Preparing a liquid crystalline dispersion of carbon nanotubes with high aspect ratio

• Keiko Kojima,
• Nodoka Kosugi,
• Hirokuni Jintoku,
• Kazufumi Kobashi and
• Toshiya Okazaki

Beilstein J. Org. Chem. 2024, 20, 52–58, doi:10.3762/bjoc.20.7

• film thickness was analyzed by laser confocal microscopy (Figure 5a, Table 1). The average thickness was ≈393 nm, whereas the edge of the film was much thicker (≈999 nm). In earlier studies, the CNTs in the dispersions were observed to flow and accumulate along the droplet's edge due to the coffee ring

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• exhibited a micromolar and submicromolar binding affinity for ds-polynucleotides and inactivated a mutant of dipeptidyl peptidase enzyme E451A. Confocal microscopy revealed that the conjugate with the longer linker entered the HeLa cell membranes and blue fluorescence was visualized as the dye accumulated

• cellular uptake and intracellular distribution of Phen-Py-1 in HeLa cells by TCS SP8 X confocal microscopy. The results showed that the dye entered the HeLa cell membranes fast, and after 1 hour of incubation at 1 µM concentration, blue fluorescence was visualized as the dye accumulated in the cell

• binding (∆rH). The reaction Gibbs energies (∆rG) were calculated by using the following equation: ∆rG = −RTln(Ka). The entropic contribution to the binding Gibbs energy was calculated by the equation: T∆rS = ∆rH − ∆rG. Confocal microscopy: HeLa cells were cultured and maintained in complete high glucose

Post-functionalization of drug-loaded nanoparticles prepared by polymerization-induced self-assembly (PISA) with mitochondria targeting ligands

• Janina-Miriam Noy,
• Fan Chen and
• Martina Stenzel

Beilstein J. Org. Chem. 2021, 17, 2302–2314, doi:10.3762/bjoc.17.148

• mitochondria target containing nanoparticles PPM-NP4-TPP and MPM-NP2-TPP were further analysed using 3D spheroid tumour models [47]. The samples were incubated with 143B and SW982 cells and the penetration profiles of the micelles were investigated using laser scanning confocal microscopy. After 3 hours of

• zwitterionic drug particles similar anticancer efficiency than that of the non-conjugated PPM-NP4 micelles. The co-localization of the TPP-variants into the mitochondria, lysosomes and nuclei were analysed using laser scanning confocal microscopy. Surprisingly, there was no improvement in mitochondria

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Synthesis of 1-indolyl-3,5,8-substituted γ-carbolines: one-pot solvent-free protocol and biological evaluation

• Premansh Dudhe,
• Mena Asha Krishnan,
• Kratika Yadav,
• Diptendu Roy,
• Krishnan Venkatasubbaiah,
• Biswarup Pathak and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2021, 17, 1453–1463, doi:10.3762/bjoc.17.101

• experiments were performed. In brief, HeLa cells were incubated with carboline 3ac (10 μM and 100 nM), and the cellular uptake was examined using confocal microscopy (λex = 405 nm; λem = 420–470 nm). Compound 3ac showed excellent cytosolic uptake in cancer cells when incubated at a 10 μM concentration (Figure

• derivative 3ac (10 nM, 100 nM, 1 μM, 10 μM, and 100 μM), the cellular uptake and distribution was monitored by using confocal microscopy (λex = 405 nm; λem range = 420–470 nm). Selected examples of compounds containing the γ-carboline core. Single-crystal XRD structure of 3ac (CCDC: 1897787). UV–vis

• , 3ca, 3ga in the breast cancer cell line, MCF7 and (B) doxorubicin against the panel of tested cancer cell lines. Dose–response curve of γ-carbolines 3ac, 3bc, 3ca, 3ga in macrophage cell line, RAW264.7. Laser scanning confocal microscopy studies (λex = 405 nm; collection range = 420–470 nm) for uptake

