Deprotonation mechanism of a single-stranded DNA i-motif

We present the detailed deprotonation mechanism of a fully protonated DNA i-motif as studied by all-atom Molecular Dynamics simulations. The associated unfolding of the i-motif is driven by the application of the Metadynamics method. The release of two protons, which stabilize the hemi-protonated cy...

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Published in:RSC advances 2014-01, Vol.4 (33), p.17110-17113
Main Authors: Smiatek, Jens, Heuer, Andreas
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Language:English
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description We present the detailed deprotonation mechanism of a fully protonated DNA i-motif as studied by all-atom Molecular Dynamics simulations. The associated unfolding of the i-motif is driven by the application of the Metadynamics method. The release of two protons, which stabilize the hemi-protonated cytosine pairs in the native i-motif, can be identified as the initial step for the occurrence of the unfolding process. By a systematic analysis of the proton motion, we are able to validate a two-step deprotonation mechanism. Our findings are in excellent agreement to experimental results that have been recently published.
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title Deprotonation mechanism of a single-stranded DNA i-motif
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