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Probing Synergistic Effects of DNA Methylation and 2'-β-Fluorination on i-Motif Stability

Hala Abou Assi1, Yu Chen Lin1, Israel Serrano2

  • 1Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.

Chemistry (Weinheim an Der Bergstrasse, Germany)
|November 3, 2017
PubMed

Insights

Recent studies suggest DNA i-motif structures are crucial for telomere biology and gene regulation. This study found that specific modified nucleosides, 5-methyl-2'-deoxy-2'-fluoro-arabinocytidine and 2'-deoxy-2'-fluoro-arabinocytidine, stabilize i-motif structures at physiological pH.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Genetics

Background:

  • DNA i-motif structures are increasingly recognized for their roles in telomere maintenance and gene transcription.
  • Understanding the factors influencing i-motif stability is crucial for exploring their biological functions.

Purpose of the Study:

  • To investigate the impact of four cytidine nucleoside modifications on DNA i-motif structure and stability.
  • To identify modifications that promote i-motif formation and stability under physiological conditions.

Main Methods:

  • Synthesis and characterization of four modified cytidine nucleosides: 2 omino-deoxycytidine (dC), 2 omino-deoxy-5-methyl-cytidine (5-Me-dC), 2 omino-deoxy-2 omino-fluoro-arabinocytidine (2 ominoF-araC), and 2 omino-deoxy-2 omino-fluoro-5-methyl-arabinocytidine (5-Me-2 ominoF-araC).
  • pH-dependent stability measurements (pH1/2) to assess i-motif stability.
  • Nuclear Magnetic Resonance (NMR) spectroscopy to elucidate the structural basis of stabilization.

Main Results:

  • The base pair 5-Me-2 ominoF-araC:2 ominoF-araC formed i-motif structures with a pH1/2 value of 7.34±0.3, closely matching physiological pH.
  • NMR analysis of a stable telomeric sequence (HJ-2) at pH 7.0 revealed stabilization by hybrid 5-Me-dC:2 ominoF-araC hemiprotonated base pairs.
  • The study highlights the synergistic effect of base and sugar modifications on i-motif stability.

Conclusions:

  • Specific combinations of base and sugar modifications can significantly enhance the stability of DNA i-motif structures.
  • The findings suggest that modified cytidine nucleosides can stabilize i-motif structures at physiological pH, with implications for telomere biology and gene regulation.
  • The interplay between base and sugar modifications is a key determinant of i-motif structural stability.
Keywords:
5-methylcytosinebiological chemistryepigenetic modificationsnucleosidestelomeric DNA

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