Conformationally Gated Charge Transfer in DNA Three-Way Junctions.
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.
†Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.
Yuqi
Y
Zhang
‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.|§Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States.
Ryan M
RM
Young
‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
Arun K
AK
Thazhathveetil
‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
Arunoday P N
AP
Singh
†Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.
Chaoren
C
Liu
‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
Yuri A
YA
Berlin
∥DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands.
Ferdinand C
FC
Grozema
‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
Frederick D
FD
Lewis
‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
Mark A
MA
Ratner
∥DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands.
Nicolas
N
Renaud
⊥Materials Chemistry Research Center, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.
Khatcharin
K
Siriwong
#Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain, Institut de Química Computacional, Universitat de Girona, 17071 Girona, Spain.
Alexander A
AA
Voityuk
‡Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.|§Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States.
Michael R
MR
Wasielewski
†Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.|▽Departments of Biochemistry and Physics, Duke University, Durham, North Carolina 27708, United States.
David N
DN
Beratan
D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation / Q000706:statistics & numerical data*
D004247:DNA
DNA; conformational gating,; electron transfer; nucleic acids; three-way junctions