Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative

• observed in the CD spectra, indicating that the formation of the Ag(I)-mediated base pairs as deduced from the melting curves does not influence the overall DNA topology. This is a well-known feature of the Im–Ag(I)–Im base pair [31]. Fluorescence spectroscopy assay In 2003, the ATP/AMP-binding aptamer was

• ’ terminus (Figure 4A and Figure 5). In the absence of AMP, the sequences should form a regular duplex structure, with the fluorescence of the fluorescein being quenched by the DABCYL moiety located nearby. In the presence of AMP and Ag(I), the aptamer should instead form the aptamer:AMP complex, releasing

One-pot multicomponent green Hantzsch synthesis of 1,2-dihydropyridine derivatives with antiproliferative activity

• Giovanna Bosica,
• Kaylie Demanuele,
• José M. Padrón and
• Adrián Puerta

Beilstein J. Org. Chem. 2020, 16, 2862–2869, doi:10.3762/bjoc.16.235

• reported by Cao and collaborators [19]. Catalyst characterization and recyclability The catalyst was analyzed by X-ray fluorescence (XRF) spectroscopy in order to ascertain the PW/Al2O3-support ratio. The mass percentage ratio of tungsten, which is the main component of the catalyst, and aluminium, the

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• . Accordingly, the field has developed to a stage that allows custom-design of RNA probes and tools for specific application. For example, investigations of RNA structures by NMR, EPR, or fluorescence spectroscopy require labeling of the RNA molecules with specific reporter groups [2][4][7][8][9][10]. Likewise

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• self-sorting protocols. The present mini review will provide an overview over the latest advancements in this field with a focus on reversibly switchable functions in discrete supramolecular systems. Keywords: copper; fluorescence; self-assembly; self-sorting; zinc porphyrin; Introduction Since self

• reversibility was achieved by the addition of the rhodium porphyrin 19 that reversed the system reviving the state SelfSORT-I. Since both self-sorted states exhibited a distinct fluorescence due to the changes at the zinc porphyrin sites, luminescence was used for the selective detection of DABCO in a mixture

• innovative catch–release system with multiple functions combined the ON/OFF-adjustment of silver(I) catalysis and fluorescence monitoring [59]. Actually, the ratiometric luminescence response allowed the exact monitoring of the catalytic activity. In the initial incomplete self-sorting (state SelfSORT-I

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• experiments. For that purpose, the DNA melting temperature Tm of the dye-labeled oligonucleotides F21T and Fa2T (for sequence see caption of Figure 2) was monitored by fluorescence spectroscopy, as the thermally induced unfolding of the quadruplex disrupts the Förster resonance energy transfer (FRET) between

• the ligands 4a–e on the addition of G4-DNA is the result of a sufficiently tight complexation. As this fluorescence light-up effect depends significantly on the length of the linker chain n, it is also concluded that the ligands with the strongest effect, i.e., 4c and 4d (n = 4 and 5), have a more

• the groove or loops has a direct influence on the strength and mode of the terminal π-stacking of the berberine unit. The tighter binding with better fitting of the side chain to the binding site is further supported by the observation that both ICD and the fluorescence light-up effect are the

Easy access to a carbohydrate-based template for stimuli-responsive surfactants

• Thomas Holmstrøm,
• Daniel Raydan and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2020, 16, 2788–2794, doi:10.3762/bjoc.16.229

• metal-binding event. This study was carried out by having pyrene fluorophores attached to the two non-chelating positions, giving rise to excimer fluorescence when the distance between them was decreased due to the ring flip [12]. Carbohydrates with gluco stereochemistry have also been used as templates

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

• receptors is described. We show that the binding of DNA-based artificial receptors to E. coli expressing His-tagged outer membrane protein C (His-OmpC) induces a Förster resonance energy transfer (FRET) between the dyes, which results in the generation of a unique fluorescence fingerprint. Because the

• cell decreases over time. This occurs because each bacterium continuously divides, which forces the synthetic receptors to split between the two daughter cells (Figure 2A). The manifestation of this phenomenon was experimentally validated [2] by observing a decrease in the fluorescence generated by the

