Abstract
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+ ion by possessing compact TE formation.Keywords: DNA nanomotor, G-quadruplex, Hoogsteen H-bonds, MD simulation, tetraplex.
Graphical Abstract
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