Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• the 5’-end) prone to form a G-quadruplex structure (Scheme 7). Circular dichroism studies have indicated that TBANB adopts a random coil structure while after reduction caused by chemical (Na2S2O4) or enzymatic (nitroreductase with NADH) stimuli, the formation of a G-quadruplex structure was evidenced

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

• conformations depending on conditions. Z-DNA, a GC-repeat rich, thermodynamically less preferred, left-handed helical conformation that is favored by cytosine methylation is known to form in vivo under negative supercoiling or high salt concentrations [64][65][66][67][68]. Circular dichroism is traditionally

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

• compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is

• between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably. Keywords: circular dichroism; emission-based dichroism; groove binding; intercalation; linear dichroism; non-covalent

• interactions; nucleic acids recognition; vibrational circular dichroism; Review 1. Introduction Many biological molecules are chiral and chromophoric among which the most important examples include proteins and nucleic acids. Moreover, the chiral constituents of natural biopolymers are homochiral, e.g

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• values for p-nitroanilines are affected by an induced circular dichroism effect due to the interaction between the dipole moments of the polarized chromophore guest moiety and of the cyclodextrin cavity. Therefore, these parameters provide an estimation of the time-averaged tilt angle between the

Recent progress in the racemic and enantioselective synthesis of monofluoroalkene-based dipeptide isosteres

• Myriam Drouin and
• Jean-François Paquin

Beilstein J. Org. Chem. 2017, 13, 2637–2658, doi:10.3762/bjoc.13.262

• important for the activity (Table 6). Conformational studies of the fluorinated peptide using circular dichroism also showed that the incorporation of the monofluoroalkene did not perturb the formation of the secondary structure of the peptide, which was a α-helix. Dory and co-workers wanted to study the

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

• chromophores [19][20][21]. This helical twist was evidenced by circular dichroism, in particular a strong bisignate Cotton effect for the DNA-templated pyrene assemblies [19][20]. Figure 1 shows selected examples of pyrene-modified nucleic acids and nucleosides. On the other hand, pyrene–nucleobase conjugates

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• 8c was also prepared for comparison (Scheme 5A). Measured circular dichroism (CD) spectra for the hexapeptides 8a–c (Figure 5, top) demonstrate strong negative bands at 204 nm and weak positive bands at 227 nm, which indicate a polyproline-II fold. Remarkably, this spectral shape was observed for all

• the midpoint and the top of the logD projection peak. Experimental logD values were compared to the calculated ones (Equation 5). Circular dichroism spectra were recorded in a 1 mm quartz cell at 298 K in methanol (HPLC grade) or aqueous potassium phosphate buffer (50 mM, pH 7.01 at 297 K). The

• solvent dielectric constant, ε. The trans/cis ratios were determined from the 1H and 19F NMR spectra at 298 K. Solvent set: C6D6, CDCl3, CD2Cl2, CD3OD, CD3CN, D2O. For details see Table S1 in Supporting Information File 1. Mean residue molar circular dichroism (Δε) of peptides 8–10 in methanol (left) and

Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by ¹H NMR spectroscopy

• Yoshihiro Nishida,
• Mengfei Yuan,
• Kazuo Fukuda,
• Kaito Fujisawa,
• Hirofumi Dohi and
• Hirotaka Uzawa

Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196

• among α-glycosyl 1,2-diacyl-sn-glycerols in the solution state [16]. Probably, the two gauche conformers, namely gt(+) and gg(−), are stabilized in a manner so as to permit stacking interactions between the 1,2-diacyl chains. In our previously reported circular dichroism (CD) studies [17][18], helical

• > 3JH1proS,H2 Hz). This rule is maintained among 1,2-diacetyl-, 1,2-dipalmitoyl-, and 1,2-dibenzoyl-sn-glycerols and substituents at the sn-3 position. The validity of this rule is confirmed in a comparative analysis using circular dichroism (CD) spectroscopy [17][18]. The current study applies these

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• FhuA ΔCVFtev (see MD simulation results, Figure 2C and D), ensuring the long-term stability of the protein (Figure S1, Supporting Information File 1). The aforementioned features are consistent with results from circular dichroism (CD) spectroscopy (Figure S1, Supporting Information File 1), showing

