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Reverse Watson-Crick G-G base pair in G-quadruplex formation.

Soma Mondal1, Jyotsna Bhat, Jagannath Jana

  • 1Bose Institute, Centenary Campus, Department of Biophysics, P-1/12 CIT Scheme VIIM, Kankurgachi, Kolkata-54, India. subhro_c@jcbose.ac.in.

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|November 20, 2015
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A stable dimeric G-rich structure, a precursor to G-quadruplexes, was identified. Molecular dynamics and cisplatin adduct formation confirmed reverse Watson-Crick G-G base pairing, not Hoogsteen bonds, in this intermediate.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biophysics

Background:

  • G-rich sequences are known to form G-quadruplex structures.
  • The intermediate structures and their formation pathways remain incompletely understood.

Purpose of the Study:

  • To characterize the stable intermediate dimeric G-rich form.
  • To elucidate the specific G-G base pairing within this dimeric intermediate.
  • To investigate the interaction of cisplatin with the dimeric structure.

Main Methods:

  • Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) spectrometry for detection.
  • Molecular dynamics (MD) simulations for atomic-level insights.
  • Cisplatin adduct formation studies.

Main Results:

  • A stable dimeric G-rich intermediate, a precursor to tetrameric G-quadruplexes, was detected.
  • MD simulations revealed reverse Watson-Crick G-G base pairing within the dimer.
  • Cisplatin formed a stable adduct with the dimer, supporting the absence of Hoogsteen hydrogen bonds.

Conclusions:

  • The dimeric G-rich form utilizes reverse Watson-Crick G-G base pairing.
  • This dimeric structure serves as a key intermediate in G-quadruplex formation.
  • Cisplatin binding confirms the structural characteristics of the dimeric intermediate.