Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• compounds, which have been employed in biomedical imaging and as potential DNA-targeting anticancer agents [14][15][16][17]. More recently, a benzoquinolizinium-based fluorescent dye was reported to be used as imaging agent for inflammation and for the evaluation of the physiological response to anti

A fluorescent probe for detection of Hg²⁺ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene

• Xiaoqian Chen,
• Naqin Yang,
• Yue Ma,
• Xinan Yang and
• Peihua Ma

Beilstein J. Org. Chem. 2023, 19, 864–872, doi:10.3762/bjoc.19.63

• cucurbit[n]uril fluorescent probes has become increasingly mature [9][28][29][30][31]. For example, the host–guest fluorescent probe of cucurbit[10]uril (Q[10]) and the fluorescent dye acridine (AD) was used to identify the pesticide dodine (DD) [32]; a fluorescent probe of cucurbit[10]uril (Q[10]) and

Microelectrode arrays, electrosynthesis, and the optimization of signaling on an inert, stable surface

• Kendra Drayton-White,
• Siyue Liu,
• Yu-Chia Chang,
• Sakashi Uppal and
• Kevin D. Moeller

Beilstein J. Org. Chem. 2022, 18, 1488–1498, doi:10.3762/bjoc.18.156

• peptides were placed on the array along with a fluorescent dye (LRSC, lissamine rhodamine) that was used to make sure the placement chemistry was working. The array used was coated with the borate ester diblock copolymer (Figure 2), and the peptides were attached to this polymer through a PEG-6 linker in

Synthesis, optical and electrochemical properties of (D–π)₂-type and (D–π)₂Ph-type fluorescent dyes

• Kosuke Takemura,
• Kazuki Ohira,
• Taiki Higashino,
• Keiichi Imato and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2022, 18, 1047–1054, doi:10.3762/bjoc.18.106

• Kosuke Takemura Kazuki Ohira Taiki Higashino Keiichi Imato Yousuke Ooyama Applied Chemistry Program, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan 10.3762/bjoc.18.106 Abstract The (D–π)2-type fluorescent dye OTT-2

• with two (diphenylamino)carbazole-thiophene units as D (electron-donating group)–π (π-conjugated bridge) moiety and the (D–π)2Ph-type fluorescent dye OTK-2 with the two D–π moieties connected through a phenyl ring were derived by oxidative homocoupling of a stannyl D–π unit and Stille coupling of a

• dyes [10][11][12][13][21][22][27][28][32]. In our previous work [33], we have reported the synthesis, optical and electrochemical properties of the (D–π)2Ph-type fluorescent dye OTK-2 with two (diphenylamino)carbazole-thiophene units as D–π moiety connected through a phenyl ring (Scheme 1). The ICT

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• selectively bind a hexa-histidine tag (His-tag). ODN-1 can also be modified with a second functional group (X), such as a fluorescent dye, to afford X-ODN-1 (Figure 1A and Figure 1B). In this way, the binding of X-ODN-1 to the bacteria will lead to the presentation of X on the cell surface (Figure 1A). A

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

• ]. The band at 1678 cm−1 was the characteristic feature of an antiparallel conformation of the sheet structure or the β-turn structure [61]. To further confirm the β-sheet formation, we performed a ThT fluorescence spectroscopy assay. ThT is a widely used fluorescent dye that is amyloid-specific and can

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• fluorescent dye that is tethered to an acetyllysine-containing peptide. If the acetyl moiety of the fluorophore is enzymatically hydrolyzed by HDAC8, it will produce a strongly fluorescent signal at 360 nm. Table 1 shows the percentage of HDAC8 inhibition at 100, 10, and 1 µM concentration of the designed

Chemical tuning of photoswitchable azobenzenes: a photopharmacological case study using nicotinic transmission

• Lorenzo Sansalone,
• Jun Zhao,
• Matthew T. Richers and
• Graham C. R. Ellis-Davies

Beilstein J. Org. Chem. 2019, 15, 2812–2821, doi:10.3762/bjoc.15.274

• an internal solution containing (in mM): 135 potassium gluconate, 4 MgCl2, 10 HEPES, 4 Na2-ATP, 0.4 Na2-GTP, 10 Na2-phosphocreatine, pH 7.35. The red fluorescent dye Alexa 594 (0.05 mM, ThermoFisher Scientific, Waltham, MA, USA) was added to visualize the morphology of the neurons. Normal ACSF was

