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

• DNA conjugate [16], led to 8 dye labeled fragments, all located in the non-hybridized part of the substrate. Most prominent is cleavage after G(18) (Figure 2, lane b; note the slight shift and duplication of the substrate peak compared to the hydrolysis ladder shown in lane f). The product

Eosin Y-catalyzed visible-light-mediated aerobic oxidative cyclization of N,N-dimethylanilines with maleimides

• Zhongwei Liang,
• Song Xu,
• Wenyan Tian and
• Ronghua Zhang

Beilstein J. Org. Chem. 2015, 11, 425–430, doi:10.3762/bjoc.11.48

• derivatives under organic dye Eosin Y catalysis. Swan and Roy reported the reaction using benzoyl peroxide as catalyst at low temperature as early as 1968 [42]. In 2011, Miura and co-workers achieved this transformation using a copper catalyst and air as the terminal oxidant [43]. Bian and co-workers

Efficient deprotection of F-BODIPY derivatives: removal of BF₂ using Brønsted acids

• Mingfeng Yu,
• Joseph K.-H. Wong,
• Cyril Tang,
• Peter Turner,
• Matthew H. Todd and
• Peter J. Rutledge

Beilstein J. Org. Chem. 2015, 11, 37–41, doi:10.3762/bjoc.11.6

• facilitate chromatographic purification. The parent dipyrrins are more difficult to handle but have a range of potential applications in dye and porphyrin syntheses, metal ion coordination and supramolecular chemistry [12]. Methods to enable the functionalization of dipyrrins by temporarily complexing with

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

• randomly introduced into the polymeric matrix. Recently Mamba’s group [17] described an example of fluorescent tagging of epichlorohydrin branched β-CD polymer based on a pre-branching modification approach. In his work the β-CD was first modified with an azo dye making it less soluble in water. The

• modified β-CD was then copolymerized with epichlorohydrin in a ratio that resulted in the formation of a water-soluble copolymer. The azo dye modified β-CD epichlorohydrin copolymer was used as a molecular fluorescent sensor for the detection of chloroform, one of the chlorination byproducts in water. Here

• . Fluorescent labeling of the β-CD polymer based on the reaction between the amino moieties and the isothiocyanate form of the dye (rhodamine or fluorescein). As an example of the first strategy we report the fluorescent labeling of β-CD polymer with rhodamine isothiocyanate (Scheme 2). 1) Introduction of the

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• sequence a2. As we have demonstrated already that the [2.2.2]heptamethinecyanine dye binds selectively to quadruplex DNA and that its interaction with the quadruplex is indicated by a drastic emission light-up effect [20][21], we chose the [2.2.2]heptamethinecyanine derivatives 1a–e [22] as ligands for

• thermal stability of the ILPR-DNA with respect to unfolding was also examined by emission spectroscopy in K+- and Na+-containing buffer, i.e., the melting temperature, Tm, of the dye-labelled quadruplex-forming ILPR sequence Fa2T [fluorescein-d(ACAG4TGTG4ACAG4TGTG4)-tetramethylrhodamine] was determined by

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• bromide was introduced as a part of a heterogenic two-chromophore system, to take advantage of very efficient FRET energy transfer process (77%) from fluorescein to the RNA-intercalated phenanthridinium fluorophore (Figure 8, left) [83]. The resulting fluorescent dye exhibited improved ds-RNA-marker

• properties in comparison to other phenanthridinium analogues by means of signal brightness, signal-to-background noise and increased fluorescence half-lifetime. The same dye was also applied as convenient reporter for si-RNA (Figure 8, right) [84]. In parallel the designed and tested covalently linked

• cellular uptake (Figure 11), upon which red colour of 19 accumulated in cell nuclei – intriguingly after only 2 hours fluorescence colour changed to yellow (Figure 11, right) and the dye distributed over the cytoplasm pointing out to the metabolic modification of the compound. The new, easily accessible

Host–guest-driven color change in water: influence of cyclodextrin on the structure of a copper complex of poly((4-hydroxy-3-(pyridin-3-yldiazenyl)phenethyl)methacrylamide-co-dimethylacrylamide)

• Nils Retzmann,
• Gero Maatz and
• Helmut Ritter

Beilstein J. Org. Chem. 2014, 10, 2480–2483, doi:10.3762/bjoc.10.259

• of CD–dye hydrogels by addition of metal ions, as well as the sensing of copper ions using cyclodextrin–dye rotaxane [10][11]. Herewith we thus wish to describe our recent results about the synthesis of a water-soluble polymer bearing a novel azo dye and the presumed formation of complexes with Cu

