Charge transport in DNA nanowires connected to carbon nanotubes
Abstract
DNA is perhaps the worlds most controllable nanowire, with potential applications in nanoelectronics and sensing. However, understanding of its charge transport (CT) properties remains elusive, with experiments reporting a wide range of behaviors from insulating to superconductive. Here, we report extensive first-principle simulations that account for DNA's high flexibility and its native solvent environment. The results show that the CT along the DNA's long axis is strongly dependent on DNA's instantaneous conformation varying over many orders of magnitude. In high CT conformations, delocalized conductive states extending over up to 10 base pairs are found. Their low exponential decay constants further indicate that coherent CT, which is assumed to be active only over 2–3 base pairs in the commonly accepted DNA CT models, can act over much longer length scales. We also identify a simple geometrical rule that predicts CT properties of a given conformation with high accuracy. The effect of mismatched base pairs is also considered: while they decrease conductivities of specific DNA conformations, thermally induced conformational fluctuations wash out this effect. Overall, our results indicate that an immobilized partially dried poly(G)-poly(C) B-DNA is preferable for nanowire applications.
- Authors:
-
- North Carolina State Univ., Raleigh, NC (United States). Center for High Performance Simulation and Dept. of Physics
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); North Carolina State University, Raleigh, NC (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1565367
- Alternate Identifier(s):
- OSTI ID: 1212225
- Grant/Contract Number:
- FG02-98ER45685
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Physical Review. B, Condensed Matter and Materials Physics
- Additional Journal Information:
- Journal Volume: 92; Journal Issue: 7; Journal ID: ISSN 1098-0121
- Publisher:
- American Physical Society (APS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; Materials Science; Physics
Citation Formats
Tan, Bikan, Hodak, Miroslav, Lu, Wenchang, and Bernholc, J. Charge transport in DNA nanowires connected to carbon nanotubes. United States: N. p., 2015.
Web. doi:10.1103/physrevb.92.075429.
Tan, Bikan, Hodak, Miroslav, Lu, Wenchang, & Bernholc, J. Charge transport in DNA nanowires connected to carbon nanotubes. United States. https://doi.org/10.1103/physrevb.92.075429
Tan, Bikan, Hodak, Miroslav, Lu, Wenchang, and Bernholc, J. Wed .
"Charge transport in DNA nanowires connected to carbon nanotubes". United States. https://doi.org/10.1103/physrevb.92.075429. https://www.osti.gov/servlets/purl/1565367.
@article{osti_1565367,
title = {Charge transport in DNA nanowires connected to carbon nanotubes},
author = {Tan, Bikan and Hodak, Miroslav and Lu, Wenchang and Bernholc, J.},
abstractNote = {DNA is perhaps the worlds most controllable nanowire, with potential applications in nanoelectronics and sensing. However, understanding of its charge transport (CT) properties remains elusive, with experiments reporting a wide range of behaviors from insulating to superconductive. Here, we report extensive first-principle simulations that account for DNA's high flexibility and its native solvent environment. The results show that the CT along the DNA's long axis is strongly dependent on DNA's instantaneous conformation varying over many orders of magnitude. In high CT conformations, delocalized conductive states extending over up to 10 base pairs are found. Their low exponential decay constants further indicate that coherent CT, which is assumed to be active only over 2–3 base pairs in the commonly accepted DNA CT models, can act over much longer length scales. We also identify a simple geometrical rule that predicts CT properties of a given conformation with high accuracy. The effect of mismatched base pairs is also considered: while they decrease conductivities of specific DNA conformations, thermally induced conformational fluctuations wash out this effect. Overall, our results indicate that an immobilized partially dried poly(G)-poly(C) B-DNA is preferable for nanowire applications.},
doi = {10.1103/physrevb.92.075429},
journal = {Physical Review. B, Condensed Matter and Materials Physics},
number = 7,
volume = 92,
place = {United States},
year = {Wed Aug 19 00:00:00 EDT 2015},
month = {Wed Aug 19 00:00:00 EDT 2015}
}
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Works referenced in this record:
Generalized Gradient Approximation Made Simple
journal, October 1996
- Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
- Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868
Absence of dc-Conductivity in -DNA
journal, December 2000
- de Pablo, P. J.; Moreno-Herrero, F.; Colchero, J.
