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Kinetic partitioning modulates human telomere DNA G-quadruplex structural polymorphism.

Xi Long1, Michael D Stone2

  • 1Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America.

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Summary

Folding protocols significantly impact telomere DNA G-quadruplex (GQ) structures. Kinetic partitioning, not just thermodynamics, influences the distribution of these crucial genome stability structures.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Genetics

Background:

  • Telomeres protect chromosome ends and maintain genome stability.
  • Human telomeres feature a 3' G-rich single-stranded tail capable of forming G-quadruplexes (GQs).
  • GQs can adopt diverse topological isomers, influencing their function.

Purpose of the Study:

  • To investigate the impact of different folding protocols on telomere DNA G-quadruplex conformations.
  • To analyze the kinetics of GQ folding and its relation to thermodynamic equilibrium.
  • To understand the contribution of folding kinetics to physiological GQ structures.

Main Methods:

  • Single-molecule Förster resonance energy transfer (smFRET) to study GQ conformations.
  • In situ refolding and slow cooling DNA annealing protocols were employed.
  • Kinetic analysis of GQ folding over minutes to hours.

Main Results:

  • The choice of folding protocol markedly affects observed DNA conformations.
  • In situ refolding kinetics gradually equilibrate towards slow cooling annealing distributions.
  • Low ionic strength and kinetic partitioning influence the distribution of GQ structures, favoring parallel conformations in the short term.

Conclusions:

  • Folding kinetics, alongside thermodynamics, is critical for determining telomere DNA GQ structures.
  • Kinetic partitioning during folding can lead to long-lived, non-equilibrium distributions of GQs.
  • These findings provide insights into the formation of physiological GQ structures in telomeres.