Structure and Flexibility of Copper-Modified DNA G-Quadruplexes Investigated by 19 F ENDOR Experiments at 34†GHz.

DNA G-quadruplexes (GQs) are of great interest due to their involvement in crucial biological processes such as telomerase maintenance and gene expression. Furthermore, they are reported as catalytically active DNAzymes and building blocks in bio-nanotechnology. GQs exhibit remarkable structural diversity and conformational heterogeneity, necessitating precise and reliable tools to unravel their structure-function relationships. Here, we present insights into the structure and conformational flexibility of a unimolecular GQ with high spatial resolution via electron-nuclear double resonance (ENDOR) experiments combined with Cu(II) and fluorine labeling. These findings showcase the successful application of the 19 F-ENDOR methodology at 34 GHz, overcoming the limitations posed by the complexity and scarcity of higher-frequency spectrometers. Importantly, our approach retains both sensitivity and orientational resolution. This integrated study not only enhances our understanding of GQs but also expands the methodological toolbox for studying other macromolecules.

Precise Distance Measurements in DNA G-Quadruplex Dimers and Sandwich Complexes by Pulsed Dipolar EPR Spectroscopy.

DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as π-stacked dimers and aggregates with aromatic binding partners. Reliable methods for determining the structure of these non-covalent adducts are scarce. Here, we use artificial square-planar Cu(pyridine)4 complexes, covalently incorporated into tetramolecular G-quadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu2+ -Cu2+ distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-to-tail or head-to-head stacking mode, were unambiguously distinguished. Measured distances are in full agreement with results of molecular dynamics simulations. Furthermore, intercalation of two well-known G-quadruplex binders, PIPER and telomestatin, into G-quadruplex dimers resulting in sandwich complexes was investigated, and previously unknown binding modes were discovered. Additionally, we present evidence that free G-tetrads also intercalate into dimers. Our transition metal labeling approach, combined with pulsed EPR spectroscopy, opens new possibilities for examining structures of non-covalent DNA aggregates.

Heteroleptic Coordination Environments in Metal-Mediated DNA G-Quadruplexes.

The presence of metal centers with often highly conserved coordination environments is crucial for roughly half of all proteins, having structural, regulatory, or enzymatic function. To understand and mimic the function of metallo-enzymes, bioinorganic chemists pursue the challenge of synthesizing model compounds with well-defined, often heteroleptic metal sites. Recently, we reported the design of tailored homoleptic coordination environments for various transition metal cations based on unimolecular DNA G-quadruplex structures, templating the regioselective positioning of imidazole ligandosides L I . Here, we expand this modular system to more complex, heteroleptic coordination environments by combining L I with a new benzoate ligandoside L B within the same oligonucleotide. The modifications still allow the correct folding of parallel tetramolecular and antiparallel unimolecular G-quadruplexes. Interestingly, the incorporation of L B results in strong destabilization expressed in lower thermal denaturation temperatures T m . While no transition metal cations could be bound by G-quadruplexes containing only L B , heteroleptic derivatives containing both L I and L B were found to complex CuII, NiII, and ZnII. Especially in case of CuII we found strong stabilizations of up to ΔT m = +34°C. The here shown system represents an important step toward the design of more complex coordination environments inside DNA scaffolds, promising to culminate in the preparation of functional metallo-DNAzymes.

Structure-Property Relationships in CuII -Binding Tetramolecular G-Quadruplex DNA.

A series of artificial metal-base tetrads composed of a CuII cation coordinating to four pyridines, covalently attached to the ends of tetramolecular G-quadruplex DNA strands [LA-D d(G4 )]4 (LA-D =ligand derivatives), was systematically studied. Structurally, the square-planar [Cu(pyridine)4 ] complex behaves analogously to the canonical guanine quartet. Copper coordination to all studied ligand derivatives was found to increase G-quadruplex thermodynamic stability, tolerating a great variety of ligand linker lengths (1-5 atoms) and thus demonstrating the robustness of the chosen ligand design. Only at long linker lengths, the stabilizing effect of copper binding is compensated by the loss of conformational freedom. A previously reported ligand LE with chiral backbone enables incorporation at any oligonucleotide position. We show that ligand chirality distinctly steers CuII -induced G-quadruplex stabilization. 5'-End formation of two metal-base tetrads by tetramolecular G-quadruplex [LE2 d(G)4 ]4 shows that stabilization in the presence of CuII is not additive. All results are based on UV/Vis thermal denaturation, thermal difference, circular dichroism experiments and molecular dynamics simulations.

Syntheses, Structures, and Complexation Studies of Tris(organostannyl)methane Derivatives.

The syntheses of tris(organostannyl)methanes HC(SnX n Ph(3-n))3 (1, n=0; 2, n=1, X=I; 3, n=1, X =F; 4, n=1, X=Cl; 5, n=1, X=OAc; 6, n=2, X=I; 7, n=2, X=Cl) and the organostannate complexes Et4N[HC(SnIPh2)3⋅F] (8), Ph4P[HC(SnClPh2)3⋅Cl] (9), and [Ph4P]2[HC(SnCl2Ph)3⋅2 Cl] (10) are reported. The compounds were characterized by 1H, 13C, 19F, and 119Sn NMR spectroscopy, IR spectroscopy, electrospray mass spectrometry, and (with the exception of 3) single-crystal X-ray diffraction analysis. From the reaction between 2 and AgClO4 resulted the unprecedented hexanuclear organotin oxocluster [HC{Sn(ClO4)2Ph2}2Sn(OH)2Ph]2 (11), the molecular structure of which was elucidated by using X-ray crystallography.