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Updated: Jun 26, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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ILPR G-quadruplexes formed in seconds demonstrate high mechanical stabilities.

Zhongbo Yu1, Joseph D Schonhoft, Soma Dhakal

  • 1Department of Chemistry, Kent State University, Kent, Ohio 44242, USA.

Journal of the American Chemical Society
|January 22, 2009
PubMed
Summary

Guanine-rich G quadruplexes in the insulin gene region form stable structures, potentially blocking DNA replication. These structures exhibit distinct mechanical properties and thermodynamic stability, offering insights into gene regulation.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • The insulin linked polymorphism region (ILPR) regulates insulin gene transcription.
  • Guanine-rich segments in ILPR suggest a role for G quadruplexes in gene regulation.
  • G quadruplexes are stable secondary structures formed in guanine-rich DNA sequences.

Purpose of the Study:

  • To investigate the existence and stability of G quadruplex structures within the ILPR.
  • To elucidate the mechanical and thermodynamic properties of these G quadruplexes.
  • To explore the potential functional implications of G quadruplexes in DNA replication and gene control.

Main Methods:

  • Mechanical unfolding using laser tweezers.
  • Circular dichroism (CD) spectroscopy.

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  • Jarzynski's equality analysis for thermodynamic stability.
  • Kinetic measurements for folding rates.

    • Main Results:

    • Coexistence of stable parallel and antiparallel G quadruplex structures in the ILPR at physiological salt concentrations.
    • Unfolding forces (22.6 pN parallel, 36.9 pN antiparallel) exceed helicase stall forces, supporting a role in replication blockage.
    • Antiparallel G quadruplex is thermodynamically more stable (ΔG unfold: 23 kcal/mol) than the parallel form (14 kcal/mol).
    • Both structures exhibit rapid folding kinetics (kfold: 0.4 s⁻¹ parallel, 0.3 s⁻¹ antiparallel), suggesting kinetic accessibility for gene regulation.

    Conclusions:

    • G quadruplexes in the ILPR possess significant mechanical stability and thermodynamic favorability.
    • These structures may impede DNA replication processes, leading to replication slippage.
    • The rapid folding kinetics indicate potential roles in dynamic gene regulation.
    • This study provides a mechanical framework for understanding G quadruplex function in biological systems.