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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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Antiparallel G-Quadruplex Formation Hinders Conversion to a Parallel Topology.

Jianjun Xia1, Jielin Chen1, Jiahang Zhou1

  • 1State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.

The Journal of Physical Chemistry. B
|November 5, 2024
PubMed
Summary
This summary is machine-generated.

G-quadruplexes (G4s) folding is complex. An antiparallel G4 intermediate slows parallel G4 formation, especially at lower temperatures, though sodium ions can speed up this conversion.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • G-quadruplexes (G4s) are crucial nucleic acid structures with diverse biological roles.
  • Understanding G4 folding mechanisms is vital for their application, but remains incompletely elucidated.

Purpose of the Study:

  • Investigate the folding process of a specific G-rich sequence, d[(G3T2)3G3], in potassium solutions.
  • Determine the impact of folding intermediates on the overall G4 folding kinetics and thermodynamics.

Main Methods:

  • Stopped-flow kinetic analysis to monitor folding pathways.
  • Investigated the influence of potassium and sodium ions on folding intermediates and rates.
  • Analyzed temperature-dependent folding kinetics.

Main Results:

  • The sequence d[(G3T2)3G3] forms a parallel G4 structure, potentially via an antiparallel intermediate.
  • The antiparallel G4 conformation forms rapidly but converts slowly to the stable parallel form.
  • This intermediate pathway is slower than direct folding and is temperature-dependent.
  • Sodium ions accelerate the conversion from antiparallel to parallel G4 structures.

Conclusions:

  • G4 folding involves competitive pathways, with intermediates significantly influencing overall folding rates.
  • The antiparallel G4 intermediate acts as a kinetic trap, slowing the formation of the thermodynamically preferred parallel structure.
  • Ion-specific effects (K+ vs. Na+) modulate G4 folding dynamics, highlighting the complexity of these structures in biological contexts.