Photoreversible stretching of a BAPTA chelator marshalling Ca²⁺-binding in aqueous media

• Aurélien Ducrot,
• Arnaud Tron,
• Robin Bofinger,
• Ingrid Sanz Beguer,
• Jean-Luc Pozzo and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2019, 15, 2801–2811, doi:10.3762/bjoc.15.273

• electron-transfer reaction, while ion binding blocks this quenching pathway restoring emission. Thus, ion liberation from 1 and transfer to 3 would result in a fluorescence off–on switching of the latter. To perform the ion-transfer experiment, the fluorescent dye is loaded with one equivalent of Ca2

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

• , that is at a concentration 100-fold lower than that of the cytotoxic effect. The new compound was then tested as bioimaging probe in live and fixed cells (Figure 6). As can be seen, the green fluorescent dye BTD-4APTEG was found most concentrated at the plasma membranes of the MCF-7 cells in both, live

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• decreased the viability of rat peritoneal macrophages to 67% (*P < 0.05) at 40 µM concentration. It seems that this phenomenon was not related to the fluorescent dye of compound 5, since dansyl amide itself did not change the viability of rat macrophages at both concentrations. A decrease in cell viability

Synthesis, photophysical and electrochemical properties of pyridine, pyrazine and triazine-based (D–π–)₂A fluorescent dyes

• Keiichi Imato,
• Toshiaki Enoki,
• Koji Uenaka and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2019, 15, 1712–1721, doi:10.3762/bjoc.15.167

• solvents are fairly large (Table 1). Thus, the fact indicates that the (D–π–)2A fluorescent dyes have advantageous characteristics as emitters for OLEDs and fluorescence probes for biological imaging. It is well accepted that the dipole–dipole interactions between the fluorescent dye and the solvent

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• enables them to be effective hosts for a wide range of guest molecules including organic biscarbonyl derivatives, near-infrared dyes, acenes, precious metal halide complexes, trimethylammonium ion-pairs, and saccharides. Keywords: fluorescent dye; host–guest chemistry; hydrogen bonding; hydrophobic

Synthesis and SAR of the antistaphylococcal natural product nematophin from Xenorhabdus nematophila

• Frank Wesche,
• Hélène Adihou,
• Thomas A. Wichelhaus and
• Helge B. Bode

Beilstein J. Org. Chem. 2019, 15, 535–541, doi:10.3762/bjoc.15.47

• relationship of the simple and antistaphylococcal amide nematophin from Xenorhabdus nematophila and synthetic derivatives are described. Moreover, the synthesis of intrinsic fluorescent derivatives, incorporating azaindole moieties was achieved for the first time. Keywords: azaindole; fluorescent dye; MRSA

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• facilitated the discovery of novel PqsD-targeting compounds through CuAAC-mediated conjugation of a fluorescent dye (Figure 9) [62]. Finally, Sangshetti et al. reported the discovery of linezolid-like Schiff bases, which showed promising anti-biofilm activity in the double-digit micromolar range [63]. Notably

Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• illumination in confocal laser scanning microscopy [23][25], or absorb at shorter wavelengths, where biological samples show a high background from autofluorescence [26][27]. An ideal fluorescent dye would be highly photostable in biological media, have long-wavelength absorption to minimize background

• protonation-sensitive fluorescent dye yields a rational and modular approach towards CB–dye pairs [25]. This strategy had been previously applied to carbazole, aminonaphthalenesulfonate and aminopyrene as fluorescent dyes [25][26][27][28]. Herein, we systematically explore the utility of boron-dipyrromethenes

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

• challenging tandem hairpin Py/Im polyamides which could recognize >10 base pairs with flexible linker conjugated with a fluorescent dye (either Texas Red (TR) or Cyanine 3 (Cy3)) using a Fmoc-based solid phase synthetic approach; two of the representative conjugates 23 and 24 are shown in the Figure 8 [86][87

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

• more benign procedure. The properties of the dyes as fluorescence probes for dsDNA detection were investigated and compared with those of the commercial dye TO. In TE buffer solution the dyes from the series have negligible fluorescence themselves, but they form strongly fluorescent dye–dsDNA complexes

