Kinetic and Thermodynamic Control of G-Quadruplex Polymorphism by Na+ and K+ Cations

J Phys Chem B. 2023 Aug 10;127(31):6842-6855. doi: 10.1021/acs.jpcb.3c01001. Epub 2023 Jul 28.

Abstract

G-Quadruplexes (G4s) are ubiquitous nucleic acid folding motifs that exhibit structural diversity that is dependent on cationic conditions. In this work, we exploit temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) to elucidate the kinetic and thermodynamic mechanisms by which monovalent cations (K+ and Na+) impact folding topologies for a simple G-quadruplex sequence (5'-GGG-(TAAGGG)3-3') with a three-state folding equilibrium. Kinetic measurements indicate that Na+ and K+ influence G4 formation in two distinctly different ways: the presence of Na+ modestly enhances an antiparallel G4 topology through an induced fit (IF) mechanism with a low affinity (Kd = 228 ± 26 mM), while K+ drives G4 into a parallel/hybrid topology via a conformational selection (CS) mechanism with much higher affinity (Kd = 1.9 ± 0.2 mM). Additionally, temperature-dependent studies of folding rate constants and equilibrium ratios reveal distinctly different thermodynamic driving forces behind G4 binding to K+H°bind > 0, ΔS°bind > 0) versus Na+H°bind < 0, ΔS°bind < 0), which further illuminates the diversity of the possible pathways for monovalent facilitation of G-quadruplex folding.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Cations, Monovalent
  • G-Quadruplexes*
  • Kinetics
  • Models, Molecular
  • Nucleic Acid Conformation
  • Polymorphism, Genetic
  • Potassium / chemistry
  • Sodium / chemistry
  • Temperature
  • Thermodynamics*

Substances

  • Cations, Monovalent
  • Sodium
  • Potassium