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DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context.

Aaron M Fleming1, Brandon Leonel Guerra Castañaza Jenkins1, Bethany A Buck1

  • 1Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States.

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This summary is machine-generated.

DNA damage significantly impacts the folding of potential G-quadruplex sequences (PQSs), affecting gene regulation. DNA breaks accelerate PQS folding, with implications for cellular processes like replication and repair.

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Area of Science:

  • Molecular biology
  • Genetics
  • Biochemistry

Background:

  • Potential G-quadruplex sequences (PQSs) form noncanonical DNA structures crucial for gene regulation.
  • The influence of DNA damage on PQS folding kinetics remains poorly understood.
  • Genomic DNA constraints on PQS folding are mimicked by duplex-G-quadruplex-duplex (DGD) scaffolds.

Purpose of the Study:

  • To investigate the effects of DNA base damage and strand breaks on PQS folding kinetics.
  • To analyze PQS folding within a DGD scaffold using the VEGF promoter sequence.
  • To determine the impact of damage on PQS folding relevant to cellular timescales.

Main Methods:

  • Circular dichroism (CD) spectroscopy to monitor folding kinetics.
  • 1D proton Nuclear Magnetic Resonance (1H NMR) for structural analysis.
  • Utilizing a duplex-G-quadruplex-duplex (DGD) scaffold for the VEGF promoter sequence.

Main Results:

  • Folding half-lives varied from 2 seconds to 12 minutes based on DNA damage type and location.
  • A single strand break near G-runs accelerated folding >150-fold.
  • Mg2+ ions and APE1 protein facilitated PQS folding.
  • CD and NMR confirmed G4 formation and damage-dependent folding.

Conclusions:

  • DNA damage, particularly strand breaks, significantly alters PQS folding kinetics.
  • The VEGF promoter PQS folding is sensitive to the type and position of DNA damage.
  • Measured folding half-lives are relevant to DNA replication, transcription, and repair processes.