A Nitroxide‐Tagged Platinum(II) Complex Enables the Identification of a DNA G‐Quadruplex Binding Mode

Abstract

We reported a novel strategy for investigating small molecule binding to G-quadruplexes (GQs). A newly synthesized dinuclear platinum(II) complex (Pt2L) containing a nitroxide radical was shown to selectively bind a GQ-forming sequence derived from human telomere (hTel). Using the nitroxide moiety as a spin label, electron paramagnetic resonance (EPR) spectroscopy was carried out to investigate binding between Pt2L and hTel GQ. Measurements indicated that two molecules of Pt2L bind with one molecule of hTel GQ. The inter-spin distance measured between the two bound Pt2L, together with molecular docking analyses, revealed that Pt2L predominately binds to the neighboring narrow and wide grooves of the G-tetrads as hTel adopts the antiparallel conformation. The design and synthesis of nitroxide tagged GQ binders, and the use of spin-labeling/EPR to investigate their interactions with GQs, will aid the development of small molecules for manipulating GQs involved in crucial biological processes.

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

“…[51][52][53][54][55][56][57][58] So far, few reports describe PDEPR-based investigations on G-quadruplexes, [59][60][61] including in-cell spin-labeled G-quadruplexes [62] and quadruplex-metal complex adducts. [63,64] Recently, we incorporated new Cu 2+ -based spin labels into tetramolecular DNA G-quadruplexes of varying Gtetrad count, which allowed us to determine intramolecular distances within the secondary structure with unprecedented accuracy. [65] Key to obtain such precise data was a label design in which the magnetic orbitals of the square-planar coordinated Cu 2+ cations were fixed in defined spatial orientations by equipping the four-stranded DNA construct with a set of four nitrogen donor ligands, forming a rigid chelate environment.…”

“…While PDEPR is most commonly used to determine structural constraints in protein systems, its application to distance measurements within nucleic acids has been steadily expanding [51–58] . So far, few reports describe PDEPR‐based investigations on G‐quadruplexes, [59–61] including in‐cell spin‐labeled G‐quadruplexes [62] and quadruplex‐metal complex adducts [63, 64] …”

Enhanced Stabilization of G‐Quadruplex DNA by [Ni4L6]8+ Cages with Large Rigid Aromatic Ligands

“…As shown in Figure c and d, cages 1 and 2 could induce a remarkable stabilization of antiparallel G‐quadruplex DNA in Na + buffer, and the Δ T m values were in the range 39.09–40.90 °C. The Δ T m values were unexpectedly high and make the cages fully competitive with high‐affinity G‐quadruplex binders such as polynuclear Pt II complexes , . In K + buffer, the cages exhibited Δ T m values of 29.08–31.69 °C (Table and Figure S7), and the stabilization effect on hybrid G‐quadruplex is at a high level that can be compared to those of previously reported metal complexes …”

Präzise Abstandsmessungen in DNA‐G‐Quadruplex‐Dimeren und Sandwichkomplexen über gepulste dipolare EPR‐Spektroskopie

“…Während PDEPR gewöhnlich zur Bestimmung struktureller Gegebenheiten in Proteinsystemen verwendet wird, gewinnt die Anwendung der Methode auch für Abstandsmessungen in Nukleinsäuren kontinuierlich an Popularität [51–58] . Bis jetzt schildern nur wenige Berichte PDEPR‐basierte Untersuchungen zu G‐Quadruplexen, [59–61] darunter zum Beispiel die Beschreibung von In‐Zell‐Systemen [62] und Addukten aus Quadruplexen und Metallkomplexen [63, 64] …”

“…[51][52][53][54][55][56][57][58] Bis jetzt schildern nur wenige Berichte PDEPR-basierte Untersuchungen zu G-Quadruplexen, [59][60][61] darunter zum Beispiel die Beschreibung von In-Zell-Systemen [62] und Addukten aus Quadruplexen und Metallkomplexen. [63,64] Vorkurzem berichteten wir über den Einbau eines neuen Cu 2+ -basierten Spinmarkers in tetramolekulare DNA-G-Quadruplexe mit variierender Anzahl an G-Tetraden. Die Kombination von 3'-m it 5'-Markierung erlaubte es,i ntramolekulare Abstände innerhalb der Sekundärstruktur mit beispielloser Genauigkeit zu bestimmen.…”