What stoichiometries determined by mass spectrometry reveal about the ligand binding mode to G-quadruplex nucleic acids

Abstract

G-quadruplexes (G4s) have become important drug targets to regulate gene expression and telomere maintenance. Many studies on G4 ligand binding focus on determining the ligand binding affinities and selectivities. Ligands, however, can also affect the G4 conformation. Here we explain how to use electrospray ionization mass spectrometry (ESI-MS) to monitor simultaneously ligand binding and cation binding stoichiometries. The changes in potassium binding stoichiometry upon ligand binding hint at ligand-induced conformational changes involving a modification of the number of G-quartets. We investigated the interaction of three quadruplex ligands (PhenDC3, 360A and Pyridostatin) with a variety of G4s. Electrospray mass spectrometry makes it easy to detect K displacement (interpreted as quartet disruption) upon ligand binding, and to determine how many ligand molecules must be bound for the quartet opening to occur. The reasons for ligand-induced conversion to antiparallel structures with fewer quartets are discussed. Conversely, K intake (hence quartet formation) was detected upon ligand binding to G-rich sequences that did not form quadruplexes in 1mM K alone. This demonstrates the value of mass spectrometry for assessing not only ligand binding, but also ligand-induced rearrangements in the target sequence. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

The future of telomere length in personalized medicine

“…G4s have become important drug targets that may regulate gene expression and telomere maintenance. Researchers are focusing on new methods to study the ligand binding affinities and selectivity (187) and to propose new bioactive chemotypes, identified after combined ligand-based virtual and experimental screening (188).…”

Strength in Numbers: Development of a Fluorescence Sensor Array for Secondary Structures of DNA

“…High-resolution methods such as NMR or X-ray crystallography can provide detailed structural information, but are time-consuming, require specialized equipment, and often fail if a sample presents a mixture of isoforms. Other biophysical techniques, such as thermal denaturation, [11] thermal difference spectroscopy, [12] hydrodynamic, [13] mass-spectrometric, [14][15] chromatographic [16] and gel-electrophoretic methods [17] may be employed in order to assess the secondary structure of DNA oligonucleotides; however, they provide only limited structural information and are poorly suited for high-throughput analysis. Vibrational circular dichroism (VCD) [18][19] and electronic circular dichroism (CD) spectroscopy can furnish a more detailed picture of DNA conformation (such as quantitative analysis of structural elements in G4-DNA), especially when coupled with chemometric analysis.…”

Heteroleptic Coordination Environments in Metal-Mediated DNA G-Quadruplexes

“…On the other hand, for an unfolded G-quadruplex, the main signal would correspond to the mass of the DNA strand without potassium ions. The mass spectrum shows a main signal corresponding to [htelL B 2 L I 4 +Cu+K-7H] 4− (Figure 4), thus strongly indicating a folded G-quadruplex coordinating to a Cu II or Ni II ion in the gas phase (D'Atri et al, 2015;Lecours et al, 2017).…”