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

• fluorescein dyes to target mouse major satellite DNA using thermal denaturation, gel-shift electrophoresis, circular dichroism and fluorescence spectroscopy [89][90]. Some of these fluorescent probes were found to detect target sequences in mouse living cell lines and the nuclear substructures formed by

Diels–Alder cycloadditions of N-arylpyrroles via aryne intermediates using diaryliodonium salts

• Huangguan Chen,
• Jianwei Han and
• Limin Wang

Beilstein J. Org. Chem. 2018, 14, 354–363, doi:10.3762/bjoc.14.23

• photosensitive dyes. Keywords: benzyne; cycloaddition; diaryliodonium salts; N-phenylamine; pyrrole; Introduction Pyrrole is a very useful heterocyclic substrate to produce structural attributes of valuable chemicals, functional materials and pharmaceuticals [1][2][3][4][5]. Recently, arylation of pyrrole

• synthesized in 75% yield (Scheme 2b), whose structure was determined by 2D-NMR analyses (see Supporting Information File 1). Furthermore, as a unique electron donor, the novel compound 5 may have potential applications in photosensitive dyes and OLEDs [28][29]. Interestingly, the bridged-ring compound 6 could

Recent advances on organic blue thermally activated delayed fluorescence (TADF) emitters for organic light-emitting diodes (OLEDs)

• Thanh-Tuân Bui,
• Fabrice Goubard,
• Malika Ibrahim-Ouali,
• Didier Gigmes and
• Frédéric Dumur

Beilstein J. Org. Chem. 2018, 14, 282–308, doi:10.3762/bjoc.14.18

Fluorogenic PNA probes

• Tirayut Vilaivan

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

• probe that can change its fluorescence signal in response to hybridization to its specific target. The most obvious strategy would be to employ the same principle as DNA beacons, whereby two interacting dyes are placed on a hairpin-forming PNA probe that can switch to an open conformation upon target

• hybridization [3][4]. It has been reported that short, linear PNA beacons can perform surprisingly well when compared to linear DNA beacons [40]. This could be attributed to both the ability of PNA to form a compact structure in aqueous media, thereby forcing the two dyes in close contact, and the excellent

• ) partner, and the combination of short linear PNA probes with environment-sensitive dyes, such as in light-up and forced intercalation (FIT) PNA probes. PNA probes carrying two or more interacting dyes in the same strand The very first PNA probe of this type were independently reported in 1998 by Ortiz et

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been

• becomes a spectroscopic ruler. Such an assumption is often made, both correctly and incorrectly [8][9][10], for covalently attached external nucleic acid fluorophores like Cy-, Alexa- and ATTO-dyes. This provides a powerful means for measuring long distance ranges (typically 35–90 Å) in nucleic acid

• external fluorophores like Cy-, Alexa- and ATTO-dyes as well as finally summarize some of its recent applications. The field started less than a decade ago with the introduction of the first fluorescent nucleobase analogue FRET pair, tCO–tCnitro, and we divide this review into three parts: the first one

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• measured in the vis range (>360 nm), the application of disposable plastic cuvettes can solve or at least minimize the problem. However, for dyes that strongly adhere to cuvette walls the collected chiroptical spectrum does not correspond to conditions in homogeneous solution and thus cannot be interpreted

Photocatalytic formation of carbon–sulfur bonds

• Alexander Wimmer and
• Burkhard König

Beilstein J. Org. Chem. 2018, 14, 54–83, doi:10.3762/bjoc.14.4

• . Photoredox-active metal complexes or organic dyes are used to initiate photo-induced single-electron transfer (SET) processes upon excitation with visible-light. Such photooxidations or photoreductions yield reactive organic radicals, which can undergo unique bond forming reactions, under very mild

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

• monomethine cyanine dyes 5a–d, which are analogues of the commercial dsDNA fluorescence binder thiazole orange (TO), have been synthesized. The synthesis was achieved by using a simple, efficient and environmetally benign synthetic procedure to obtain these cationic dyes in good to excellent yields

• L·mol−1·cm−1). All investigated dyes from the series are either not fluorescent or their fluorescence is quite low, but they become strongly fluorescent after binding to dsDNA. The influence of the substituents attached to the chromophores was investigated by combination of spectroscopic (UV–vis and

• fluorescence spectroscopy) and theoretical (DFT and TDDFT calculations) methods. Keywords: cyanine dyes; DFT calculations; green synthesis; nucleic acids; thiazole orange; Introduction Since the discovery by Lee and co-workers [1][2] that the old photographic dye thiazole orange, TO, (Scheme 1) has excellent

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• dyes which could be applied as FRET pair. In this case, labeling was achieved in two bioorthogonal reactions, an iEDDA and a SPAAC reaction. Furthermore, dual modification with an azido and an alkyne function enabled fluorophore/biotin labeling using a combination of SPAAC and CuAAC reaction. Efficient

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

• characterized environment-dependent fluorescence. This property, together with the facile synthetic accessibility, makes it and its derivatives useful for a number of applications, e.g., as materials for organic electronics [1], dyes for mechanochromic materials [2], and fluorescent monomers for polymer