• the transmembrane region could not be achieved, leading to an incomplete coverage of the hydrophobic belt. D) Water molecules in the first solvation sphere (<5 Å) are partly covering the hydrophobic belt of FhuA ΔCVFtev using 126 MPD molecules. MPD, 2-methyl-2,4-pentanediol. Circular dichroism spectra

Cycloheximide congeners produced by Streptomyces sp. SC0581 and photoinduced interconversion between (E)- and (Z)-2,3-dehydroanhydrocycloheximides

• Li Yang,
• Ping Wu,
• Jinghua Xue,
• Huitong Tan,
• Zheng Zhang and
• Xiaoyi Wei

Beilstein J. Org. Chem. 2017, 13, 1039–1049, doi:10.3762/bjoc.13.103

• conformers of both stereoisomers were subjected to TDDFT calculations of the electronic circular dichroism (ECD) spectra. As shown in Figure 3, the calculated ECD spectra of (4R,6R,αS)-1 and (4R,6R,αR)-1 were similar to one another and both in good agreement with the measured spectrum of 1, which indicated a

Interactions between shape-persistent macromolecules as probed by AFM

• Johanna Blass,
• Jessica Brunke,
• Franziska Emmerich,
• Cédric Przybylski,
• Vasil M. Garamus,
• Artem Feoktystov,
• Roland Bennewitz,
• Gerhard Wenz and
• Marcel Albrecht

Beilstein J. Org. Chem. 2017, 13, 938–951, doi:10.3762/bjoc.13.95

• formation, which might prevent the accessibility of the CD-moieties located on the polymer backbone, was avoided by the presence of pyridine as a non-polar solvent. Both NOESY NMR experiments and circular dichroism (results not shown) do not indicate any significant interaction of the CDs and the aromatic

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• close chiral anion-pair complexes would then undergo a chiral counterion-controlled asymmetric reaction with a nucleophile. This proposal was validated experimentally, and a chloride-induced conformational switch to form a helical backbone was experimentally observed by circular dichroism (CD) during

Characterization of the synthetic cannabinoid MDMB-CHMCZCA

• Carina Weber,
• Stefan Pusch,
• Dieter Schollmeyer,
• Sascha Münster-Müller,
• Michael Pütz and
• Till Opatz

Beilstein J. Org. Chem. 2016, 12, 2808–2815, doi:10.3762/bjoc.12.279

• samples. For this purpose, we used analytical methods such as NMR, tandem mass spectrometry, vibrational and electronic circular dichroism spectroscopy (VCD and ECD), as well as chiral HPLC. Results and Discussion Pure MDMB-CHMCZCA (3) was obtained as a so-called “research chemical” (RC) from an online RC

• ECD spectra were obtained on a J-815 circular dichroism spectropolarimeter (Jasco) in a 1 mm (path length) quartz glass cuvette and a spectral range of 400–185 nm. The measurements were carried out with an acetonitrile solution of MDMB-CHMCZCA (0.25 mmol/L), a scan speed of 20 nm/min and 8 repetitions

• . The baseline was corrected by subtraction of a solvent spectrum recorded with the same parameters. Vibrational spectroscopy The infrared (IR) and vibrational circular dichroism (VCD) spectra were recorded with a Tensor 27 IR spectrometer (Bruker Optics) equipped with a PMA50 module for polarization

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• group of Yamamoto studied the effect of β-, γ-, G1-β-, and Me-α-CD on the thermal stability of an aqueous buffered solution of chicken egg white lysozyme by circular dichroism and fluorescence spectroscopy [91]. The thermal stability is significantly lowered in the presence of β-, γ-, and G1-β-CD

Inhibition of peptide aggregation by means of enzymatic phosphorylation

• Kristin Folmert,
• Malgorzata Broncel,
• Hans v. Berlepsch,
• Christopher H. Ullrich,
• Mary-Ann Siegert and
• Beate Koksch

