Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• fluorescent probes via their labeling by commercial and "home-made" fluorescent dyes bearing azide groups. It was noted that yields of alkyne-modified MGBs were higher (50–83%) compared to those of azide modified MGBs (≈40%). The other variant for insertion of terminal azide or alkyne groups into the

Indenopyrans – synthesis and photoluminescence properties

• Andreea Petronela Diac,
• Ana-Maria Ţepeş,
• Albert Soran,
• Ion Grosu,
• Anamaria Terec,
• Jean Roncali and
• Elena Bogdan

Beilstein J. Org. Chem. 2016, 12, 825–834, doi:10.3762/bjoc.12.81

• derivatives have been found to act as potential candidates for electroluminescent devices due to their fluorescent properties. Fluorescent dyes have lately attracted considerable interest owing to their wide range of applications in various fields. For example, naphthopyrans (e.g. 3,3-diphenyl-3H-naphtho[2,1

New synthetic strategies for xanthene-dye-appended cyclodextrins

• Milo Malanga,
• Andras Darcsi,
• Mihaly Balint,
• Gabor Benkovics,
• Tamas Sohajda and
• Szabolcs Beni

Beilstein J. Org. Chem. 2016, 12, 537–548, doi:10.3762/bjoc.12.53

• fluorophores for labeling in order to assess if these versatile molecules cross biological barriers (e.g., cell membrane, blood–brain barrier) and to follow their distribution in living matter [3]. Among the fluorescent dyes, the group of fluorophores based on xanthene scaffolds is one of the most popular. Two

• spectrum resulted in the proposed model (shown in Figure 8) for the intermolecular inclusion mode of the compound. Conclusion A novel green synthetic strategy for obtaining single isomer, xanthene-appended cyclodextrin was developed. The synthetic approach is based on commercially available fluorescent

• dyes and coupling agents, thus having clear potential for multigram scale-up. The mild, aqueous conditions, as well as the simplicity of the synthesis, make these reactions attractive tools for the preparation of fluorescent cyclodextrins connected through an amide bond. The obtained products were

Smart molecules for imaging, sensing and health (SMITH)

• Bradley D. Smith

Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274

• development of squaraine rotaxanes as a novel family of deep-red fluorescent dyes with extremely high brightness and stability [35][36]. A key finding was the importance of the interlocked rotaxane structure for protecting the encapsulated squaraine from chemical attack by water. Squaraine rotaxanes can be

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• a third component fluorescent dyes [10] were coupled to the polymers simultaneously with the bioactive and the cell-penetrating peptides in order to enable the monitoring of cellular uptake and intracellular distribution of the peptide–polymer conjugate. Until now, various polymer carriers have been

Design, synthesis and photochemical properties of the first examples of iminosugar clusters based on fluorescent cores

• Mathieu L. Lepage,
• Antoine Mirloup,
• Manon Ripoll,
• Fabien Stauffert,
• Anne Bodlenner,
• Raymond Ziessel and
• Philippe Compain

Beilstein J. Org. Chem. 2015, 11, 659–667, doi:10.3762/bjoc.11.74

• diverse analytes and in relevant biosensing and bioimaging applications [73]. One critical aspect for the evaluation of biological activities using fluorescent dyes (e.g., the deprotonated form of 4-methylumbelliferone) [74] is to determine their spectroscopic features in different environments (local pH

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

• derivatives incorporating fluorescent dyes for sensing applications [22][23][24][25]. Looking to extend these systems to incorporate an F-BODIPY motif, we have synthesized the Boc-protected triazolyl-cyclam/F-BODIPY derivatives 3 and 4 from 2,4-dimethyl-1H-pyrrole (5), 4-nitrobenzaldehyde (6, Scheme 2A) and 4

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

• profiling (ABPP); bioorthogonal; click chemistry; mass defect; molecular probe; Introduction Fluorescent dyes are widely used for detection and monitoring in the fields of chemistry, biochemistry, molecular biology, medicine and material sciences. Due to sensitive and selective detection methods and

• unproblematic toxicology they have almost completely replaced radioactive tags. Widely used representatives include dansyl chloride, fluoresceins, rhodamines and boron-dipyrromethenes (BODIPYs) [1]. Dansyl chloride, with a maximum UV–vis absorption at 369 nm, is one of the first extrinsic fluorescent dyes

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

• fluorescent dyes – intercalating Sybr Green I and pending cyanine-5 (Figure 5). For the scenario of experiment F (Figure 2) the complex formation kinetics drops even further, but the brightness reaches a plateau at ≈2 × 105 kHz. The by far slowest complex formation is observed in case of experiment D (Figure

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• peptide sequence for analytical investigations (Figure 4). These tools can be spin and radioactive labels, bioactive molecules (such as biotin) or fluorescent dyes. The paramagnetic substance TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) (Figure 5) was manually coupled to NPY

Studies on the photodegradation of red, green and blue phosphorescent OLED emitters

• Susanna Schmidbauer,
• Andreas Hohenleutner and
• Burkhard König

Beilstein J. Org. Chem. 2013, 9, 2088–2096, doi:10.3762/bjoc.9.245

• . While fluorescent dyes normally emit from their singlet excited states (at room temperature) and therefore can only utilize singlet excitons, phosphorescent organotransition metal dopants emit from their triplet excited states. In addition phosphorescent organotransition metal dopants are able to

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

• . To provide new tools for imaging of mitochondria in vivo, we synthesized novel hydrophobic analogues of the red fluorescent dyes rhodamine B and rhodamine 101 that replace the carboxylate with a methyl group. Compared to the parent compounds, methyl analogues termed HRB and HR101 exhibit slightly red

Synthesis of glycoconjugate fragments of mycobacterial phosphatidylinositol mannosides and lipomannan

• Benjamin Cao,
• Jonathan M. White and
• Spencer J. Williams

Beilstein J. Org. Chem. 2011, 7, 369–377, doi:10.3762/bjoc.7.47

• substantially less nonspecific interaction with proteins over other fluorescent dyes [45]. Using alkynyl-NBD 30 (prepared in one step from NBD chloride and propargylamine) [34], the disaccharide 1 and trisaccharides 2 and 3 were coupled upon treatment with CuSO4, sodium ascorbate and the Cu(I)-stabilizing

Miniemulsion polymerization as a versatile tool for the synthesis of functionalized polymers

• Daniel Crespy and
• Katharina Landfester

Beilstein J. Org. Chem. 2010, 6, 1132–1148, doi:10.3762/bjoc.6.130

• resonance imaging (MRI) in polyurethane, polyurea, and crosslinked dextran shells [117][118]. No significant difference in the relaxation time (T1) between the encapsulated agent and the contrast agent in solution could be detected therefore making the capsules good candidates for MRI. Fluorescent dyes as

Chromo- and fluorophoric water-soluble polymers and silica particles by nucleophilic substitution reaction of poly(vinyl amine)

• Katja Hofmann,
• Ingolf Kahle,
• Frank Simon and
• Stefan Spange

Beilstein J. Org. Chem. 2010, 6, No. 79, doi:10.3762/bjoc.6.79

• concerning its synthesis and purification. An alternative pathway is the chemical modification of commercially available polymers containing reactive groups which can react with fluorescent dyes [6]. Poly(vinyl amine)s (PVAm) are copolymers made by the hydrolysis of poly(vinyl formamide) (PVFA). Fully

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32