• ions and CD in aqueous media under respect of color change. Findings The aim of this work was to synthesize the polymerizable azo dye N-(4-hydroxy-3-(pyridin-3-yldiazenyl)phenethyl)methacrylamide (5) which should potentially be able to form stable azo–metal complexes in aqueous solutions. Therefore

• tyramine (1) was selectively methacrylated at room temperature followed by a diazotation coupling with 3-aminopyridine (4) leading to N-(4-hydroxy-3-(pyridin-3-yldiazenyl)phenethyl)methacrylamide (5). Subsequently, the azo dye containing polymer 7 was synthesized through free radical copolymerization of 5

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• was emitted by NBD/DDY/catalase, which is probably due to very low fluorescence quantum yields reported for NBD derivatives of primary amines in water [39]. Furthermore, NBD (9) is not suitable for standard SDS-PAGE (12% gels) as the dye smears and therefore potentially covers fluorescent signals of

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• complexes consisting of various DNA duplexes and the fluorescent dye were studied with respect to the kinetics of their formation as well as to their stability against perfusion. Keywords: artificial lipid bilayers; lipo-oligonucleotide duplexes; nucleic acids; Sybr Green I; Introduction The post

• Cy5 dye at 635 nm (Figure 2). Then, a Sybr Green I (3) solution in dimethyl sulfoxide (≈1 µg/mL) was added to the cis compartment of the slide. In the first experiment (A) laser irradiation of the intercalated dye was performed at 470 nm. In orienting experiments Sybr Green I was irradiated at 470 nm

• , in order to see if this dye stains the complementary DNA strands 4 + 5, which are known to form a duplex at the bilayer membrane [19]. Firstly, we evaluated the optimal measuring conditions such as the volume, the Sybr Green I concentration as well as of the lipo-oligonucleotides. At this point we

End group functionalization of poly(ethylene glycol) with phenolphthalein: towards star-shaped polymers based on supramolecular interactions

• Carolin Fleischmann,
• Hendrik Wöhlk and
• Helmut Ritter

Beilstein J. Org. Chem. 2014, 10, 2263–2269, doi:10.3762/bjoc.10.235

• broad variety of applications [36][37][38][39]. An adequate guest molecule for β-CD is the well-known indicator dye phenolphthalein [40]. In addition to its relatively high affinity to β-CD, this molecule undergoes a decolorization in basic solution as the complexation induces a re-lactonization of the

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• necessary to assess the structure of the AP dye/polynucleotide complex. Application of the most informative methods like NMR and X-ray crystallography was hampered by the tendency of the AP dye/DNA complexes to form colloidal systems at c > 0.1 mM, which neither crystalized nor were suitable for NMR studies

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• , pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA

• label that can change its fluorescence in response to its altered micro-environment [7][8][9]. Nile red is a member of the benzophenoxazine dye family which exhibits several interesting features including a high photostability, high fluorescence quantum yield, broad working pH range, long excitation and

• emission wavelengths, and solvatochromic properties [10]. Applications of Nile red as a staining dye in histology [11][12] and as a probe for the sensing of polarity and hydrophobicity [13] are well-known. Nile red has been used as a DNA label, either as a base modifier [14][15][16], a base replacement [17

Homogeneous and heterogeneous photoredox-catalyzed hydroxymethylation of ketones and keto esters: catalyst screening, chemoselectivity and dilution effects

• Axel G. Griesbeck and
• Melissa Reckenthäler

Beilstein J. Org. Chem. 2014, 10, 1143–1150, doi:10.3762/bjoc.10.114

• Axel G. Griesbeck Melissa Reckenthaler University of Cologne, Department of Chemistry, Organic Chemistry, Greinstr. 4, D-50939 Köln, Germany; Fax: +49(221)470 5057 10.3762/bjoc.10.114 Abstract The homogeneous titanium- and dye-catalyzed as well as the heterogeneous semiconductor particle

• -pentyrolactone and not the corresponding seven-membered lactone. The primary product from hydroxymethylation was also isolated from the reaction of the ε-keto ester 25 [40]. Heterogeneous and dye-sensitized photocatalysis The results with the semiconductor particle TiO2 P25 under low catalyst loading conditions

• transfer at the first or second oxidation event. The pinacolization route II is favoured for heterogeneous and dye-catalyzed conditions. Interestingly, the combination of TiO2 P25 with an organic dye prefers largely the hydrogenation route III [45]. On the surface of the relatively large semiconductor

Organic synthesis using photoredox catalysis

• Axel G. Griesbeck

Beilstein J. Org. Chem. 2014, 10, 1097–1098, doi:10.3762/bjoc.10.107

• other Ru or Ir complexes) with strong MLCT transitions, organic dyes such as xanthene, porphyrine or phthalocyanine dyes (e.g., eosin Y), and colloidal semiconductor particles (e.g., TiO2) [1][2][3][4][5][6][7][8][9]. In addition, combinations of light-absorbing materials have been studied such as dye