• security systems that can generate (pseudo) random fluorescence patterns [4][5][6]. Originally, the pattern-generating probes (or ID-probes [24]) were designed to detect multiple different analytes and their combinations [24][25][26]. In a later stage, we showed that the unique emission fingerprints

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

• of anthracene tagged imidazolium receptors responded to ATP through an amplified fluorescence quenching [60]. Based on these results, we wanted to develop similar self-assembled systems which would show a “turn-on” response in the presence of ATP or other phosphate analytes. The current design of

• compact arrangement of the stacked pyrene chromophores and this restriction of internal motion might have resulted in a higher excimer intensity [71]. In order to see whether the presence of other phosphate analytes interfered in ATP detection, fluorescence enhancements of PBIm12 (75 µM), for only ATP (50

• fluorescence experiments applying the time correlated single photon counting (TCSPC) method. 1H and 13C NMR were performed on Jeol 400 MHz and Bruker 500 MHz spectrometers. Mass spectra were recorded in a Bruker mass spectrometer. SEM images was recorded by using the instrument CARL ZEISS (model SUPRA 55VP

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

• and 4 h. While the control cells (without adding 1 or 2) showed little fluorescence, the cells treated with RPE and 1 or 2 started to show many red fluorescent puncta inside the cells after 2 h. The puncta remained inside the cells at 4 h and showed little change (Figure 6). These results indicate

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

• sensing [1][2][3][4][5][6]. The analyte can be detected by relying on the enhancement of the Raman scattering intensity, if it is bound close to the gold surface (surface enhanced Raman scattering, SERS), for example, or by the release from the metal surface of a chromophore the fluorescence of which is

Synthesis and characterization of S,N-heterotetracenes

• Astrid Vogt,
• Florian Henne,
• Christoph Wetzel,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2020, 16, 2636–2644, doi:10.3762/bjoc.16.214

• (Table 1). Fluorescence quantum yields were far below 1% except for hexacene 22, which showed a very moderate value of 1.9%. This result is in line with the series of S,N-heteroacenes where noticeable fluorescence started with heptacene SN7 (ϕem = 19%) reaching 93% for the longest tridecamer SN13 [17][37

• ', and SN4''. UV–vis absorption spectra of TTA, Hex-SN4 9, Pr-SN4'' 33 and fluorescence spectrum of 33 in THF at rt (left) and corresponding cyclic voltammograms in dichloromethane/tetrabutylammonium hexafluorophosphate (0.1 M), 100 mV/s (right). Energy diagram of the frontier molecular orbitals of

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

• -fullerene in co-organic solvents and aqueous solution was investigated by fluorescence spectroscopy and ultraviolet-visible spectroscopy. The association stoichiometry of the complexes TBTQ-(OG)6 with C60 and TBTQ-(OG)6 with C70 was found to be 1:1 with binding constants of Ka = (1.50 ± 0.10) × 105 M−1 and

• order to investigate the host–guest relationship between TBTQ-(OG)6 and fullerenes, fluorescence titration experiments were performed in toluene/DMSO 1:1 (v/v), in which both the host and the guest components could be dissolved, instead of in water. As shown in Figure 2, the spectrum of TBTQ-(OG)6

• concentration of the fullerenes C60 and C70 increase, the emission is significantly quenched, indicating the photoinduced energy transfer from TBTQ-(OG)6 to the fullerenes [47][48]. Molar ratio plots (see Figure S16, Supporting Information File 1) on the basis of the fluorescence titration experiments suggested

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• the lines and decreases the signal intensities even more. In addition, the stabilization of the 14-3-3 peptide interaction in the presence of the ligand was confirmed by biochemical assays such as isothermal titration calorimetry (ITC) and fluorescence anisotropy. On a quest for modulators of 14-3-3

• fluorescence screening, yielding less false positive hits due to ligand aggregation or auto-fluorescence, while at the same time identifying the ligand binding site. Specific amino acid labeling For larger and intrinsically disordered proteins (IDPs), signal overlap in 1H,15N-HSQC/TROSY-HSQC spectra becomes a

• for measuring binding affinities, such as isothermal titration calorimetry (ITC) or fluorescence anisotropy/polarization, are only able to provide an averaged KD. Outlook In the last two decades, additional NMR methods have been developed to extend the size limits of NMR spectroscopy to very large