• MitoTracker Red®, an established fluorescent mitochondrial marker (Figure 6BC and Figure 7BC, respectively). To quantify the co-localization of 4 and 5 dyes and MitoTracker Red® the Manders (MCC) and Pearson (PCC) correlation coefficient were used [37]. The calculated values of MCC were 0.83 ± 0.12 (for 4

• in deionized water. The dyes were added in 1 to 3 equivalent steps compared to the concentration of the template strand. The percentage of DMSO changed with every addition up to a maximum of about 5% in the sample solution, so the DMSO was neglected in the blank subtraction. To achieve a good

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

• pigments [2], DPPs have significantly infiltrated organic electronics as functional dyes. The number of recently appeared review articles [3][4][5][6][7][8] clearly demonstrates their wide application potential, which spans organic solar cells (OSC), organic field-effect transistors (OFET), organic light

One-pot syntheses of blue-luminescent 4-aryl-1H-benzo[f]isoindole-1,3(2H)-diones by T3P^® activation of 3-arylpropiolic acids

• Melanie Denißen,
• Alexander Kraus,
• Guido J. Reiss and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 2340–2351, doi:10.3762/bjoc.13.231

• class particularly attractive for the development of novel sensors and fluorescent dyes [38], for instance 6-chloro-2,3-naphthaleneimide derivatives were successfully used for labeling amino acids, and for studying peptide protein interactions [39]. Even the superficial attachment to a binding domain

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• Phthalocyanines and subphthalocyanines are attracting attention as functional dyes that are applicable to organic solar cells, photodynamic therapy, organic electronic devices, and other applications. However, phthalocyanines are generally difficult to handle due to their strong ability to aggregate, so this

• years, the term “functional dyes” was proposed [9][10][11]. Functional dye is a generic name for dyes that exceed the framework of coloration and show various chemical and physical responses. In modern times, unlike the concept of colorants in the past, dyes have been developed for various applications

• based on their unique functions. Phthalocyanines are also expected to be applied as functional dyes. A series of compounds having a macrocyclic π-conjugated system including porphyrin are known as functional dyes. In particular, phthalocyanines have a wide range of functions and are expected to serve as

Curcuminoid–BF₂ complexes: Synthesis, fluorescence and optimization of BF₂ group cleavage

• Henning Weiss,
• Jeannine Reichel,
• Helmar Görls,
• Kilian Rolf Anton Schneider,
• Mathias Micheel,
• Michael Pröhl,
• Michael Gottschaldt,
• Benjamin Dietzek and
• Wolfgang Weigand

Beilstein J. Org. Chem. 2017, 13, 2264–2272, doi:10.3762/bjoc.13.223

• .13.223 Abstract Eight difluoroboron complexes of curcumin derivatives carrying alkyne groups containing substituents have been synthesized following an optimised reaction pathway. The complexes were received in yields up to 98% and high purities. Their properties as fluorescent dyes have been

• investigated. Furthermore, a strategy for the hydrolysis of the BF2 group has been established using aqueous methanol and sodium hydroxide or triethylamine. Keywords: BF2 complex; curcumin; dyes; fluorescence; hydrolysis; spectroscopy; Introduction In recent years curcumin, a pigment naturally occurring in

• attention regarding their properties as fluorescent dyes with fluorescence quantum yields of up to 60% and Stokes shifts of up to 5000 cm−1 [9]. Additionally, the incorporation of the BF2 group forces the β-diketone unit into the enol form, which leads to increased rigidity and enhanced photostability of

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

• substituted benzyl alcohols. Although benzyl alcohol is industrially produced by reduction of benzaldehyde, this aldehyde is considered as the second most important flavoring molecule after vanillin, due to its variety of applications in cosmetics, perfumes, food, dyes, agrochemicals and pharmaceuticals [41

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• substituted poly(acrylate)s, PAAADen, PAAADhn and PAAADddn, respectively, such that the ratio of β-CDen to adamantyl substituents is ca. 3:1. The variation of the characteristics of the complexation of the dyes methyl red, methyl orange and ethyl orange in these three networks and by β-cyclodextrin, β-CD, and

• PAAβ-CDen alone provides insight into the factors affecting dye complexation. The rates of release of the dyes through a dialysis membrane from the three aqueous networks show a high dependence on host–guest complexation between the β-CDen substituents and the dyes as well as the structure and the

• substitution of PAAβ-CDen. Thus, when host–guest complexation between the poly(acrylate) substituents of the network is complete, ca. two thirds of the β-CDen substituents remain available to complex other hydrophobic species exemplified by the dyes methyl red, MR, methyl orange, MO, and ethyl orange, EO

Oxidative dehydrogenation of C–C and C–N bonds: A convenient approach to access diverse (dihydro)heteroaromatic compounds

• Santanu Hati,
• Ulrike Holzgrabe and
• Subhabrata Sen

Beilstein J. Org. Chem. 2017, 13, 1670–1692, doi:10.3762/bjoc.13.162

• an important class of compounds [1]. A large variety of such compounds are discovered so far and their therapeutic potential in diverse disease models has been thoroughly investigated [2]. For example thiazoles and oxazoles are found in various bioactive natural products, organic dyes and