- Physical Review Letters, Vol. 85, Issue 23
Charge-Transfer and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide as a Base-Pair Surrogate
journal, October 2008
- Zeidan, Tarek A.; Carmieli, Raanan; Kelley, Richard F.
- Journal of the American Chemical Society, Vol. 130, Issue 42
Sensitivity of DNA-Mediated Electron Transfer to the Intervening π-Stack: A Probe for the Integrity of the DNA Base Stack
journal, May 1997
- Hall, Daniel B.; Barton, Jacqueline K.
- Journal of the American Chemical Society, Vol. 119, Issue 21
DNA-mediated charge transport for DNA repair
journal, October 2003
- Boon, E. M.; Livingston, A. L.; Chmiel, N. H.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 22
Direct Conductance Measurement of Single DNA Molecules in Aqueous Solution
journal, June 2004
- Xu,
- Nano Letters, Vol. 4, Issue 6
Ab initio study of electron transport in dry poly(G)-poly(C) -DNA strands
journal, September 2010
- Pemmaraju, C. D.; Rungger, I.; Chen, X.
- Physical Review B, Vol. 82, Issue 12
Linear-response formulation for mesoscopic systems with arbitrary interactions
journal, October 1992
- Datta, Supriyo
- Physical Review B, Vol. 46, Issue 15
Polarons in DNA
journal, April 2000
- Conwell, E. M.; Rakhmanova, S. V.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 9
Unified model for conductance through DNA with the Landauer-Büttiker formalism
journal, February 2013
- Qi, Jianqing; Edirisinghe, Neranjan; Rabbani, M. Golam
- Physical Review B, Vol. 87, Issue 8
Conductivity of a single DNA duplex bridging a carbon nanotube gap
journal, February 2008
- Guo, Xuefeng; Gorodetsky, Alon A.; Hone, James
- Nature Nanotechnology, Vol. 3, Issue 3
Long-range oxidative damage to cytosines in duplex DNA
journal, December 2004
- Shao, F.; O'Neill, M. A.; Barton, J. K.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 52
Scalable molecular dynamics with NAMD
journal, January 2005
- Phillips, James C.; Braun, Rosemary; Wang, Wei
- Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
Ultrafast Dynamics in DNA-Mediated Electron Transfer: Base Gating and the Role of Temperature
journal, December 2003
- O'Neill, Melanie A.; Becker, Hans-Christian; Wan, Chaozhi
- Angewandte Chemie, Vol. 115, Issue 47
Comparison of Electronic Transport Measurements on Organic Molecules
journal, November 2003
- Salomon, A.; Cahen, D.; Lindsay, S.
- Advanced Materials, Vol. 15, Issue 22
Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects
journal, May 2005
- Voityuk, Alexander A.
- The Journal of Chemical Physics, Vol. 122, Issue 20
Direct measurement of electrical transport through single DNA molecules of complex sequence
journal, August 2005
- Cohen, H.; Nogues, C.; Naaman, R.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 33
Electrical Resistance of Long Conjugated Molecular Wires
journal, June 2008
- Ho Choi, S.; Kim, B.; Frisbie, C. D.
- Science, Vol. 320, Issue 5882
Intermediate tunnelling–hopping regime in DNA charge transport
journal, February 2015
- Xiang, Limin; Palma, Julio L.; Bruot, Christopher
- Nature Chemistry, Vol. 7, Issue 3
Colloquium : The quest for high-conductance DNA
journal, January 2004
- Endres, R. G.; Cox, D. L.; Singh, R. R. P.
- Reviews of Modern Physics, Vol. 76, Issue 1
Mechanisms for DNA Charge Transport
journal, March 2010
- Genereux, Joseph C.; Barton, Jacqueline K.
- Chemical Reviews, Vol. 110, Issue 3
Temperature Dependence of Electrochemical DNA Charge Transport: Influence of a Mismatch
journal, January 2013
- Wohlgamuth, Chris H.; McWilliams, Marc A.; Slinker, Jason D.
