Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• ), which matched the ones of the independently formed complexes of these ligands with DNA (see above). In the case of 3e–g, the binding event was also confirmed by CD spectroscopy, namely by the formation of weak ICD signals (Figure 7B, cf. Supporting Information File 1, Figure S7B). Because of the very

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• , and polynucleotide binding affinity has been investigated by UV–vis, fluorescence and CD spectroscopy and molecular modeling. Further, binding of Phen-Py-1 to human dipeptidyl peptidase III enzyme was investigated by fluorescence spectroscopy and microcalorimetric measurements. Results and Discussion

• and probability of contact, including steric shielding and charge–charge interactions [41]. Circular dichroism (CD) experiments CD spectroscopy was chosen to monitor conformational changes of polynucleotide's secondary structure induced by small molecule binding [42]. Compounds Phen-Py-1 and Phen-Py-2

BINOL as a chiral element in mechanically interlocked molecules

• Matthias Krajnc and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

• unit on the helicity of the polyacetylene was investigated by CD spectroscopy. Here, no chiral induction was observed for the ammonium species 32, while the N-acylated polymers 33 showed clear Cotton effects in the absorption range of the polymer main chain (490 nm), demonstrating an effective

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• - instead of 7-bromotryptophan yielded the expected stapled peptide P1a. Next, the secondary structures of the two stapled peptides P1a and P1b were investigated by CD spectroscopy. Unfortunately, both peptides did not show enhanced helical conformation in water. To get more information about the structure

• data [72]. Moreover, the epimerization by the conditions of SMC is unlikely as it has been excluded by total hydrolysis of a late-stage SMC modified RGD peptide [67]. Analysis of the secondary structures of the cyclic peptides P2–P4 by CD spectroscopy also did not show a significantly increased α

• were investigated by CD spectroscopy and an increased helicity was observed for both peptides. In particular, P5.2 shows the characteristic signature of an α-helix with the tendency of minima at λ = 208 and 222 nm and a maximum at λ = 190 nm (Figure 1). The CD spectra provided calculated helicities of

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

• into oligonucleotides resulted in the formation of unstable duplexes with complementary DNA and RNA strands whereas four consecutive incorporations led to increased duplex stability due to an efficient stacking of heteroaromatic triazoles as revealed by CD spectroscopy and molecular dynamics

Analogs of the carotane antibiotic fulvoferruginin from submerged cultures of a Thai Marasmius sp.

• Birthe Sandargo,
• Leon Kaysan,
• Rémy B. Teponno,
• Christian Richter,
• Benjarong Thongbai,
• Frank Surup and
• Marc Stadler

Beilstein J. Org. Chem. 2021, 17, 1385–1391, doi:10.3762/bjoc.17.97

• antibiotic fulvoferruginin (1), fulvoferruginins B–F (2–6). The structures of these sesquiterpenoids were elucidated using HRESIMS, 1D and 2D NMR, as well as CD spectroscopy. Assessing the bioactivity, fulvoferruginin emerged as a potent cytotoxic agent of potential pharmaceutical interest. Keywords

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• 5a–e in the presence of ct DNA were examined with flow linear dichroism (LD) and circular dichroism (CD) spectroscopy (Figure 5, Figure S6, Supporting Information File 1). The binding of ligands 5a–e resulted in the development of negative LD signals at 350–355 nm and 420–429 nm clearly indicating an

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• concentration, high sensitivity 19F NMR has been employed to offer unique opportunities for their sampling and characterization in situ [50]. Prosser et al. demonstrated the utility of this approach when employing a combination of variable temperature (VT) 19F NMR analysis and CD spectroscopy to study the near

• ionization and ion mobility), CD spectroscopy and atomic force microscopy, the authors were able to obtain detailed information about the size and secondary structure associated with some of the soluble intermediates. These included: large β-sheet oligomers formed immediately after solubilization (oligomer

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• the effect of sulfate modification on the self-assembly properties of the dendritic peptide amphiphiles were performed using circular dichroism (CD) spectroscopy and electron transmission microscopy (TEM) as well as cryogenic TEM. Finally, the binding affinity of the sulfated supramolecular polymers

• mixture was subsequently purified by size exclusion chromatography to yield 85% of the oligosulfated monomer II. Characterization of the supramolecular polymers of I and II The self-assembly behavior of the peptide-based materials can be readily investigated using CD spectroscopy. The supramolecular

• from CD spectroscopy, we decided to carry out the TEM experiments in solutions of neutral pH and physiological ionic strength, to efficiently screen the repulsive charges at the surface of the sulfated dendritic peptide amphiphile II. For the dry TEM experiments we preferred 10 mM or 20 mM TRIS buffer