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• . observed by confocal microscopy that the A-1 aptamer entered gp160-positive cells and suggested that receptor-mediated endocytosis could be the mechanism of entry, such a notion was not definitively demonstrated as the mechanism of uptake [35]. In addition, observed differences between these aptamers could

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

• 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

• synthesised possessing four or five N+ or four Ts modifications and a fluorescent label (6-FAM) at the 3ʼ-end (Table 1) was tested. Asynchronously growing NIH3T3 mouse fibroblasts were incubated with the ONs for 12 hours, fixed in 4% paraformaldehyde before the cells were processed for fluorescent confocal

• 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

Potent hemithioindigo-based antimitotics photocontrol the microtubule cytoskeleton in cellulo

• Alexander Sailer,
• Franziska Ermer,
• Yvonne Kraus,
• Rebekkah Bingham,
• Ferdinand H. Lutter,
• Julia Ahlfeld and
• Oliver Thorn-Seshold

Beilstein J. Org. Chem. 2020, 16, 125–134, doi:10.3762/bjoc.16.14

• network within cells treated with HITubs and documented the resulting disruption of the physiological MT network integrity, and consequently also changes in cell morphology by confocal microscopy. Cells exposed to HITub-4 (1 μM) in the dark or under λ = 530 nm illumination (to maintain exclusively Z

• antiproliferative potencies at λ = 450 and 530 nm/dark conditions (75 ms pulsing every 15 s). b) EC50 values of HITubs from cellular antiproliferation assays under dark conditions and at λ = 450 nm. The ratio of lit/dark EC50 values shows the fold change in photoswitchable bioactivity. Confocal microscopy images of

Plasma membrane imaging with a fluorescent benzothiadiazole derivative

• Pedro H. P. R. Carvalho,
• Jose R. Correa,
• Karen L. R. Paiva,
• Daniel F. S. Machado,
• Jackson D. Scholten and
• Brenno A. D. Neto

Beilstein J. Org. Chem. 2019, 15, 2644–2654, doi:10.3762/bjoc.15.257

• (pH 7.4) at room temperature and the coverslips were mounted over glass slides using ProLong Gold Antifade (Invitrogen, OR, USA) according to the manufacturer’s recommendations. These two main samples (of live and fixed cells) were analyzed using confocal microscopy and excited using 405 nm wavelength

• . Afterwards, the cells were washed three times in PBS and the samples were mounted over glass slides by using antifade agent Prolong Gold (Invitrogen, OR, USA) according to the manufacture’s recommendations. The samples were analyzed using confocal microscopy. CellMask was excited at 633 nm wavelength and the

Novel solid-phase strategy for the synthesis of ligand-targeted fluorescent-labelled chelating peptide conjugates as a theranostic tool for cancer

• Sagnik Sengupta,
• Mena Asha Krishnan,
• Premansh Dudhe,
• Ramesh B. Reddy,
• Bishnubasu Giri,
• Sudeshna Chattopadhyay and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2018, 14, 2665–2679, doi:10.3762/bjoc.14.244

• bioconjugates a potential theranostic tool for cancer. The newly synthesized bioconjugates 13 and 17, that can selectively target PSMA+ and FR+ cancers, were further evaluated by performing in vitro studies using laser scanning confocal microscopy on PSMA+ LNCaP cells, FR+ epithelial CHO-β cells and PSMA−, FR

• folate receptors. The in vitro uptake study has been performed using laser scanning confocal microscopy and the bioconjugates are found to be delivered specifically to cells expressing corresponding cell surface proteins. The small molecule targeted imaging probes prepared in this study are designed for

• remove unbound conjugates, confocal images were acquired using a laser scanning confocal microscopy (FV 1000, Olympus) by excitation at 559 nm (yellow diode laser) and emission at 618 nm. Author’s Contributions Sagnik Sengupta (SS) chemically synthesized and characterized the targeting ligands and

