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 language | English |
|---|---|
| Pages (from-to) | 2434-2438 |
| Number of pages | 5 |
| Journal | Journal of Physical Chemistry Letters |
| Volume | 6 |
| Issue number | 13 |
| DOIs | |
| Publication status | Published - Jul 2 2015 |
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Keywords
- conformational gating
- DNA
- electron transfer
- nucleic acids
- three-way junctions
ASJC Scopus subject areas
- Materials Science(all)
Cite this
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 journal › Article
}
TY - JOUR
T1 - Conformationally Gated Charge Transfer in DNA Three-Way Junctions
AU - Zhang, Yuqi
AU - Young, Ryan M.
AU - Thazhathveetil, Arun K.
AU - Singh, Arunoday P N
AU - Liu, Chaoren
AU - Berlin, Yuri A.
AU - Grozema, Ferdinand C.
AU - Lewis, Frederick D.
AU - Ratner, Mark A
AU - Renaud, Nicolas
AU - Siriwong, Khatcharin
AU - Voityuk, Alexander A.
AU - Wasielewski, Michael R
AU - Beratan, David N.
PY - 2015/7/2
Y1 - 2015/7/2
N2 - 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.
AB - 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.
KW - conformational gating
KW - DNA
KW - electron transfer
KW - nucleic acids
KW - three-way junctions
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UR - http://www.scopus.com/inward/citedby.url?scp=84947582541&partnerID=8YFLogxK
U2 - 10.1021/acs.jpclett.5b00863
DO - 10.1021/acs.jpclett.5b00863
M3 - Article
VL - 6
SP - 2434
EP - 2438
JO - Journal of Physical Chemistry Letters
JF - Journal of Physical Chemistry Letters
SN - 1948-7185
IS - 13
ER -