Conformationally Gated Charge Transfer in DNA Three-Way Junctions

Yuqi Zhang, Ryan M. Young, Arun K. Thazhathveetil, Arunoday P N Singh, Chaoren Liu, Yuri A. Berlin, Ferdinand C. Grozema, Frederick D. Lewis, Mark A Ratner, Nicolas Renaud, Khatcharin Siriwong, Alexander A. Voityuk, Michael R Wasielewski, David N. Beratan

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among well stacked conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups (extenders) lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.

Original languageEnglish
Pages (from-to)2434-2438
Number of pages5
JournalJournal of Physical Chemistry Letters
Volume6
Issue number13
DOIs
Publication statusPublished - Jul 2 2015

Fingerprint

Charge transfer
DNA
deoxyribonucleic acid
charge transfer
Conformations
simulation
Transport properties
Molecular structure
Polyethylene glycols
Molecular dynamics
Switches
glycols
polyethylenes
molecular structure
switches
transport properties
Kinetics
molecular dynamics
Computer simulation
kinetics

Keywords

  • conformational gating
  • DNA
  • electron transfer
  • nucleic acids
  • three-way junctions

ASJC Scopus subject areas

  • Materials Science(all)

Cite this

Zhang, Y., Young, R. M., Thazhathveetil, A. K., Singh, A. P. N., Liu, C., Berlin, Y. A., ... Beratan, D. N. (2015). Conformationally Gated Charge Transfer in DNA Three-Way Junctions. Journal of Physical Chemistry Letters, 6(13), 2434-2438. https://doi.org/10.1021/acs.jpclett.5b00863

Conformationally Gated Charge Transfer in DNA Three-Way Junctions. / Zhang, Yuqi; Young, Ryan M.; Thazhathveetil, Arun K.; Singh, Arunoday P N; Liu, Chaoren; Berlin, Yuri A.; Grozema, Ferdinand C.; Lewis, Frederick D.; Ratner, Mark A; Renaud, Nicolas; Siriwong, Khatcharin; Voityuk, Alexander A.; Wasielewski, Michael R; Beratan, David N.

In: Journal of Physical Chemistry Letters, Vol. 6, No. 13, 02.07.2015, p. 2434-2438.

Research output: Contribution to journalArticle

Zhang, Y, Young, RM, Thazhathveetil, AK, Singh, APN, Liu, C, Berlin, YA, Grozema, FC, Lewis, FD, Ratner, MA, Renaud, N, Siriwong, K, Voityuk, AA, Wasielewski, MR & Beratan, DN 2015, 'Conformationally Gated Charge Transfer in DNA Three-Way Junctions', Journal of Physical Chemistry Letters, vol. 6, no. 13, pp. 2434-2438. https://doi.org/10.1021/acs.jpclett.5b00863
Zhang Y, Young RM, Thazhathveetil AK, Singh APN, Liu C, Berlin YA et al. Conformationally Gated Charge Transfer in DNA Three-Way Junctions. Journal of Physical Chemistry Letters. 2015 Jul 2;6(13):2434-2438. https://doi.org/10.1021/acs.jpclett.5b00863
Zhang, Yuqi ; Young, Ryan M. ; Thazhathveetil, Arun K. ; Singh, Arunoday P N ; Liu, Chaoren ; Berlin, Yuri A. ; Grozema, Ferdinand C. ; Lewis, Frederick D. ; Ratner, Mark A ; Renaud, Nicolas ; Siriwong, Khatcharin ; Voityuk, Alexander A. ; Wasielewski, Michael R ; Beratan, David N. / Conformationally Gated Charge Transfer in DNA Three-Way Junctions. In: Journal of Physical Chemistry Letters. 2015 ; Vol. 6, No. 13. pp. 2434-2438.
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