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

• analyzed by FACSDiVa (BD Bioscience) 5.0 software. Confocal microscopy imaging Cells were seeded to cover glass containing (thickness 1, Assistant, Karl Hecht GmbH & Co KG, Sondheim/Rhön Germany) 24-well plates one day prior to the experiment in complete cell medium. Treatment was performed in serum-free

• K2 by CytoPainter Lysosomal Staining Kit - Deep Red Fluorescence (abcam, Cambridge, UK), according to the manufacturer’s instructions. Confocal microscopy was carried out using a Zeiss LSM 710 system (Carl Zeiss Microscopy GmbH, Jena, Germany) with a 40× oil objective. Images were processed by

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

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

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• internalisation studies with HepG2 cells [29]. The green CDs were non-toxic to cells at concentrations of up to 625 μg/mL and exposures of 72 h. Laser scanning confocal microscopy (LSCM) demonstrated cell internalization, making these materials a good candidate as a bioimaging agent. In 2011 Qu et al. developed a

• the CDs, while significant toxicity was seen at concentrations at and above 400 μg/mL. CDs (100 μg/mL) were also incubated with HepG2 for 24 h and laser scanner confocal microscopy (LCSM) was used to image the internalization of the CDs within the cells using the green, yellow and red channels

A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

• Heidi-Kristin Walter,
• Bettina Olshausen,
• Ute Schepers and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2017, 13, 127–137, doi:10.3762/bjoc.13.16

• handheld UV lamp. Confocal microscopy of HeLa cells after transfection with DNA2aD1–DNA3rD5 (row 1), DNA2rD1–DNA3aD8 (row 2), DNA2aD2–DNA3aD8 (row 3) and DNA2rD4–DNA3aD8 (row 4). The visualization was performed using a Leica TCS-SPE (DMi8) inverted microscope with an ACS APO 63×/1.30 oil objective. For

A self-assembled cyclodextrin nanocarrier for photoreactive squaraine

• Ulrike Kauscher and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2016, 12, 2535–2542, doi:10.3762/bjoc.12.248

• : Additional measurements and methods. Acknowledgments Financial support from the DFG EXC 1003 Cells in Motion–Cluster of Excellence, Münster, Germany is gratefully acknowledged. We thank Lena Fischer-Riepe for her help with confocal microscopy.

A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 125–138, doi:10.3762/bjoc.12.14

• ]. Thus, compound 28 (Figure 9b) was prepared and found to inhibit formation of the MBNL-CUGexp nuclear foci in DM1 model cells. Indeed, it was possible to follow live cells and watch the foci dissolve in real time using time-lapse confocal microscopy [77]. The logical next step was increasing affinity

Multivalent dendritic polyglycerolamine with arginine and histidine end groups for efficient siRNA transfection

• Fatemeh Sheikhi Mehrabadi,
• Hanxiang Zeng,
• Mark Johnson,
• Cathleen Schlesener,
• Zhibin Guan and
• Rainer Haag

Beilstein J. Org. Chem. 2015, 11, 763–772, doi:10.3762/bjoc.11.86

• maintaining its low cytotoxicity (Figure 4). Cellular uptake and confocal microscopy The cellular uptake and localization of fluorescently labeled siRNA/AAdPG complexes were quantified using flow cytometry and confocal microscopy (Figure 6). By comparing the cellular uptake of dPG-NH2 functionalized solely

• transfection media, the cells were trypsinized and collected via centrifugation. The transfected cells were analyzed by FACS to determine the mean Cy3-fluoroscence of each sample. Confocal microscopy Unmodified NIH 3T3 fibroblast cells were seeded at a density of 10,000 cells/well on an 8-well chamber slide

A versatile δ-aminolevulinic acid (ΑLA)-cyclodextrin bimodal conjugate-prodrug for PDT applications with the help of intracellular chemistry

• Chrysie Aggelidou,
• Theodossis A. Theodossiou,
• Antonio Ricardo Gonçalves,
• Mariza Lampropoulou and
• Konstantina Yannakopoulou