Beilstein J. Org. Chem. 2016, 12, 2462–2470, doi:10.3762/bjoc.12.240

• of phosphorylation, time-dependent CD (circular dichroism) measurements were performed. To ensure comparable and reproducible starting conditions, a disaggregation and concentration validation assay using HFIP (1,1,1,3,3,3-hexafluoropropan-2-ol) was performed. Thus, all aggregates that may have

• solution was stored at −20 °C. Circular dichroism CD spectra were recorded by using a Jasco J-810 spectropolarimeter (Jasco, Gross-Umstadt, Germany) at 24 °C (Jasco PTC-348W1 peltier thermostat) using 0.2 mm path length Quartz Suprasil cuvettes (Hellma, Müllheim, Germany). After background correction, the

Determination of the absolute stereostructure of a cyclic azobenzene from the crystal structure of the precursor containing a heavy element

• Reji Thomas and
• Nobuyuki Tamaoki

Beilstein J. Org. Chem. 2016, 12, 2211–2215, doi:10.3762/bjoc.12.212

• date there have been several spectroscopic, diffraction methods developed to determine the absolute stereostructure of chiral molecules [26][27][28][29][30][31][32][33][34][35]. The non-empirical methods employed to determine the absolute configuration of a molecule include circular dichroism, exciton

• chirality methods [28][29], NMR spectroscopy [30][31][32], X-ray diffraction [33][34][35], etc. In addition to these methods, many researchers explored a combination of vibrational circular dichroism and quantum mechanical calculations to determine the absolute stereostructures [36][37][38]. Among various

• known chirality to obtain the target molecule. We could determine the stereostructure of the cyclic azobenzene by comparing the HPLC data obtained with a chiral column and the circular dichroism (CD) spectra of the product obtained by reduction of the enantiopure precursor and the target molecule

New furoisocoumarins and isocoumarins from the mangrove endophytic fungus Aspergillus sp. 085242

• Ze’en Xiao,
• Senhua Chen,
• Runlin Cai,
• Shao’e Lin,
• Kui Hong and
• Zhigang She

Beilstein J. Org. Chem. 2016, 12, 2077–2085, doi:10.3762/bjoc.12.196

• methyl protons H-4' and H-5' to C-2', and chelated hydroxy proton 8-OH to C-8, C-7, and C-8a (Figure 2). The negative circular dichroism at 265 nm (Figure 5) suggested R configuration at C-3, by comparison with data for isocoumarin derivatives described in the literature [13]. Thus, asperisocoumarin E (5

Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291

• Peng Zhang,
• Xiao-Ming Li,
• Xin-Xin Mao,
• Attila Mándi,
• Tibor Kurtán and
• Bin-Gui Wang

Beilstein J. Org. Chem. 2016, 12, 2012–2018, doi:10.3762/bjoc.12.188

• time-dependent density functional theory-electronic circular dichroism (TDDFT-ECD) calculations. A similar compound, whose planar structure was previously described but the relative and absolute configurations and 13C NMR data were not reported, was also identified and was tentatively named as

From supramolecular chemistry to the nucleosome: studies in biomolecular recognition

• Marcey L. Waters

Beilstein J. Org. Chem. 2016, 12, 1863–1869, doi:10.3762/bjoc.12.175

• attractive scaffold because a two-state approximation for folding was reasonable in most cases and the β-hairpin is far more amenable to NMR analysis than α-helices, which were usually characterized by Circular Dichroism (CD). Additionally, because the sidechains in β-hairpins interdigitate, they provide

Artificial Diels–Alderase based on the transmembrane protein FhuA

• Hassan Osseili,
• Daniel F. Sauer,
• Klaus Beckerle,
• Marcus Arlt,
• Tomoki Himiyama,
• Tino Polen,
• Akira Onoda,
• Ulrich Schwaneberg,
• Takashi Hayashi and
• Jun Okuda

Beilstein J. Org. Chem. 2016, 12, 1314–1321, doi:10.3762/bjoc.12.124

• (polyethylene-polyethylene glycol), SDS (sodium dodecyl sulfate), TEV (Tobacco Etch Virus), MALDI–TOF–MS (matrix-assisted laser desorption/ionisation and time-of-flight mass spectrometry), FhuAΔCVFtev (FhuA Δ1-159_C545_V548_F501_tev), CD (circular dichroism), ESI-MS (electrospray ionization-mass spectrometry

