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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

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A pH-Responsive Topological Switch Based on a DNA Quadruplex-Duplex Hybrid.

Yoanes Maria Vianney1, Jagannath Jana1, Klaus Weisz1

  • 1Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489, Greifswald, Germany.

Chemistry (Weinheim an Der Bergstrasse, Germany)
|March 18, 2024
PubMed
Summary
This summary is machine-generated.

This study reveals a novel DNA structure that changes shape with pH, forming unique quadruplex-duplex hybrids. This reversible pH-dependent folding offers potential for developing new biosensors.

Keywords:
G-quadruplexesNMR spectroscopymolecular switchquadruplex-duplex junctiontopology

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • Guanine-rich oligonucleotides can form G-quadruplex structures.
  • Telomeric sequences are known to fold into G-quadruplexes.
  • Hybrid structures combining quadruplex and duplex DNA offer unique functionalities.

Purpose of the Study:

  • To investigate the pH-dependent folding of a modified human telomeric oligonucleotide.
  • To characterize the structural transitions and the formation of quadruplex-duplex hybrids.
  • To explore the potential of this architecture as a pH-sensing system.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy for high-resolution structure determination.
  • pH titration experiments in a potassium-containing buffer.
  • Conformation-sensitive optical readout using thiazole orange dye.

Main Results:

  • The oligonucleotide exhibits pH-dependent folding into distinct quadruplex-duplex hybrid structures.
  • At acidic pH, a chair-type quadruplex conformation is observed.
  • A transition to a (3+1) hybrid topology with a duplex stem-loop occurs near neutral pH, stabilized by adenine protonation and a non-canonical base quartet.
  • The structural transition is reversible and can be optically monitored.

Conclusions:

  • A novel quadruplex-duplex hybrid architecture demonstrates reversible pH-dependent structural transitions.
  • Adenine protonation plays a critical role in stabilizing the acidic conformation.
  • This system shows promise as a pH sensor within the physiological range of 7±1.