Synthesis of 1,4-benzothiazinones from acylpyruvic acids or furan-2,3-diones and o-aminothiophenol

• Ekaterina E. Stepanova,
• Maksim V. Dmitriev and
• Andrey N. Maslivets

Beilstein J. Org. Chem. 2020, 16, 2322–2331, doi:10.3762/bjoc.16.193

• studies on biological activity, chemosensors, and fluorescence, were developed via the reaction of furan-2,3-diones or acylpyruvic acids in the presence of carbodiimides with o-aminothiophenols. The target enaminones were formed together with pharmaceutically interesting 2-hydroxy-2H-1,4-benzothiazin-3(4H

• potential Cu2+ chemosensors [14], and their BF2 chelates, as multicolor fluorescence complexes, some of which exhibited aggregation-induced emission (AIE) properties [15]. In addition, enaminones I and II proved themselves to be versatile and available building blocks for the synthesis of various

• fused to 1,4-benzothiazin-2-one moieties, which may be interesting for studies on biological activity, chemosensors, and fluorescence. The first approach is based on the reaction of furan-2,3-diones 5 with o-aminothiophenols 1 in acetonitrile. This approach gave less side products, but the yields of

Chan–Evans–Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

• Viktor M. Tkachuk,
• Oleh O. Lukianov,
• Mykhailo V. Vovk,
• Isabelle Gillaizeau and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2020, 16, 2304–2313, doi:10.3762/bjoc.16.191

• pyrimidin-2(1H)-ones 5a–e exhibit fluorescence properties with emission of λmax = 490–532 nm in CH2Cl2 solution. In order to analyze the effect exerted on the Chan–Evans–Lam arylation by 4-, 5-, and 6-substituents on the pyrimidine ring and also aiming at the further functionalization of pyrimidin-2(1H)-one

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• ][12][13][14]. Among dyestuffs classes, the push-pull fluorescent dyes are renowned to own such special behaviors. The push-pull dyes generate higher charge delocalization upon excitation, thus enhance both polarizability and fluorescence emission [12][13][14][18]. The charge delocalization upon

• frontier molecular orbitals of the dyes are shown in Figure S92 in Supporting Information File 1. Solvatochromic studies on emissions were also done to gain insights into the photophysical behavior of the new push-pull dyes bearing free amino and azomethine groups. Therefore, the fluorescence spectra of

• all dyes 3–7 and 8–12 were recorded in the same solvents of various polarities that were used in the UV–vis studies, and the results are summarized in Table 1 and Table S1 (Supporting Information File 1). All dyes showed fluorescence properties and there was no direct correlation of the increase of

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

• solution-based synthetic route. PBA-BODIPY dextran assembles into nanoparticles of around 200 nm by hydrophobic interactions. The resulting PBA-BODIPY dextran nanoparticles retain an apolar interior as proved by pyrene fluorescence, suitable for the encapsulation of hydrophobic drugs with high

• shoulder at shorter wavelength (λabs = 364 nm) is typical for a symmetric dye. Normalized fluorescence spectra of conjugate Dex-1b were recorded at two different excitation wavelengths (λexc = 380 and 460 nm) and they are shown in Figure 3B and Figure S2 (Supporting Information File 1). The maximum

• assemblies of the conjugate Dex-1b a simple experiment with pyrene was conducted. It is well known that the fluorescence spectrum of pyrene is very sensitive to the polarity of the environment [37]. Indeed, the ratio (I1/I3) between the first (I1 = 372 nm) and the third bands (I3 = 383 nm) in the emission

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• microarray scanner (for example, Genepix 4400A). Microarray scanners are fluorescence scanners which utilize laser technology, such that the excitation wavelength is generated by specific lasers. Commonly used laser wavelengths are 488 nm, 532 nm, 594 nm and 635 nm, which match with usual fluorophore labels

• the slide. Thus, high-resolution images (2.5–10 μm/pixel) yield adequate data points for glycan microarray spots to provide lower standard deviations between replicate spots. The fluorescence intensity of the spots can be fine-tuned by controlling the laser power (also called LP) and the