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

Nitration of 5,11-dihydroindolo[3,2-b]carbazoles and synthetic applications of their nitro-substituted derivatives

• Roman A. Irgashev,
• Nikita A. Kazin,
• Gennady L. Rusinov and
• Valery N. Charushin

Beilstein J. Org. Chem. 2017, 13, 1396–1406, doi:10.3762/bjoc.13.136

• -dihydroindolo[3,2-b]carbazole (indolo[3,2-b]carbazole, ICZ) has been successfully used as a basic structural fragment of perspective electroluminescent, hole-transporting materials and light-harvesting dyes for organic light emitting diodes (OLEDs) [7][8][9][10][11][12][13], organic field-effect transistors

Detection of therapeutic radiation in three-dimensions

• John A. Adamovics

Beilstein J. Org. Chem. 2017, 13, 1325–1331, doi:10.3762/bjoc.13.129

• leuco dye, which is radiolytically oxidized to a dye absorbing at 630 nm. Keywords: dosimeters; leuco dyes; polymers; radiation; triarylmethane synthesis; Introduction Radiotherapy treatment is a complex 3D process, which is the principle treatment modality for most cancers [1]. The two main types of

• dosimeter would be firm in structure and tissue equivalent [14]. This review describes such a 3D dosimeter, which we have been studying since 2004, composed primarily of the polymer polyurethane containing a radiochromic leuco dye and a radical initiator [15]. Review Leuco dyes and radical initiators Our

• initial studies focused on a broad class of compounds referred to as leuco dyes which switch between two chemical forms of which one is colorless. The transformations are caused by the in put of energy either from heat, light or change in pH [16]. The leuco dyes by themselves are not oxidized at clinical

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

• , sensitivity and good spatio-temporal resolution altogether [5]. From the plethora of known fluorescent compounds, there are widely used small organic fluorophores, such as BODIPY dyes. BODIPYs are fluorescent dyes based on the 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene scaffold, which have recently

• experienced increased attention in chemistry [6][7][8][9][10] and life science applications [11][12][13]. On the grounds of high fluorescence quantum yield, narrow spectral characteristics, and sufficient chemical stability, BODIPYs have been utilized for example as laser dyes, tags of small organic molecules

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

• diameter range can be obtained [4]. Moreover, this synthetic procedure allows to introduce different types of carbohydrates and other ligands (i.e., polyethylene chains, lipids, peptides, DNA, RNA or fluorescent dyes) in controlled ratios [4]. A modification of this technique consists in the application of

Synthesis of tetrasubstituted pyrazoles containing pyridinyl substituents

• Josef Jansa,
• Ramona Schmidt,
• Ashenafi Damtew Mamuye,
• Laura Castoldi,
• Alexander Roller,
• Vittorio Pace and
• Wolfgang Holzer

Beilstein J. Org. Chem. 2017, 13, 895–902, doi:10.3762/bjoc.13.90

• ], agrochemicals [5], dyes [6], fluorescent materials [7][8] and ligands of complexing agents [9][10][11]. Multiaryl-substituted pyrazoles are of special interest, with some drug molecules such as the nonsteroidal anti-inflammatory agent Lonazolac [12] or the well-known COX-2 inhibitor Celecoxib [13] as prominent

Energy down converting organic fluorophore functionalized mesoporous silica hybrids for monolith-coated light emitting diodes

• Markus Börgardts and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 768–778, doi:10.3762/bjoc.13.76

• molecules with inorganic silica hosts [11][20]. Therefore, a terminal triethoxysilyl group has to be coupled to luminescent dyes with blue, green, and red emission characteristics for generating hybrid materials with white light emission based upon additive color mixing. A rapid and versatile

• (Figure 1a). Neglecting energy transfer between the luminophores superposition of the emission spectra of the three dyes covers the whole range of the visible region (400–800 nm) (Figure 1b). The three dyes were additionally analyzed with respect to their CIE chromaticity coordinates, i.e., their

• attributed to an inhomogeneous line broadening in the solid state. As benzofurazane and Nile red dyes exhibit solvatochomism, their spectral properties are clearly affected by incorporation into the polar silica environment. A detailed study of the spectral properties and solvatochromism of the Nile red

Isoxazole derivatives as new nitric oxide elicitors in plants

• Anca Oancea,
• Emilian Georgescu,
• Florentina Georgescu,
• Alina Nicolescu,
• Elena Iulia Oprita,
• Catalina Tudora,
• Lucian Vladulescu,
• Marius-Constantin Vladulescu,
• Florin Oancea and
• Calin Deleanu

Beilstein J. Org. Chem. 2017, 13, 659–664, doi:10.3762/bjoc.13.65

• -disubstituted isoxazoles on nitric oxide and reactive oxygen species generation in Arabidopsis tissues was studied using specific diaminofluoresceine dyes as fluorescence indicators. Keywords: chemical elicitor; 1,3-dipolar cycloaddition; isoxazole; nitric oxide; nitrile oxide; reactive oxygen species