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2000
Volume 13, Issue 1
  • ISSN: 1573-4137
  • E-ISSN: 1875-6786

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.

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/content/journals/cnano/10.2174/1573413712666160720110526
2017-02-01
2025-07-05
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/content/journals/cnano/10.2174/1573413712666160720110526
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  • Article Type:
    Research Article
Keyword(s): DNA nanomotor; G-quadruplex; Hoogsteen H-bonds; MD simulation; tetraplex
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