes was 150 nm in width and 30 nm in height. We evaluated the biological activity of

• construct 6 and its liposomal formulation, both of which showed immunomodulatory properties in primary rat macrophages. The uptake and intracellular distribution of construct 6 and its liposomal formulation was monitored by means of live-cell fluorescence microscopy in two cancer cell lines. The

• the prepared liposomes with incorporated construct 6 was performed by atomic force microscopy (AFM) analysis in a tapping mode in 2D and 3D arrangement, see Figure 4 (Supporting Information File 1, section 3). We confirmed the successful preparation of liposomes, the average size of which was 150 nm

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• biology and the investigation of macromolecular structure and function relationships. Major contributions also came from considerable advances in high resolution NMR spectrometry and electron microscopy along with the continuous evolution of synchrotron radiation and free electron laser light sources

• electron microscopy). Figure 15 displays the reconstruction of the full macromolecular complex as a flexible arrangement of three mannose/heptose-specific dimers flanked by two fucose-specific TNF-α-like trimers [48]. This study (along with many other examples) highlights the potential of SAXS to decipher

Correlation of surface pressure and hue of planarizable push–pull chromophores at the air/water interface

• Frederik Neuhaus,
• Fabio Zobi,
• Gerald Brezesinski,
• Marta Dal Molin,
• Stefan Matile and
• Andreas Zumbuehl

Beilstein J. Org. Chem. 2017, 13, 1099–1105, doi:10.3762/bjoc.13.109

• using fluorescence microscopy, grazing-incidence angle X-ray diffraction, and infrared reflection–absorption spectroscopy. An increase of the lateral membrane pressure leads to a well-packed layer of the ‘flipper’ mechanophores and a clear change in hue above 18 mN/m. The fluorescent probes had no

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

• containing mannose-binding receptors) [46] and thyroglobulin in serum [47] and to study the internalization pathway in dendritic cells, employing confocal laser microscopy (CLSM) and flow cytometry [48]. Moreover, even techniques based on light scattering, like dark field microscopy (DFM), resulted

• relevance. Long et al. [50] developed a simple procedure to analyze in real-time the carbohydrate–protein interaction at the single NP level, using for the first time an unusual technique such as the dark field microscopy, DFM (Figure 3). Briefly, the method is based on the interaction among 60 nm AuNPs

• microscopy. The interaction among ConA-functionalized AuNPs (60 nm) and dextran-coated AuNPs (20 nm) are detected by DFM. Reprinted with permission from [50]. Copyright 2015 American Chemical Society. Copper-free cycloaddition (SPAAC) of azido galactoside on cyclooctyne and schematic depiction of Au surface

Aggregation behaviour of a single-chain, phenylene-modified bolalipid and its miscibility with classical phospholipids

• Simon Drescher,
• Vasil M. Garamus,
• Christopher J. Garvey,
• Annette Meister and
• Alfred Blume

Beilstein J. Org. Chem. 2017, 13, 995–1007, doi:10.3762/bjoc.13.99

• was studied as a function of temperature using transmission electron microscopy (TEM), differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy, and small angle neutron scattering (SANS). We show that our new bolalipid self-assembles into nanofibres, which transform into

• side by side within the fibrous aggregate but slightly twisted relative to each other leading to a helical super structure of the fibres. This helicity was previously confirmed by cryo-transmission electron microscopy (cryo-TEM), high resolution atomic force microscopy (AFM) [26], and Monte Carlo

• were vigorously vortexed at 60 °C to obtain a homogeneous suspension. Transmission electron microscopy (TEM) The samples were prepared by spreading 5 µL of the bolalipid suspension (c = 0.05 mg mL−1 in case of pure bolalipid, c = 60 µM in case of lipid mixtures) onto a copper grid coated with a Formvar