Background: The DNA tetraplex (TE) nanomotor is a new nanomotor family constructed
through self-assembly of guanine-rich (G-rich) single strand DNA and produces controlled motion at
the molecular scale.
Objective and Method: In this study, the TE conformation stability of single strand 15-mer G-rich
DNA, GGTTGGTGTGGTTGG, was studied in atomic scale using molecular dynamics simulation
method for the aim of potential application in empowering nanosystems/nanoswitchers.
Results and Conclusion: The study of dynamic behavior of TE conformation indicated that the 15-
mer G-rich DNA is stabilized by eight Hoogsteen hydrogen bonds between NH…O and NH…N
groups resulted in higher-order G-quadruplex conformation as an integral part of TE structure.
Moreover, the higher-order G-quadruplex produces steric hindrance in the ion-free state, disorganizing
rearrangement of Hoogsteen H-bonds leads to “wobble TE” conformation. Data showed that in
the absence of the coordinated K+
, the G bases initially tend to fluctuate and rotate while in the presence
of coordinated ion, the system intends to form compact rigid TE. We propose the single strand
15-mer G-rich DNA as a nanomotor with maximum efficiency in attaching coordinated K+
possessing compact TE formation.