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• base pairs away from the 5’ and 3’ ends of the aptamer. The aptamer derivatives 1cf and 1df contain one Im:Im pair directly adjacent to the central binding pocket. For 1cf, the Im:Im pair is located towards the termini, whereas in derivative 1df it is close to the loop region. Melting curves and CD

• spectroscopy To evaluate whether the Ag(I)-mediated base pairs are indeed formed in the aptamer derivatives, melting curves and circular dichroism (CD) spectra were recorded in the presence of increasing amounts of Ag(I). The DNA melting is expected to occur when the loop structure of the aptamers opens up. In

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• examined with photometric and fluorimetric titrations, thermal DNA denaturation analysis, and CD spectroscopy. The results from the spectrometric titrations indicated the formation of 2:1 or 1:1 complexes (ligand:G4-DNA) with log Kb values of 10–11 (2:1) and 5–6 (1:1), which are typical for berberine

• the absence of ds26 as clearly indicated by only a small decrease of the melting temperature of ΔΔTm = 1.8 °C (Figure 2; cf. Supporting Information File 1, Figure S4). CD spectroscopy The interactions of the ligands 4a–e with G4-DNA 22AG and a2 were also examined with circular dichroism (CD

• . Additional information about the complex formation between the ligands and the quadruplex DNA forms 22AG and a2 was provided by CD spectroscopy. The changes of the CD spectrum of 22AG upon the addition of derivatives 4a–e clearly indicate a shift of the equilibrium between the different quadruplex forms of

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• intercalators, particularly those which have substituents protruding into either the major or minor grooves (or both) [29]. For a more detailed structural analysis of the complexes, CD spectroscopy was applied [12][13]. It should be noted that due to the distance between the asymmetric atom and NDI or GCP

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• cations and water molecules from the DNA/RNA grooves [44][45] by side arms interacting with the grooves and thereby supporting the binding. Circular dichroism experiments CD spectroscopy is an ideal method to get insight into the changes of the polynucleotide secondary structure upon binding of small

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• structure (Figure 1a) [54][55][56]. To support the results obtained from CD spectroscopy, FTIR spectroscopy was performed in D2O (pH 7.4). The appearance of two intense peaks at 1629 and 1678 cm−1 in the amide I region (Figure 1b) suggested an intermolecular antiparallel β-sheet arrangement [57][58][59][60

• between 1800 and 1500 cm−1, with 200 accumulations at a resolution of 0.4 cm−1. CD spectroscopy CD experiments were performed on a JASCO J-1500 spectropolarimeter equipped with a Peltier module as a temperature controller. The experiments were carried out in buffer solutions at different pH values. The

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

• Sarah Kölsch,
• Heiko Ihmels,
• Jochen Mattay,
• Norbert Sewald and
• Brian O. Patrick

Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13

• absorption and CD spectroscopy (Figure 10). In the course of the photoreaction, the formation of 3b was indicated by the emergence of its characteristic long-wavelength absorption band, whose shape and shift matched its DNA-bound form. The association of the released monomer 3b with DNA was also clearly

A chiral self-sorting photoresponsive coordination cage based on overcrowded alkenes

• Constantin Stuckhardt,
• Diederik Roke,
• Wojciech Danowski,
• Edwin Otten,
• Sander J. Wezenberg and
• Ben L. Feringa

Beilstein J. Org. Chem. 2019, 15, 2767–2773, doi:10.3762/bjoc.15.268

• with high symmetry is formed by chiral self-sorting without any sign of the formation of diastereomeric mixtures. To further confirm the self-sorting behavior of these cage structures, CD spectroscopy was performed. A linear dependence of CD amplitude on the ee of ligand stable Z-1 was found, which can

• corresponding stable isomer. Supporting Information Supporting Information File 538: Experimental procedures, compound characterization, CD spectroscopy, binding studies, NMR studies of the photochemical and thermal isomerizations, X-ray crystallography, computational details and Cartesian coordinates of DFT

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• splitting was noticed for [1(ʟ-, ᴅ/ʟ-LysOMe)2]MeOH (Figure S29, Supporting Information File 1). CD spectroscopy was further used to analyze complexation processes. For complexes 1(LysOMe)2, 1(ArgOMe)2, and 1(HisOMe)2 the CD effects are observed for bands at 300 nm – in the region where chiral components are

• methanol and methanol/water mixture but not in DMSO. We have also shown that chirality of guests is reflected at the hosts’ structures by diastereomeric splitting of methylene protons (CH2SO3−, f) and by induction of considerable CD effects. These results demonstrate that CD spectroscopy can be a very

