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

Abstract

DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as p-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 Gquadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu 2+-Cu 2+ distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-totail 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.

Paramagnetic Chemical Probes for Studying Biological Macromolecules

“…A related spin label ( L ) was used to label DNA quadruplexes with Cu­(II) forming a Cu­(pyridine) 4 complex (Figure ). , While initial studies used the racemic form of the tag, later studies employed the ( S ) isomer for distance measurements. A DNA quadruplex can also be labeled with a large dinuclear platinum­(II) complex linked to TEMPO …”

Going the dHis-tance: Site-Directed Cu2+ Labeling of Proteins and Nucleic Acids

“…This result is especially intriguing given the localized nature of Cu 2+ in the labeling scheme, the large spectral width and high anisotropy of the metal ion, and observations on rigid nitroxide pairs and nitroxide–Cu 2+ and Cu 2+ –Cu 2+ systems. ,, Orientational effects for the dHis label have recently been thoroughly understood through the combination of EPR experimentation, force-field parametrized MD simulations, and quantum mechanical calculations . Cu 2+ binding to dHis is elastic, and MD simulations show fluctuations in the bond lengths and bond angles between the Cu 2+ center and its coordinating atoms, as shown in Figure B .…”

In‐Cell Characterization of the Stable Tyrosyl Radical in E. coli Ribonucleotide Reductase Using Advanced EPR Spectroscopy

“…As orientation selectivity,which occurs when dipolar spectrum is dependent on the selected g-tensor S3). Angewandte Chemie orientations, [28] was reported previously for the in vitro Y 122 C-Y 122 C pair, [29] we employed orientation-selective DEER spectroscopy.T hree DEER traces were recorded at distinct gtensor orientations covering the whole EPR line,a nd the obtained dipolar traces were summed (see SI 2.7). Fouriertransform of in-cell and in vitro summed traces led to almost ideal Pake patterns (SI 2.7).…”