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SARS-CoV‑2 RNA's Dual Identity: G‑Quadruplex versus Hairpin.

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Computational analysis reveals SARS-CoV-2 G-quadruplexes dynamics. Pseudouridine presence near G-quadruplexes stabilizes hairpins but destabilizes G-quadruplex structures, potentially unwinding them.

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Area of Science:

  • Computational biology
  • Structural biology
  • Virology

Background:

  • High-resolution structural characterization of G-quadruplexes remains challenging despite biophysical assay advancements.
  • SARS-CoV-2 contains potential G-quadruplex forming regions critical for viral function.

Purpose of the Study:

  • To computationally investigate the 2D and 3D geometry, energetics, and dynamics of a specific SARS-CoV-2 G-quadruplex.
  • To examine the influence of pseudouridine on G-quadruplex and hairpin stability.

Main Methods:

  • Bioinformatic tools were employed to predict structures.
  • Analysis of G-quadruplex and hairpin dynamics, relative stability, and impact of pseudouridine.
  • Investigation of Hoogsteen connections' role in G-quadruplex stabilization.

Main Results:

  • Predicted 2D and 3D structures for four G4-Quadruplexes and three hairpins.
  • Hypothesized that Hoogsteen connections are crucial for G-quadruplex dynamic stability.
  • Observed that pseudouridine enhances hairpin stability and destabilizes G-quadruplexes, potentially causing unwinding.

Conclusions:

  • The number of Hoogsteen connections is a critical determinant of G-quadruplex dynamic stability.
  • Pseudouridine's proximity to SARS-CoV-2 G-quadruplexes can significantly alter nucleic acid structure and stability.