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G-triplex structure and formation propensity.

Linda Cerofolini1, Jussara Amato2, Andrea Giachetti3

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The first experimental G-triplex DNA structure of a thrombin binding aptamer (TBA) fragment was determined. This G-triplex folding is stabilized by potassium ions and provides insight into guanine-rich sequences in vivo.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Oligonucleotide Chemistry

Background:

  • G-triplex DNA structures are increasingly recognized for their biological relevance.
  • Thrombin binding aptamer (TBA) folding intermediates have been computationally predicted.
  • Experimental evidence for G-triplex folding in TBA fragments was previously limited.

Purpose of the Study:

  • To determine the solution structure of a 3' end TBA-truncated 11-mer oligonucleotide (11-mer-3'-t-TBA).
  • To provide the first experimental G-triplex DNA structure stabilized by potassium ions.
  • To compare the experimental structure with computationally predicted models.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy
  • Circular Dichroism (CD) spectroscopy
  • Differential Scanning Calorimetry (DSC)
  • X-ray crystallography (implied by structure determination)

Main Results:

  • The solution structure of 11-mer-3'-t-TBA revealed a stable G-triplex DNA conformation.
  • This G-triplex is stabilized by a network of Hoogsteen-like hydrogen bonds and potassium ions.
  • The experimental structure closely matched metadynamics predictions, with minor loop differences.
  • Only 11-mer-3'-t-TBA among tested constructs formed a stable G-triplex.

Conclusions:

  • 11-mer-3'-t-TBA adopts a stable G-triplex DNA conformation.
  • Potassium ions are crucial for stabilizing this G-triplex structure.
  • The findings support the in vivo occurrence of G-triplex folding intermediates in human guanine-rich sequences.