Tricky Topology: Persistence of Folded Human Telomeric i-Motif DNA at Ambient Temperature and Neutral pH

• Main Authors: Mahmoud A. S. Abdelhamid, Zoë A. E. Waller
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2020-01-01
• Series: Frontiers in Chemistry
• Subjects: i-motif; cytosine; quadruplex; DNA; topology; kinetics
• Online Access: https://www.frontiersin.org/article/10.3389/fchem.2020.00040/full

i-Motifs are four-stranded DNA structures formed from sequences rich in cytosine, held together by hemi-protonated cytosine-cytosine base pairs. These structures have been utilized extensively as pH-switches in DNA-based nanotechnology. Recently there has been an increasing interest in i-motif structures in biology, fuelled by examples of when these can form under neutral conditions. Herein we describe a cautionary tale regarding handling of i-motif samples. Using CD and UV spectroscopy we show that it is important to be consistent in annealing i-motif DNA samples as at neutral pH, i-motif unfolding kinetics is dependent on the time allowed for annealing and equilibration. We describe how the quadruplex structure formed by the human telomeric i-motif sequence can be shown to form and persist in the same conditions of neutral pH and ambient temperature in which, once at thermodynamic equilibrium, it exists predominantly as a random coil. This study has implications not only for work with i-motif DNA structures, but also in the uses and applications of these in nanotechnological devices.