Julita Eilmes

Design, synthesis and spectroscopic properties of crown ether-capped dibenzotetraaza[14]annulenes Design, synthesis and spectroscopic properties of crown ether-capped dibenzotetraaza[14]annulenes

The first series of discrete multichromophore arrays of dibenzotetraaza[14]annulene (DBTAA), containing flexible bridges, have been synthesized in 40–46% isolated yields. The key asymmetrical intermediates, carrying two distinctly addressable functionalities (ROH vs. ROCH₂–CC–H and R(CH₂)_nBr vs. ROCH₂–CC–H) at the macrocycle periphery, were synthesized in moderate to high (30–78%) isolated yields. Facile synthetic protocols developed for the synthesis of discrete DBTAA arrays offer several advantages such as operational simplicity and easy post-synthetic workup that overcome the need for laborious chromatographic purification. All new compounds were characterized by microanalysis, mass spectrometry, UV-Vis, FTIR-ATR, and ¹H and ¹³C NMR spectroscopy. Structural features were briefly discussed with emphasis on several potential applications.

A macrocyclic precursor featuring highly reactive propargylic moieties was prepared via Williamson etherification in good yields of 54–65%. Organometallic methodology paired with protective metal insertion served as the foundation for better DBTAA exploitation through copper(I)-mediated coupling. Glaser–Hay and Glaser–Eglinton coupling conditions were applied to the direct synthesis of a cyclic strapped ligand and its corresponding dimer in 44% and 30% yields respectively. Mechanistic insight into cyclic dimer formation is discussed with emphasis on the kinetic effective molarities which reveal that the working concentration regime profoundly affects the final product's distribution. Both macrocyclic zinc(II) precursor and the corresponding inherently chiral strapped ligand are structurally characterized by single-crystal X-ray diffraction. Strapped enantiomers communicate in a solid state through the inherently chiral π-surfaces and display preferential self-recognition, leading to both homochiral MM and PP stereoisomers with pronounced helicity.

The first known cofacial dimers, based on covalently linked dibenzotetraaza[14]annulenes, were synthesized in reasonable 35–40% yields, without recourse to high-dilution techniques.

Thermodynamic studies of ligand binding to human telomere (ht) DNA quadruplexes, as a rule, neglect the involvement of various ht-DNA conformations in the binding process. Therefore, the thermodynamic driving forces and the mechanisms of ht-DNA G-quadruplex-ligand recognition remain poorly understood. In this work we characterize thermodynamically and structurally binding of netropsin (Net), dibenzotetraaza[14]annulene derivatives (DP77, DP78), cationic porphyrin (TMPyP4) and two bisquinolinium ligands (Phen-DC3, 360A-Br) to the ht-DNA fragment (Tel22) AGGG(TTAGGG)₃ using isothermal titration calorimetry, CD and fluorescence spectroscopy, gel electrophoresis and molecular modeling. By global thermodynamic analysis of experimental data we show that the driving forces characterized by contributions of specific interactions, changes in solvation and conformation differ significantly for binding of ligands with low quadruplex selectivity over duplexes (Net, DP77, DP78, TMPyP4; K_Tel22 ≈ <K_dsDNA) and for highly selective quadruplex-specific ligands (Phen-DC3, 360A-Br; K_Tel22 > K_dsDNA). These contributions are in accordance with the observed structural features (changes) and suggest that upon binding Net, DP77, DP78 and TMPyP4 select hybrid-1 and/or hybrid-2 conformation while Phen-DC3 and 360A-Br induce the transition of hybrid-1 and hybrid-2 to the structure with characteristics of antiparallel or hybrid-3 type conformation.

An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA.

Among three novel DBTAA derivatives only the DBTAA–propyl–adenine conjugate 1 showed recognition of the consecutive oligo dT sequence by increased affinity and specific induced chirooptical response in comparison to other single stranded RNA and DNA; whereby of particular importance is the up until now unique efficient differentiation between dT and rU. At variance, its close analogue DBTAA–hexyl–adenine 2 did not reveal any selectivity between ss-DNA/RNA pointing out the important role of steric factors (linker length); moreover non-selectivity of the reference compound (3, lacking adenine) stressed the importance of adenine interactions in the 1 selectivity.

The first synthesis of the bis(2-hydroxybenzoyl)dinaphthotetraaza[14]annulene ligand and its O,O-bis-alkylated derivatives containing a decanedioxy bridging moiety, pendant bis-alkoxy groups as well as dicationic butoxypyridinium substituents is reported. The synthetic procedures, full analytical and spectroscopic characterisation (NMR, MS and IR) and crystal structures of the new products are described. The crystal structures show that naphthylene moieties incorporated into the investigated derivatives provide additional opportunities for non-covalent interactions between the molecules.