Beilstein J. Org. Chem. 2014, 10, 2414–2420, doi:10.3762/bjoc.10.251

• -cyclodextrin, with an average degree of substitution, DS = 3. Delivery of water-soluble, colorless 2 to cells resulted in intense red fluorescence registered by confocal microscopy, evidently due to the engagement of the intracellular machinery towards formation of PpIX. Conjugate 2 was further complexed with

• . MCF7 cells were incubated with the colorless conjugate solution for 4 h, to allow conversion of prodrug 1 into PpIX [5][18]. Indeed, upon confocal microscopy imaging of the treated cells (λex = 568 nm), intense red fluorescence was observed (Figure 2), demonstrating that either (i) cell internalization

• isothiocyanate-labeled 1-adamantylamine (Figure 3). The characteristic confocal microscopy images revealed red fluorescence upon excitation at λex = 568 nm, as well as green fluorescence upon excitation at 488 nm. Following superimposition of the two fluorescence channels it could be concluded that PpIX

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

• 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

A peptidic hydrogel that may behave as a “Trojan Horse”

• Nicola Castellucci,
• Giorgio Sartor,
• Natalia Calonghi,
• Carola Parolin,
• Giuseppe Falini and
• Claudia Tomasini

Beilstein J. Org. Chem. 2013, 9, 417–424, doi:10.3762/bjoc.9.44

• confocal microscopy, fluorescent hydrogels were prepared, introducing the fluorescent dansyl moiety into the mixture. Keywords: amino acids; confocal microscopy; controlled release; hydrogel; low molecular weight hydrogelator; Introduction Drug delivery is an important topic in the finding of successful

• collected some information on the ability of fluorescent hydrogels 6–9 to cross the cellular membrane of the cancer cells, by means of confocal microscopy (Figure 4). It is worth mentioning that gel 6 is made of B, while gels 7–9 are made of A, doped with one of the dansyl containing compounds B–D. IGROV-1

• proliferation were studied after 24 h of treatment. Cell viability was determined by propidium iodide dye exclusion. Confocal laser scanning microscopy: For confocal microscopy, IGROV 1 were grown on glass coverslips for 24 h before being exposed to hydrogels 6, 7, 8 and 9 for 30 min. Cells were washed in PBS

Hydrophobic analogues of rhodamine B and rhodamine 101: potent fluorescent probes of mitochondria in living C. elegans

• Laurie F. Mottram,
• Safiyyah Forbes,
• Brian D. Ackley and
• Blake R. Peterson

Beilstein J. Org. Chem. 2012, 8, 2156–2165, doi:10.3762/bjoc.8.243

• differences exist between the calculated and measured values, the relative trends illustrate how structural modifications of these compounds are likely to affect fluorophore solubility and cellular permeability. Imaging of fluorophores in vivo by confocal microscopy To visualize the absorption and

• , mitochondria and nuclei, and occasionally was observed in the cytosol of cells of living animals. Unlike all of the other fluorophores tested, HRB 9 and HR101 10 engendered strong fluorescence in vivo after 2 h at concentrations as low as 100 pM. Higher magnification confocal microscopy (60× objective) using a

• of the HRB 9 and HR101 10 fluorophores. Partition constants of fluorophores. Supporting Information Supporting Information File 336: Supplementary time-lapse confocal microscopy video showing dynamics of mitochondrial fusion and fission in a living adult C. elegans animal imaged after treatment with

Sexithiophenes as efficient luminescence quenchers of quantum dots

• Christopher R. Mason,
• Yang Li,
• Paul O’Brien,
• Neil J. Findlay and
• Peter J. Skabara

Beilstein J. Org. Chem. 2011, 7, 1722–1731, doi:10.3762/bjoc.7.202

• LEDs and photovoltaic cells [19][20][21][22][23]. Previously, we reported the synthesis and characterisation of CdS quantum dots in polystyrene beads, in which beads ranging in size from 100 nm to 500 μm were prepared and confocal microscopy showed an even distribution of CdS throughout the polymer