Template-assembled synthetic G-quadruplex (TASQ): a useful system for investigating the interactions of ligands with constrained quadruplex topologies.
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.
Murat
Pierre
P
Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9, France.
Bonnet
Romaric
R
Van der Heyden
Angéline
A
Spinelli
Nicolas
N
Labbé
Pierre
P
Monchaud
David
D
Teulade-Fichou
Marie-Paule
MP
Dumy
Pascal
P
Defrancq
Eric
E
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000138:chemical synthesis* / Q000737:chemistry*; D054856:G-Quadruplexes; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry*; D011166:Porphyrins / Q000737:chemistry*; D011401:Promoter Regions, Genetic; D013329:Structure-Activity Relationship; D020349:Surface Plasmon Resonance
D008024:Ligands; D009841:Oligonucleotides; D011166:Porphyrins; D004247:DNA