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Large-Scale Conformational Analysis Explains G-Quadruplex Topological Landscape.

Michał Jurkowski1, Mateusz Kogut1, Michał Olewniczak1

  • 1Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza St 11/12, Gdańsk 80-233, Poland.

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G-quadruplexes (G4) can form 26 topologies, but only 14 are observed. Long-distance loops and G4 helicity limit G4 folding, explaining observed patterns and aiding G4 structure design.

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Area of Science:

  • * Molecular biology
  • * Structural biology
  • * Bioinformatics

Background:

  • * G-quadruplexes (G4) are four-stranded DNA structures crucial for genome stability and transcription.
  • * G4s are abundant in the human genome, playing vital roles in gene regulation.
  • * Only 14 of 26 theoretical G4 folding topologies have been experimentally observed, raising questions about accessibility and formation determinants.

Purpose of the Study:

  • * To investigate the energetic accessibility of G4 folding topologies.
  • * To identify molecular factors governing G4 folding patterns.
  • * To provide a geometric explanation for the observed G4 topological landscape.

Main Methods:

  • * Computational exploration of G4 conformational space using 128 DNA sequences.
  • * In silico folding procedure to generate nearly 20,000 unique G4 conformations.
  • * Foldability evaluation of G4 conformations across 26 theoretical topologies.

Main Results:

  • * Significant differences in foldability were observed among the 26 theoretical G4 topologies.
  • * Long-distance propeller loops in 12 topologies impose loop length constraints, hindering formation.
  • * G4 helicity governs the occurrence of long-distance propeller loops, influencing folding preferences in right-handed and left-handed G4s.

Conclusions:

  • * The study provides a geometric explanation for G4 folding patterns and topological landscape.
  • * Long-distance loop length and G4 helicity are key determinants of G4 folding.
  • * Findings offer insights for the rational design of G4 structures with specific topologies.