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

• functionality. Thus, this synthetic route represents the first successful Cu-mediated coupling reaction of berberine substrates. The DNA-binding properties of the 10-O-arylberberine derivatives with duplex and quadruplex DNA were studied by thermal DNA denaturation experiments, spectrometric titrations as well

• as CD and LD spectroscopy. Fluorimetric DNA melting analysis with different types of quadruplex DNA revealed a moderate stabilization of the telomeric quadruplex-forming oligonucleotide sequence G3(TTAG3)3. The derivatives showed a moderate affinity towards quadruplex DNA (Kb = 5–9 × 105 M−1) and ct

• DNA (Kb = 3–5 × 104 M−1) and exhibited a fluorescence light-up effect upon complexation to both DNA forms, with slightly higher intensity in the presence of the quadruplex DNA. Furthermore, the CD- and LD-spectroscopic studies revealed that the title compounds intercalate into ct DNA and bind to G4

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

• with one representative ligand from the series that such berberine–adenine conjugates exhibit a selective binding, specifically a selectivity to quadruplex DNA in competition with duplex DNA, and a preferential thermal stabilization of the G4-DNA forms 22AG and KRAS. Notably, the experimental data do

• ; DNA recognition; G4-DNA; nucleic acids; Introduction In nucleic acids chemistry, quadruplex DNA (G4-DNA) has been established as an attractive target [1][2][3]. This noncanonical DNA form is assembled through stacking of at least two guanine quartets and has been observed with highly diverse

• , G4-DNA-targeting ligands are searched for that bind selectively and sufficiently strong to quadruplex DNA and thereby influence the biological function of G-rich DNA sequences [17][18][19][20][21][22]. Among the numerous classes of compounds, mostly related to traditional DNA binders, that have been

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

• Xiao Xie,
• Michela Zuffo,
• Marie-Paule Teulade-Fichou and
• Anton Granzhan

Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183

• rapid topological classification of G4-DNA structures. Keywords: fluorescent probes; G-quadruplex DNA; G-quadruplex RNA; nucleic acids; styryl dyes; Introduction Development of fluorescent probes for G-quadruplex (G4) DNA and RNA is an active research area. In fact, these non-canonical nucleic acid

Synthesis of 9-arylalkynyl- and 9-aryl-substituted benzo[b]quinolizinium derivatives by Palladium-mediated cross-coupling reactions

• Siva Sankar Murthy Bandaru,
• Darinka Dzubiel,
• Heiko Ihmels,
• Mohebodin Karbasiyoun,
• Mohamed M. A. Mahmoud and
• Carola Schulzke

Beilstein J. Org. Chem. 2018, 14, 1871–1884, doi:10.3762/bjoc.14.161

• pH-sensitive light-up probe. Photometric and fluorimetric titrations of duplex and quadruplex DNA to 9-(arylethynyl)benzo[b]quinolizinium derivatives revealed a significant binding affinity of these compounds towards both DNA forms with binding constants of Kb = 0.2–2.2 × 105 M−1. Keywords: DNA

• topoisomerase inhibitors [5]. More recently, much interest in this research area is focused on the non-canonical quadruplex DNA (G4-DNA) [6][7][8]. Mostly based on the principles and requirements of ligands that bind to duplex DNA, numerous G4-DNA ligands have been developed to study their selectivity and

• binding properties towards G4-DNA because of the biological importance of G4-DNA [9][10][11][12][13]. Along these lines, we and others have established the class of annelated quinolizinium derivatives as versatile ligands that bind to duplex, triplex and quadruplex DNA depending on their shape and size

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

• (groove binders, intercalators and alkylating agents), which includes both classical DNA binders and new advancements in the recent years (with emphasis on research advances reported in the last five years). For a focused work, we have excluded triplex and quadruplex DNA binders for this review. In

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• -b′′′]tetraquinolizinium (5) and thiazole orange (6) were studied. It is demonstrated with absorption, fluorescence and CD spectroscopy that all investigated ligands bind with relatively high affinity to the ILPR-quadruplex DNA a2 (0.2–5.5 × 106 M−1) and that in most cases the binding parameters of

• ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences. Keywords: DNA ligands; fluorescent probes; ILPR; nucleic acids; quadruplex DNA; Introduction The “insulin-linked polymorphic region” (ILPR) is a physiologically relevant G-rich DNA sequence

• observation that insulin associates with quadruplex DNA [10]. In particular, it was assumed that the formation of quadruplex structures affects the transcriptional activity, because the position of the ILPR in the promoter region of the gene represents a stake close to the transcription process [9][11][12

Stereoselectively fluorinated N-heterocycles: a brief survey

• Xiang-Guo Hu and
• Luke Hunter

Beilstein J. Org. Chem. 2013, 9, 2696–2708, doi:10.3762/bjoc.9.306

• [21]. For example, O’Hagan and co-workers investigated the pyrrolidine-containing molecules 9 and 10 (Figure 3) as ligands of G-quadruplex DNA [22]. The non-fluorinated ligand 9 had some conformational disorder because the pyrrolidine rings were able to interconvert between exo and endo puckers. In

• influenced by a C–F…N+ charge–dipole interaction. Fluorination ridifies the pyrrolidine rings of ligand 10, with several consequences for its G-quadruplex DNA binding properties. Proline 11 readily undergoes a ring-flip process, but (4R)-fluoroproline 12 is more rigid because of hyperconjugation (σCH → σ*CF