Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies

Abstract

A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a pi-stacking binding mode showed a higher binding affinity for intermolecular-like G-quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G-quadruplex DNA over the duplex DNA. A numerical parameter, termed the G-quadruplex binding mode index (G4-BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G-quadruplex 1 against intramolecular G-quadruplex 2. The G-quadruplex binding mode index (G4-BMI) of a ligand is defined as follows: G4-BMI=K(D)(intra)/K(D)(inter), where K(D)(intra) is the dissociation constant for intramolecular G-quadruplex 2 and K(D)(inter) is the dissociation constant for intermolecular G-quadruplex 1. In summary, the present work has demonstrated that the use of parallel-constrained quadruplex topology provides more precise information about the binding modes of ligands.

Assessment of selectivity of G-quadruplex ligands via an optimised FRET melting assay

“…In addition, it is critical that ligands do not bind to duplex DNA. The G-quadruplex Binding Model Index (G4-BMI) has been used to discriminate between ligands with a tetrad-stacking mode and those classified as groove and/or loop binders [26]. Determination of G4-BMI relies on surface plasmon resonance measurements performed on surfaces modified with constrained DNA G-quadruplexes.…”

“…In principle, selectivity could arise from interactions involving features that differ from one G-quadruplex topology or structure to another. However, neither TmPyP4 with a G4-BMI of 8 [26], nor distamycin with a G4-BMI of 1.2 bind selectively to a particular G-quadruplex topology [26,27].…”

Efficient Inhibition of Telomerase by Nickel–Salophen Complexes

“…We used am ethodb ased on the concept of template-assembled synthetic G-quadruplexes. [19] Basically,t hree oligonucleotides were assembled on at emplate that constrains them to adopt different topologies:T he G-quadruplex model A,f ormed by four interacting parallel strands d(TTAGGGT);a ni ntramolecular G-quadruplex model B d(GGG(TTAGGG) 3 TT), which mimics the human telomeric sequence;a nd ah airpin duplex C.A ss hown in Ta ble 1, all the complexes are selectivef or G-quadruplexes. They exhibit as light preference for the G-quadruplex A,w here the top quartet is more accessible (absence of loop).…”

Porphyrins in complex with DNA: Modes of interaction and oxidation reactions

“…Porphyrin H 2 -TMPyP4 interacts with telomeric G-quadruplex models with a relatively high binding constant, in the order of Ka~10 6 -10 8 M -1 [97,101,[106][107][108]. The binding of H 2 -TMPyP4 to the c-myc promoter parallel quadruplex is tighter with a binding constant of Ka~10 8 -10 9 M -1 [109].…”