Deepak Koirala, Soma Dhakal, Beth Ashbridge, Yuta Sannohe, Raphaël
Rodriguez, Hiroshi Sugiyama, Shankar Balasubramanian, and Hanbin Mao
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 Kd of
490 ± 80 nM. The free-energy change of binding obtained from a
Hess-like process provides an identical Kd for pyridostatin and
a Kd 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.
Journal: Nature Chemistry
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