On the mechanism of photocatalytic reactions with eosin Y

• Michal Majek,
• Fabiana Filace and
• Axel Jacobi von Wangelin

Beilstein J. Org. Chem. 2014, 10, 981–989, doi:10.3762/bjoc.10.97

• eosin Y solutions prompted us to further investigate this behaviour. The organic dye eosin Y can exist in four different structures in solution: the spirocyclic form EY1, the neutral EY2, the monoanionic EY3, and the dianionic form EY4 (Scheme 3). Eosin Y contains two relatively acidic protons (pKa 2.0

• , 3.8 in water) [25] which can be easily abstracted to give dianionic EY4. Lack of clarity exists in many publications on photoredox catalysis with regard to the nature of the employed dye. The authors either report the use of “eosin Y, spirit soluble” – which can be EY1 or EY2 according to the Sigma

• acidity of most Brønsted acids in DMSO [28]. These observations lead to the conclusion that photoredox reactions catalyzed by eosin Y (or similar organic dyes) cannot be discussed without strict specification of the employed form of the dye and the reaction conditions. Conclusive mechanistic proposals of

Tailoring of organic dyes with oxidoreductive compounds to obtain photocyclic radical generator systems exhibiting photocatalytic behavior

• Christian Ley,
• Julien Christmann,
• Ahmad Ibrahim,
• Luciano H. Di Stefano and
• Xavier Allonas

Beilstein J. Org. Chem. 2014, 10, 936–947, doi:10.3762/bjoc.10.92

• Christian Ley Julien Christmann Ahmad Ibrahim Luciano H. Di Stefano Xavier Allonas Laboratory of Macromolecular Photochemistry and Engineering, University of Haute Alsace, 3b rue Alfred Werner, 68093 Mulhouse, France 10.3762/bjoc.10.92 Abstract The combination of a dye which absorbs the photon

• , an electron acceptor and an electron donor leading to energy conversion through electron transfer, was the basis of the so called three-component systems. In this paper, an experimental work combining Rose bengal dye with a triazine derivative as electron acceptor and ethyl 4-(dimethylamino)benzoate

• as electron donor, will underline the benefit of the photocyclic behavior of three-component systems leading to the dye regeneration. A thermodynamic approach of the photocycle is presented, followed by a mechanistic and computational study of ideal photocycles, in order to outline the specific

Nonanebis(peroxoic acid): a stable peracid for oxidative bromination of aminoanthracene-9,10-dione

• Vilas Venunath Patil and
• Ganapati Subray Shankarling

Beilstein J. Org. Chem. 2014, 10, 921–928, doi:10.3762/bjoc.10.90

• was surmised that in the presence of oxidant these substrates form a diimine type product (similar to oxidative hair dye mechanism) [33], which makes the ring unreactive towards electrophilic substitution. Since Oxone and 50% hydrogen peroxide showed good results with substrate 1a, we have checked the

Metal and metal-free photocatalysts: mechanistic approach and application as photoinitiators of photopolymerization

• Jacques Lalevée,
• Sofia Telitel,
• Pu Xiao,
• Marc Lepeltier,
• Frédéric Dumur,
• Fabrice Morlet-Savary,
• Didier Gigmes and
• Jean-Pierre Fouassier

Beilstein J. Org. Chem. 2014, 10, 863–876, doi:10.3762/bjoc.10.83

• , potential toxicity and limited availability of these structures, metal-free organic dye compounds (e.g., Eosin-Y, Nile Red, Alizarine Red S, perylene derivative or Rhodamine B etc.) were recently proposed for cooperative asymmetric organophotoredox catalysis [13][14]. Photoredox catalysis was then

• dye Vi [61][62] or an anthracene derivative (e.g. bis[(triisopropylsilyl)ethynyl]anthracene) [54][55] as PIC, Ph2I+ as eA and TTMSS as Add (see the simplified Scheme 9 based on Scheme 6). Using violanthrone-79/Ph2I+/TTMSS allowed, for the first time, the formation of an initiating cationic species

Continuous flow nitration in miniaturized devices

• Amol A. Kulkarni

Beilstein J. Org. Chem. 2014, 10, 405–424, doi:10.3762/bjoc.10.38

• preservative and also as an insecticide. 4-Amino-2-nitrophenol and 2-nitro-p-phenylenediamine are components of permanent hair dye products and fur dye. Several aniline derivatives are also used for the synthesis of various dyes [9], the first one being the aniline Yellow [10] reported in 1880. The history of

