Evaluation of binding selectivities and affinities of platinum‐based quadruplex interactive complexes by electrospray ionization mass spectrometry

Abstract

The quadruplex binding affinities and selectivities of two large π-surface PtII phenanthroimidazole complexes, as well as a smaller π-surface platinum bipyridine complex and a larger RuII complex, were evaluated by electrospray ionization mass spectrometry. Circular dichroism (CD) spectroscopy was used to determine the structures of various quadruplexes and to study the thermal denaturation of the quadruplexes in the absence and presence of the metal complexes. In addition, chemical probe reactions with glyoxal were used to monitor the changes in the quadruplex conformation because of association with the complexes. The platinum phenanthroimidazole complexes show increased affinity for several of the quadruplexes with elongated loops between guanine repeats. Quadruplexes with shorter loops exhibited insubstantial binding to the transition metal complexes. Similarly binding to duplex and single strand oligonucleotides was low overall. Although the ruthenium-based metal complex showed somewhat enhanced quadruplex binding, the PtII complexes had higher quadruplex affinities and selectivities that are attributed to their square planar geometries. The chemical probe reactions using glyoxal indicated increased reactivity when the platinum phenanthroimidazole complexes were bound to the quadruplexes, thus suggesting a conformational change that alters guanine accessibility.

Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry

“…Combining ESI-MS with the use of chemical probes (57,58) that react with and modify nucleic acids in a structure-dependent manner provides a more versatile approach to investigating ligandbinding sites and understanding how interactions of ligands with DNA can alter its conformation. Chemical probes in conjunction with ESI-MS have been used for both RNA and DNA substrates (44,(59)(60)(61). Investigation of the impact of ligand binding on DNA conformations was first reported for reactions of KMnO 4 , an oxidizing agent that reacts primarily by attacking the double bond of thymine to produce a mixture of diol and an alpha-hydroxylketone product, which leads to product mass shifts of 34 and 32 Da, respectively (Figure 10) (61).…”

“…The interactions of three platinum-based complexes-bipyridine ethylenediamine platinum(II) (Pt1), phenylphenanthroimidazole ethylenediamine platinum(II) (Pt2), and naphthylphenanthroimidazole ethylenediamine platinum(II) (Pt3) (see Figure 9)-with quadruplex DNA were evaluated by ESI-MS (44). These complexes were designed to incorporate extended aromatic pi surface areas to enhance their end-stacking interactions with quadruplex DNA.…”

“…Another chemical probe strategy that proved to be useful for the investigation of conformation changes of DNA upon ligand binding entails the use of glyoxal (44). In this approach, solutions containing various DNA structures (i.e., an intermolecular four-stranded quadruplex, its constituent single strand, or complexes composed of a quadruplex with a platinum compound) were incubated with glyoxal, a reagent that selectively reacts with accessible guanines.…”

Spectroscopic probing of recognition of the G-quadruplex in c-kit promoter by small-molecule natural products

“…In order to clearly illustrate the binding affinities of small molecules (P1-P12) to the G-quadruplex (G4), a parameter, IRa [18][19][20][21], is introduced as the intensity ratio of all complex ions The IRa value is 1.00 when all the G-quadruplex ions are binded with small molecules. The closer the IRa value to 1.00, the higher the binding affinity of small molecules to the G-quadruplex.…”

“…Phan and coworkers studied the structure of this G-rich sequence in K + solution by NMR spectroscopy, and found that this G-rich sequence can form a G-quadruplex containing three G-tetrad layers [15]. In this study, we used electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy [16][17][18][19][20][21] to probe the formation and recognition of the G-quadruplex from d(A 1 GGGA 5 GGGCG 10 CTGGG 15 AGGAG 20 GG) (named as S1) in the promoter region of human c-kit oncogene.…”