Three new trixane glycosides obtained from the leaves of Jungia sellowii Less. using centrifugal partition chromatography

• Luíse Azevedo,
• Larissa Faqueti,
• Marina Kritsanida,
• Antonia Efstathiou,
• Despina Smirlis,
• Gilberto C. Franchi Jr,
• Grégory Genta-Jouve,
• Sylvie Michel,
• Louis P. Sandjo,
• Raphaël Grougnet and
• Maique W. Biavatti

Beilstein J. Org. Chem. 2016, 12, 674–683, doi:10.3762/bjoc.12.68

• Armen Instrument (Saint-Avé, France) fitted with a 1000 mL rotor containing 2016 twin-cells, equipped with a gradient pump and a 50 mL loop injection 6-way valve. Electronic circular dichroism (ECD) spectra were recorded in acetonitrile using a Jasco XLC 3195CD detector. Plant material The leaves of J

Self and directed assembly: people and molecules

• Tony D. James

Beilstein J. Org. Chem. 2016, 12, 391–405, doi:10.3762/bjoc.12.42

• electrochemistry [77]. The system has also been used with Eric Anslyn (University of Texas at Austin) to determine the ee of amines using circular dichroism (CD) spectroscopy [78]. The system was more recently used to measure the ee of amines using fluorescence [79]. The UK Office of Science and Innovation (OSI

Interactions of cyclodextrins and their derivatives with toxic organophosphorus compounds

• Sophie Letort,
• Sébastien Balieu,
• William Erb,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2016, 12, 204–228, doi:10.3762/bjoc.12.23

• CDs. The correlation between inclusion parameters and catalytic properties of CDs was studied by induced circular dichroism (ICD) of the inclusion complexes using rotational-strength analysis method. ICD analysis underlines a change of the environment in the cavity due to the formation of the

Bifunctional phase-transfer catalysis in the asymmetric synthesis of biologically active isoindolinones

• Antonia Di Mola,
• Maximilian Tiffner,
• Francesco Scorzelli,
• Laura Palombi,
• Rosanna Filosa,
• Paolo De Caprariis,
• Mario Waser and
• Antonio Massa

Beilstein J. Org. Chem. 2015, 11, 2591–2599, doi:10.3762/bjoc.11.279

• to obtain both the enantiomers of chiral bioactive compounds. In this case, we focused on (R,R)-8a, which afforded the required (S)-7 (the absolute configuration has been previously determined by vibrational circular dichroism) [31]. Asymmetric synthesis of 9 by decarboxylation of (S)-7 Although

Chiroptical properties of 1,3-diphenylallene-anchored tetrathiafulvalene and its polymer synthesis

• Masashi Hasegawa,
• Junta Endo,
• Seiya Iwata,
• Toshiaki Shimasaki and
• Yasuhiro Mazaki

Beilstein J. Org. Chem. 2015, 11, 972–979, doi:10.3762/bjoc.11.109

• systems having strong chiroptical properties because they have great potential for use in optical devices involving polarized light [1][2][3]. Chiral response, in electronic circular dichroism (ECD) based on an exciton coupling between two adequate π-chromophores, can express a pronounced chiroptical

• −341 (c 0.83 in CH2Cl2), respectively. Figure 2 depicted the electronic circular dichroism (ECD) spectra of the enantiomers of (+)/(−)-3 and (+)/(−)-9, and their UV–vis absorption spectra. The ECD spectrum of the (−)-9 enantiomer exhibited a clear bisignate CD curve with a negative peak at 274 nm and a

• -IA3 column (20 Ø × 250 mm). The optical rotations were measured with JASCO P-1300 spectropolarimeter in 1 dm quartz cell at 24 °C. Electronic circular dichroism (ECD) spectra were recorded on JASCO J-725 spectrodichrometer. The spectra were combined after the baseline correction of each measurement