Synthesis, enantioseparation and photophysical properties of planar-chiral pillar[5]arene derivatives bearing fluorophore fragments

• Guojuan Li,
• Chunying Fan,
• Guo Cheng,
• Wanhua Wu and
• Cheng Yang

Beilstein J. Org. Chem. 2019, 15, 1601–1611, doi:10.3762/bjoc.15.164

• dichroism (CD) spectroscopy. The first fraction showing negative CD signals was assigned to the Sp conformer and the second fraction showing positive CD signals was assigned to the Rp conformer. Aggregation behaviors of the enantiopure chiral pillar[5]arene derivatives were investigated by adding water into

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• , whereas by the use of visible light the stretched trans,trans-isomer is formed. By means of quantum chemical calculations and CD spectroscopy we could show that the trans→cis isomerization is spatially directed; that means that one of the two different macrocycles performs a definite clockwise rotation to

• investigation of the separated compounds. Therefore, the single HPLC peaks were collected and measured within a few minutes by CD spectroscopy. The purity of the separated isomers was tested as follows: after collection of the single HPLC peaks and a waiting time of about 20 min, HPLC chromatograms of the

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• oligonucleotides hybridized to complementary DNA or RNA disclosed a significant destabilization of both duplex types (ΔTm/mod = −1.6 to −5.5 °C). However, in the DNA/RNA hybrid the amount of destabilization could be reduced by multiple insertions of the modified unit. In addition, CD spectroscopy of the

• destabilization might be accounted to repulsive electrostatic interactions between the equatorial fluorine atom and the 5’-oxygen. CD spectroscopy of the duplexes disclosed that the helical structure of the modified oligonucleotides paired to complementary DNA was still of a B-type, whereas an intermediate A/B

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• attributed to the conformational restriction of the sugar [62][64]. The Gibbs free energy of duplex formation corresponded well with the observed Tm values. CD spectroscopy Circular dichroism of ON1–7 paired with DNA or RNA was recorded to further analyze their helical conformation and to compare it with

Olefin metathesis catalysts embedded in β-barrel proteins: creating artificial metalloproteins for olefin metathesis

• Daniel F. Sauer,
• Johannes Schiffels,
• Takashi Hayashi,
• Ulrich Schwaneberg and
• Jun Okuda

Beilstein J. Org. Chem. 2018, 14, 2861–2871, doi:10.3762/bjoc.14.265

• different analytical methods [56]. Structural integrity of the β-barrel fold was confirmed by CD spectroscopy. ICP–OES was used to determine the metal content. A little less than one metal center per protein molecule was found to be present. Additional absorption bands in the UV–vis spectra around λ = 380

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• scaffold had on its conformation. We utilized circular dichroism (CD) spectroscopy to evaluate the main structural motifs of the different analogs. Since only conserved modifications were introduced to the CSP1 sequence, we did not expect significant changes to the overall structural characteristics

• modulators. Our analysis also revealed that the binding pockets of the aromatic side-chains in CSP1 are likely optimally occupied by the current residues (Phe) and should thus be retained to maintain high affinity to the ComD1 receptor. Lastly, structural analysis using CD spectroscopy of the CSP1 analogs

• absorbance of ortho-nitrophenol (ONP). Abs550 is the scatter from cell debris, which, when multiplied by 1.75 approximates the scatter observed at 420 nm. t is the duration of incubation with ONPG in minutes, v is volume of lysate in milliliters, and Abs600 reflects cell density. Circular dichroism (CD

Design and biological characterization of novel cell-penetrating peptides preferentially targeting cell nuclei and subnuclear regions

• Anja Gronewold,
• Mareike Horn and
• Ines Neundorf

Beilstein J. Org. Chem. 2018, 14, 1378–1388, doi:10.3762/bjoc.14.116

• ; B = 0.1% TFA in acetonitrile) over 45 min and a flow rate of 6 mL·min−1. All peptides were obtained with purities >99%. CD spectroscopy All peptides were analyzed in 10 mM potassium phosphate buffer (pH 7.0) with or without the addition of TFE (1:1 dilution) using a peptide concentration of 20 µM

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• investigated by CD spectroscopy. The following properties of TxT NAA-modified DNA oligonucleotides were reported [72]: (i) they formed reasonably stable duplexes with complementary counterstrands, in particular with native DNA; (ii) the influence of the spatial orientation of the positive charge, i.e., of the

• largely insensitive to the presence of a single base mismatch in the counterstrand, thus indicating that electrostatic attraction overruled Watson–Crick base-pairing specificity in these cases. CD spectroscopy indicated that both 55a and 55b formed double-helical duplex structures with complementary DNA