title: A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands.
abstract: Ligands that stabilize the formation of telomeric DNA G-quadruplexes have potential as cancer treatments, because the G-quadruplex structure cannot be extended by telomerase, an enzyme over-expressed in many cancer cells. Understanding the kinetic, thermodynamic and mechanical properties of small-molecule binding to these structures is therefore important, but classical ensemble assays are unable to measure these simultaneously. Here, we have used a laser tweezers method to investigate such interactions. With a force jump approach, we observe that pyridostatin promotes the folding of telomeric G-quadruplexes. The increased mechanical stability of pyridostatin-bound G-quadruplex permits the determination of a dissociation constant K(d) of 490 ± 80 nM. The free-energy change of binding obtained from a Hess-like process provides an identical K(d) for pyridostatin and a K(d) of 42 ± 3 µM for a weaker ligand RR110. We anticipate that this single-molecule platform can provide detailed insights into the mechanical, kinetic and thermodynamic properties of liganded bio-macromolecules, which have biological relevance.
authors.affiliation: Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Koirala
authors.forename: Soma
authors.initials: S
authors.lastname: Dhakal
authors.forename: Beth
authors.initials: B
authors.lastname: Ashbridge
authors.forename: Yuta
authors.initials: Y
authors.lastname: Sannohe
authors.forename: Raphaël
authors.initials: R
authors.lastname: Rodriguez
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
authors.forename: Shankar
authors.initials: S
authors.lastname: Balasubramanian
authors.forename: Hanbin
authors.initials: H
authors.lastname: Mao
mesh_terms: D000634:Aminoquinolines / Q000138:chemical synthesis / Q000737:chemistry*; D004247:DNA / Q000378:metabolism; D054856:G-Quadruplexes; D006801:Humans; D007700:Kinetics; D008024:Ligands; D010080:Oxazoles / Q000737:chemistry; D010848:Picolinic Acids / Q000138:chemical synthesis / Q000737:chemistry*; D019098:Telomerase / Q000037:antagonists & inhibitors / Q000378:metabolism; D016615:Telomere / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000634:Aminoquinolines; D008024:Ligands; C567961:N2,N6-bis(4-(2-aminoethoxy)quinolin-2-yl)-4-((4-fluorobenzyl)oxy)pyridine-2,6-dicarboxamide; D010080:Oxazoles; D010848:Picolinic Acids; C567962:pyridostatin; C431888:telomestatin; D004247:DNA; D019098:Telomerase