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

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

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

Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway

• Jessica L. Bell,
• Andrew J. Haak,
• Susan M. Wade,
• Yihan Sun,
• Richard R. Neubig and
• Scott D. Larsen

Beilstein J. Org. Chem. 2013, 9, 966–973, doi:10.3762/bjoc.9.111

• , click ligation of a fluorescent dye, and gel electrophoresis revealed specific labeling of a single 24 kDa band that could be blocked with an active competitor. Future work will focus on identifying the labeled protein(s). Keywords: CCG-1423; click ligation; photoaffinity labeling; Rho pathway

Superstructures of fluorescent cyclodextrin via click-reaction

• Arkadius Maciollek,
• Helmut Ritter and
• Rainer Beckert

Beilstein J. Org. Chem. 2013, 9, 827–831, doi:10.3762/bjoc.9.94

• the elongated noncovalent polymeric structures collapse. Keywords: fluorescent dye; cyclodextrins; host–guest interaction; supramolecular polymer; Introduction Most small heterocyclic molecules show low fluorescence. However, as we reported earlier, substituted 4-hydroxythiazoles have a high

Expeditious, mechanochemical synthesis of BODIPY dyes

• Laramie P. Jameson and
• Sergei V. Dzyuba

Beilstein J. Org. Chem. 2013, 9, 786–790, doi:10.3762/bjoc.9.89

• pestle and mortar, with yields that are comparable to those obtained via traditional routes that typically require reaction times of several hours to days. Keywords: BODIPY; condensation; fluorescent dye; mechanochemistry; solvent-free; Introduction BODIPY dyes are fluorescent organic molecules, which

Design of a novel tryptophan-rich membrane-active antimicrobial peptide from the membrane-proximal region of the HIV glycoprotein, gp41

• Evan F. Haney,
• Leonard T. Nguyen,
• David J. Schibli and
• Hans J. Vogel

Beilstein J. Org. Chem. 2012, 8, 1172–1184, doi:10.3762/bjoc.8.130

• micelle-bound form, resulting in the insertion of the Trp side chain into the hydrophobic core of the micelle. Calcein leakage All four peptides were tested for their ability to induce the release of the self-quenching fluorescent dye, calcein, from calcein-encapsulated LUVs [14][15]. All of the peptides

Control over molecular motion using the cis–trans photoisomerization of the azo group

• Estíbaliz Merino and
• María Ribagorda

Beilstein J. Org. Chem. 2012, 8, 1071–1090, doi:10.3762/bjoc.8.119

• fluorescent dye close to the photoswitch giving rise to a fluorescence change upon isomerization. The introduction of azobenzene-modified biomolecules in zebrafish proved that the photochemistry of azobenzenes was similar in vivo and in vitro, and that appropriate azobenzenes could be stable in vivo for days

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

• markers are suitable for particle–cell interactions and can be followed by LSM and FACS measurements. Thus, polyurethane/urea capsules produced in inverse miniemulsion were used to encapsulate a fluorescent dye with 90% efficiency [119]. Carboxymethylation was performed on the particle surface followed by

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