Computational Probing of Watson–Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine

DNA
breathing is a local conformational fluctuation spontaneously occurring
in double-stranded DNAs. In particular, the possibility of individual
base pairs (bps) in duplex DNA to flip between alternate bp modes,
i.e., Watson–Crick (WC)-like and Hoogsteen (HG)-like, at relevant
time scales has impacted DNA research fields for many years. In this
study, to computationally probe effects of chemical modification on
the DNA breathing, we present a free energy landscape of spontaneous
thermal transitions between WC and HG bps in a free DNA duplex containing
N1-methylated adenine (m1A). For the current free energy computation,
a variant of well-tempered metadynamics simulation was extensively
performed for a total of 40 μs to produce free energy surfaces.
The free energy profile indicated that, upon the chemical modification
of adenine, the HG bp (m1A·T) was located in the most favorable
conformation (96.7%); however, the canonical WC bp (m1A·T) was
distorted into two WC-like bps of WC* (2.8%) and WC** (0.5%). The
conformational exchange between these two minor WC-like bps occurs
with the first hundred nanoseconds. The transition between WC-like
and HG bp features multiple transition pathways displaying various
extents of base flipping in combination with glycosidic rotation.
Analysis of the simulated ensemble showed that the m1A-induced changes
of the backbone and sugar pucker were in a reasonable agreement with
previous results inferred from NMR experiments. Also, this study revealed
that the formation of the stable HG bp upon the mutation alters the
characteristics of dynamic fluctuations of the neighboring WC residues
of m1A. We expect this simulation approach to be a robust computational
scheme to complement and guide future high-resolution experiments
on many outstanding issues of duplex DNA breathing.