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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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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, UT 84112-0850 United States.

Biorxiv : the Preprint Server for Biology
|January 31, 2024
PubMed
Summary
This summary is machine-generated.

DNA damage significantly impacts the folding of potential G-quadruplex sequences (PQS), influencing gene regulation. This study quantifies these effects on PQS folding kinetics within a specific DNA structure.

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Area of Science:

  • Molecular biology
  • Genetics
  • Biochemistry

Background:

  • Potential G-quadruplex sequences (PQS) form non-canonical DNA structures crucial for gene regulation.
  • The impact of DNA damage on PQS folding kinetics and subsequent gene regulation remains poorly understood.
  • Understanding these mechanisms is vital for comprehending DNA stability and cellular processes.

Approach:

  • Investigated DNA base damage and strand breaks effects on PQS folding kinetics using a duplex-G-quadruplex-duplex (DGD) scaffold mimicking genomic DNA.
  • Monitored folding kinetics via circular dichroism (CD), measuring folding half-lives under various damage conditions.
  • Utilized 1D proton nuclear magnetic resonance (1H-NMR) and CD analyses to confirm G-quadruplex (G4) formation and folding dependencies.

Key Points:

  • Folding half-lives varied from 2 seconds to 12 minutes, dependent on DNA damage type and location.
  • Magnesium ions (Mg2+) and the G4-binding protein APE1 accelerated PQS folding.
  • A strand break near the G-rich regions accelerated folding over 150-fold compared to undamaged DNA.

Conclusions:

  • DNA damage, particularly strand breaks, profoundly influences PQS folding kinetics.
  • The study confirms G4 motif formation in the VEGF promoter DGD construct, dependent on damage.
  • Measured folding half-lives are relevant to DNA replication, transcription, and repair processes.