• the relevance of nitration for the dye and colorant industry covers more than a century. Nitro derivatives of the toluene diisocynate are employed in the manufacturing of flexible polyurethane foams, which are used in transformation, furniture, and carpet underlay. 2,4,6-Trinitrotoluene is a military

Cyclic phosphonium ionic liquids

• Sharon I. Lall-Ramnarine,
• Joshua A. Mukhlall,
• James F. Wishart,
• Robert R. Engel,
• Alicia R. Romeo,
• Masao Gohdo,
• Sharon Ramati,
• Marc Berman and
• Sophia N. Suarez

Beilstein J. Org. Chem. 2014, 10, 271–275, doi:10.3762/bjoc.10.22

• would be exposed to extreme conditions, such as environmental exposure to high temperatures or exposure to extreme electromagnetic radiation (as in a dye-sensitized solar cell or ionizing radiation as in the recycling of spent nuclear fuel). ILs can play important roles in both of these latter areas [16

Synthesis of nucleotide–amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach

• Tatyana V. Abramova,
• Olga B. Morozova,
• Vladimir N. Silnikov and
• Alexandra V. Yurkovskaya

Beilstein J. Org. Chem. 2013, 9, 2898–2909, doi:10.3762/bjoc.9.326

• model compound conjugates of the amino acid, nucleotide, and dye residues, where key participants (dye, amino acid, and nucleoside) have to be drawn together mimicking the biologically important DNA repair processes. To fulfill the requirements of the photo-induced TR CIDNP experiments, a synthetic

• conjugates consisting of amino acid, nucleotide, and dye residues including linkers of different lengths (Figure 1). Target compounds 1–8 have been synthesized by the phosphotriester block liquid phase synthesis (LPS). Results and Discussion Design of model compounds Our previous studies revealed a great

• detection of elusive radicals in biomolecules using model compounds, where key participants of the reaction (dye, amino acid, and nucleoside) are spatially drawn together mimicking the biologically important DNA repair processes. Guanosine is the most easily oxidized nucleoside [12] in photoreactions of

Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

• Regina Berg and
• Bernd F. Straub

Beilstein J. Org. Chem. 2013, 9, 2715–2750, doi:10.3762/bjoc.9.308

• ligands [45]. The authors used the newly developed ligand system in a bioconjugation reaction with a virus. The exterior surface of the coat protein of cowpea mosaic virus was labelled with 60 azide groups as shown in Scheme 3 [45]. Then, the reaction with an alkyne-functionalized dye was carried out in

New syntheses of 5,6- and 7,8-diaminoquinolines

• Maroš Bella and
• Viktor Milata

Beilstein J. Org. Chem. 2013, 9, 2669–2674, doi:10.3762/bjoc.9.302

• -nitroaniline or 3-chloroaniline. Initially, 7,8-diaminoquinoline was prepared by Renshaw et al. [5] by coupling 7-aminoquinoline with benzenediazonium chloride followed by the reduction of the resulting azo-dye with SnCl2·2H2O. The second method relies on the Skraup reaction [6] of 3-nitroaniline affording 7

The chemistry of isoindole natural products

• Klaus Speck and
• Thomas Magauer

Beilstein J. Org. Chem. 2013, 9, 2048–2078, doi:10.3762/bjoc.9.243

• yellow 139 (12), which is sold by BASF as Paliotol® Yellow K 1841 belongs to the class of highly resistant and effective 1,3-disubstituted isoindoline dyes. Recently, the use of isoindoles as red to near-infrared fluorophores was reported [12]. Another interesting isoindole-based dye, 25, arises from the

The chemistry of amine radical cations produced by visible light photoredox catalysis

• Jie Hu,
• Jiang Wang,
• Theresa H. Nguyen and
• Nan Zheng

Beilstein J. Org. Chem. 2013, 9, 1977–2001, doi:10.3762/bjoc.9.234

• . König and coworkers showed that the same aza-Henry reaction can be catalyzed by the organic dye Eosin Y to afford the aza-Henry product 18 (Scheme 5) [67]. In addition to nitroalkanes, dialkyl malonates and malononitrile can be used as pronucleophiles to provide β-diester amine 19 and α-aminonitrile 20

• . The authors proposed a mechanism similar to that proposed by Stephenson and coworkers for the aza-Henry reaction catalyzed by the Ir complex (Scheme 3). The Tan group simultaneously reported that another organic dye, Rose Bengal (RB), can be used in place of Eosin Y to catalyze the aza-Henry reaction

• dark after 4 h irradiation. This observation supports the formation of hydroperoxide intermediate 21. Tan and coworkers employed a cocatalyst system composed of the organic dye Rose Bengal and graphite oxide (GO) for α-cyanation of N-aryltetrahydroisoquinolines (Scheme 7) [70]. The use of GO as