posted on 2020-03-31, 13:34authored byVorasit Vongsutilers, Yoko Shinohara, Gota Kawai
Methylation of cytosine has been
known to play a significant role
in epigenetic regulation. 5-Methylcytosine was among the first base
modification that was discovered for the capability to facilitate
B/Z-DNA transition as observed in CG repeated tracks. A study on gene
repression by Z-DNA prone sequence as in ADAM-12 has ignited our research
interest for the Z-DNA role in epigenetics. Ten eleven translocation
family proteins are responsible to catalyze 5-methylcytosine to produce
oxidative products including 5-hydroxymethylcytosine, 5-formylcytosine,
and 5-carboxycytosine, which each may have unique function rather
than the sole purpose of 5-methylcytosine clearance. Although the
Z-DNA-promoting effect of 5-methylcytosine was well established, the
effect of its oxidative products on Z-DNA remain unknown. In this
study, the Z-DNA-promoting effect of 5-hydroxymethylcytosine, 5-formylcytosine,
and 5-carboxycytosine on the CG decamer model were investigated along
with known Z-DNA stabilizers, 5-methylcytosine and 8-oxoguanine. Experimental
results from circular dichroism (CD) and NMR indicates that all oxidative
products of 5-methylcytosine hinder B/Z-DNA transition as high salt
concentration suitable to stabilize and convert unmodified CG decamer
to Z-DNA conformation is insufficient to facilitate the B/Z-DNA transition
of CG decamer containing 5-hydroxymethylcytosine, 5-formylcytosine,
or 5-carboxycytosine. Molecular dynamic simulation and free energy
calculation by MM-PBSA are in agreement with the experimental finding
that 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine
destabilize Z-DNA conformation of CG decamer, in contrast to its precursor.
Investigation of Z-DNA switch-on/switch-off regulated by 5-methylcytosine
and its oxidative products is a further step to elucidate the potential
of epigenetic regulated via Z-DNA.