Tuning the pH Response of i-Motif DNA Oligonucleotides

Chembiochem. 2015 Jul 27;16(11):1647-56. doi: 10.1002/cbic.201500182. Epub 2015 Jun 30.


Cytosine-rich single-stranded DNA oligonucleotides are able to adopt an i-motif conformation, a four-stranded structure, near a pH of 6. This unique pH-dependent conformational switch is reversible and hence can be controlled by changing the pH. Here, we show that the pH response range of the human telomeric i-motif can be shifted towards more basic pH values by introducing 5-methylcytidines (5-MeC) and towards more acidic pH values by introducing 5-bromocytidines (5-BrC). No thermal destabilisation was observed in these chemically modified i-motif sequences. The time required to attain the new conformation in response to sudden pH changes was slow for all investigated sequences but was found to be ten times faster in the 5-BrC derivative of the i-motif.

Keywords: bromocytidine; cytosine-rich DNA; i-motifs; methylcytidine; nanodevices; pH sensors; telomeric DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / chemistry
  • Base Sequence
  • Cytosine / analogs & derivatives
  • Cytosine / chemistry
  • DNA, Single-Stranded / chemistry*
  • DNA, Single-Stranded / genetics
  • Humans
  • Hydrogen-Ion Concentration
  • Kinetics
  • Nucleotide Motifs*
  • Oligodeoxyribonucleotides / chemistry*
  • Oligodeoxyribonucleotides / genetics
  • Telomere / genetics
  • Temperature


  • DNA, Single-Stranded
  • Oligodeoxyribonucleotides
  • 5-bromocytosine
  • 5-Methylcytosine
  • Cytosine