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

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

• dsDNA2r. Especially in case of D2 ΦF could be significantly improved from 27% to 45%, and in case of D4 from 9% to 16%. This is remarkable and clearly shows that the arabino-configured nucleoside 2 provides the structurally optimized anchor for fluorescent dye interactions with the DNA. Obviously, placing

Biomimetic synthesis and HPLC–ECD analysis of the isomers of dracocephins A and B

• Viktor Ilkei,
• András Spaits,
• Anita Prechl,
• Áron Szigetvári,
• Zoltán Béni,
• Miklós Dékány,
• Csaba Szántay Jr,
• Judit Müller,
• Árpád Könczöl,
• Ádám Szappanos,
• Attila Mándi,
• Sándor Antus,
• Ana Martins,
• Attila Hunyadi,
• György Tibor Balogh,
• György Kalaus (†),
• Hedvig Bölcskei,
• László Hazai and
• Tibor Kurtán

Beilstein J. Org. Chem. 2016, 12, 2523–2534, doi:10.3762/bjoc.12.247

• increase P-gp inhibitory activity [18]. Based on the unaltered accumulation of rhodamine 123, a P-gp substrate fluorescent dye, in the P-gp transfected L5178MDR cells, we observed that none of the synthesized compounds inhibits this transporter. The antioxidant activity of dracocephins A and B was also

Bright molecules for sensing, computing and imaging: a tale of two once-troubled cities

• A. Prasanna de Silva

Beilstein J. Org. Chem. 2015, 11, 2774–2784, doi:10.3762/bjoc.11.298

• naturally harnesses the diversity available in each of the three modules. For instance, the lumophore could be a fluorescent dye [3][24], a room temperature phosphor [25][26], or a lanthanide-based emitter [27][28]. Colleagues showed that even a quantum dot [29] would fit the bill. The receptor could be an

Preparation of Pickering emulsions through interfacial adsorption by soft cyclodextrin nanogels

• Shintaro Kawano,
• Toshiyuki Kida,
• Mitsuru Akashi,
• Hirofumi Sato,
• Motohiro Shizuma and
• Daisuke Ono

Beilstein J. Org. Chem. 2015, 11, 2355–2364, doi:10.3762/bjoc.11.257

• hydrophilic DM-β-CD and lipophilic benzene parts, may be affected by their hydrophilic and lipophilic balance of the nanogels. Identification of the CD nanogel assembly at the interface Adsorption of a CD nanogel at the oil–water interface in the emulsion phase was identified using a fluorescent dye-labeling

Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)

• Friederike Danneberg,
• Alice Ghidini,
• Plamena Dogandzhiyski,
• Elisabeth Kalden,
• Roger Strömberg and
• Michael W. Göbel

Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55

• (0.66 mmol/g) even manual synthesis routinely yielded milligram amounts of the purified final product. This compares favorably to the yield of DNA conjugates we have studied earlier [16]. Cleavage experiments were run with Cy5-labeled RNA, the fluorescent dye permitting the detection and quantification

Synthetic strategies for the fluorescent labeling of epichlorohydrin-branched cyclodextrin polymers

• Milo Malanga,
• Mihály Bálint,
• István Puskás,
• Kata Tuza,
• Tamás Sohajda,
• László Jicsinszky,
• Lajos Szente and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 3007–3018, doi:10.3762/bjoc.10.319

• problem of residual unreacted amino groups in the polymer was the use of an excess of the fluorescent dye (at least 2 fold the molar amount of the approximated amino groups), diluted solution for improving the solubility of the dye and long reaction time. The optimization of these reaction conditions can

• and the amount is less than 0.1% w/w (Supporting Information File 1, Figure S30). A slight deviation from the strategy based on pre-branching modification is represented in Scheme 5. According to this approach the fluorescent dye is introduced into the β-CD monomer [29] and the resulting fluoresceinyl

• (i.e., RBIT, NBF-Cl, FITC) or nucleophilic fluorescent dye (i.e., coumarin) into the polymers, respectively. The key intermediate azido-modified polymers have been used as precursor of the amino-modified polymers, but they can be considered as versatile substrates for cycloaddition reactions as well