• photomultiplier tube gain (also called PMT Gain). The image produced is saved as a TIFF image, usually with headers which describe the scanner settings used to acquire the image, and the intensity at each pixel is saved as the relative fluorescence units (RFU) for those scan settings. Spot alignment and data

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• the DNA/RNA conjugate NDI-GCP2 showed also aggregation along the ds-polynucleotide and AFM and DLS demonstrated that NDI-GCP2 has pronounced ds-DNA condensation ability. Keywords: AFM; circular dichroism; DNA/RNA recognition; fluorescence; guanidinio-carbonyl-pyrrole; naphthalene diimide

• monitoring, fluorescence is still the most popular method [8][9][10][11]. However, many new techniques or established ones with increased sensitivity are constantly improved or developed to report complementary to fluorescence. For instance, circular dichroism (CD) spectropolarimetry, highly sensitive to

• chiral properties of the DNA or RNA helical structures [12][13], could also take advantage of induced CD spectrum (ICD) in the visible spectrum range of small achiral dyes, which they show only upon binding to DNA/RNA [14]. Moreover, with recent advances in fluorescence emission-based polarisation

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• cleavage reactions [80] and 1,5-HAT [81] and iii) the excited state of the simple organic molecule target can possess an ultrashort lifetime [82] that precludes photochemistry in favor of photophysical or nonradiative deactivation, e.g., fluorescence or internal conversion (IC). Instead of direct UV

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• critical process parameters that control the glycosylation critical quality attributes. The advances made in protocols for capillary electrophoresis-laser-induced fluorescence (CE-LIF) measurements of antibody N-glycans have increased the potential for generating large datasets of N-glycosylation values

• description of the glycans, their relative abundance, and most importantly be high-throughput in terms of quantity, comprehensiveness, and speed of data generation. Capillary electrophoresis-laser-induced fluorescence (CE-LIF) is a glycomic analytical technology that has been adapted for automated and high

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA. Keywords: amino acid–fluorophore conjugate; circular dichroism; DNA/RNA recognition; fluorescence; intercalation; naphthalene diimide

• colourless and non-fluorescent core-unsubstituted NDI with a new charge transfer band with an absorption maximum in the visible spectral range and a high fluorescence quantum yield (up to 58%) [23][25]. Further, the 2-amino substituent offers the possibility to connect various amino acid side chains, thus

• stability of similar NDI compounds is greater in weakly acidic buffer solution over a longer period of time [24]. Compounds 3a,b, and 5 revealed absorption maxima of 518–540 nm with molar extinction coefficients of nearly 10000 M−1 cm−1 (Figure 2). Further, 3a,b, and 5 show strong fluorescence at 573–602 nm

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

• fluorescence spectroscopy assay were used to investigate the formation of secondary structures from PEP-1 during the self-assembly. The CD spectrum of PEP-1 at pH 7.4 (PBS buffer, c = 5.0 × 10−4 M) showed an intense negative band at around 226 nm that indicated the characteristic signature of a β-sheet-rich

• ]. 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

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

• aqueous solvents was evaluated by a series of experimental studies, such as NMR, UV, CD, and fluorescence titrations [23][25]. The Schmuck cation indeed showed a much higher affinity towards carboxylates, with dissociation constants of KD ≈ 1 mM (4: 620 µM; 5: 1.3 mM) compared to simple acylguanidinium

• ][58] has been suggested to further improve the standards set by the CAPA [59]. Standard high-throughput (HT) screening has been used regularly to facilitate studies on cellular uptake [60]. In standard assays, a single macroscopic parameter, usually the fluorescence intensity, is automatically

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• glycosylation is described. Two short-chain glycolipid analogs that mimic the naturally occurring substrate mannosyl phosphoryl dolichol exhibit either photoreactive and clickable properties or allow the use of a fluorescence readout. Both probes consist of a hydrophilic mannose headgroup that is linked to a

• structure in which the citronellyl–dodecanyl linker is located in the phospholipid membrane, and the mannose and the NBD are positioned in the surrounding aqueous medium. The close proximity of the NBD fluorophore to the membrane–water interface [30][31] allows for fluorescence-based scramblase assays