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

• within the binding site. The binding mode of the benzo[c]quinolizinium derivatives 3c,e–g with DNA was further examined with circular dichroism (CD) and linear dichroism (LD) spectroscopy (Figure 6 and Supporting Information File 1, Figures S12–S14). Hence, with increasing ligand-DNA ratio (LDR) weak

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

• = 77.2 ppm). Elemental analyses: HEKAtech EUROEA combustion analyzer, determined by Rochus Breuer, Organische Chemie I, Universität Siegen. Mass spectra (ESI): Finnigan LCQ Deca (U = 6 kV; working gas: Ar; auxiliary gas: N2; temperature of the capillary: 200 °C). Circular dichroism (CD) and linear

• dichroism (LD): Chirascan CD spectrometer, Applied Photophysics. Flow-LD: High Shear Cuvette Cell Accessory (Applied Photophysics); the LD samples were recorded in a rotating cuvette with a shear gradient of 1200 s−1. Melting points: Büchi 545 (Büchi, Flawil, CH). Materials Berberrubine (1b) was synthesized

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

• –d were further investigated by circular dichroism (CD) and flow linear dichroism (LD) spectroscopy [74][75] in phosphate buffer at different ligand-to-DNA ratios (LDR). The mixtures of compounds 3a–d with ct DNA showed clear induced circular dichroism (ICD) and LD bands in the absorption region of

• at 473 nm and 583 nm, respectively, in the presence of DNA, along with a weaker positive signal at 346 nm (Figure 4A1). For LD spectroscopic analysis, the DNA molecules were oriented in a hydrodynamic field of a rotating couette (flow linear dichroism). The corresponding LD spectra were the result of

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

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

• the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be

• 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

• [5]. As nucleic acids are characterized by a dominant helical chirality and exhibit a rather small set of secondary structures, each characterized by a different polarization spectroscopy signature, they are convenient targets to monitor structural changes induced by outer stimuli. Linear dichroism