- Analytical Chemistry, Vol. 85, Issue 3
DNA charge transport over 34 nm
journal, January 2011
- Slinker, Jason D.; Muren, Natalie B.; Renfrew, Sara E.
- Nature Chemistry, Vol. 3, Issue 3
Direct measurement of electrical transport through DNA molecules
journal, February 2000
- Porath, Danny; Bezryadin, Alexey; de Vries, Simon
- Nature, Vol. 403, Issue 6770
Density-functional method for nonequilibrium electron transport
journal, March 2002
- Brandbyge, Mads; Mozos, José-Luis; Ordejón, Pablo
- Physical Review B, Vol. 65, Issue 16, Article No. 165401
Electronic energy delocalization and dissipation in single- and double-stranded DNA
journal, March 2007
- Buchvarov, I.; Wang, Q.; Raytchev, M.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 12
Towards grid-based density-functional theory methods: Optimized nonorthogonal orbitals and multigrid acceleration
journal, July 2000
- Fattebert, J. -L.; Bernholc, J.
- Physical Review B, Vol. 62, Issue 3
PNA versus DNA: Effects of Structural Fluctuations on Electronic Structure and Hole-Transport Mechanisms
journal, September 2008
- Hatcher, Elizabeth; Balaeff, Alexander; Keinan, Shahar
- Journal of the American Chemical Society, Vol. 130, Issue 35
Rapid Electron Tunneling Through Oligophenylenevinylene Bridges
journal, February 2001
- Sikes, H. D.
- Science, Vol. 291, Issue 5508
CASSCF/CAS-PT2 Study of Hole Transfer in Stacked DNA Nucleobases
journal, May 2006
- Blancafort, Lluís; Voityuk, Alexander A.
- The Journal of Physical Chemistry A, Vol. 110, Issue 20
Toward DNA Conductivity: A Theoretical Perspective
journal, May 2010
- Mallajosyula, Sairam S.; Pati, Swapan K.
- The Journal of Physical Chemistry Letters, Vol. 1, Issue 12
Polarons in DNA Oligomers
journal, January 2010
- Kucherov, Victor M.; Kinz-Thompson, Colin D.; Conwell, Esther M.
- The Journal of Physical Chemistry C, Vol. 114, Issue 3
Effect of hydration on electrical conductivity of DNA duplex: Green’s function study combined with DFT
journal, February 2012
- Maeda, Yaku; Okamoto, Akisumi; Hoshiba, Yasuhiro
- Computational Materials Science, Vol. 53, Issue 1
Long-range photoinduced electron transfer through a DNA helix
journal, November 1993
- Murphy, C.; Arkin, M.; Jenkins, Y.
- Science, Vol. 262, Issue 5136
Evidence of Formation of Adenine Dimer Cation Radical in DNA: The Importance of Adenine Base Stacking
journal, April 2010
- Kobayashi, Kazuo
- The Journal of Physical Chemistry B, Vol. 114, Issue 16
Hole Size and Energetics in Double Helical DNA: Competition between Quantum Delocalization and Solvation Localization
journal, January 2002
- Kurnikov, I. V.; Tong, G. S. M.; Madrid, M.
- The Journal of Physical Chemistry B, Vol. 106, Issue 1
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
journal, September 2003
- Lu, X. -J.
- Nucleic Acids Research, Vol. 31, Issue 17
Study of single-nucleotide polymorphisms by means of electrical conductance measurements
journal, November 2005
- Hihath, J.; Xu, B.; Zhang, P.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 47
Charge Transport in DNA Via Thermally Induced Hopping
journal, December 2001
- Bixon, Mordechai; Jortner, Joshua
- Journal of the American Chemical Society, Vol. 123, Issue 50
Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling
journal, July 2001
- Giese, Bernd; Amaudrut, Jérôme; Köhler, Anne-Kathrin
- Nature, Vol. 412, Issue 6844
Effect of Solvation on Hole Motion in DNA
journal, February 2002
- Basko, D. M.; Conwell, E. M.
- Physical Review Letters, Vol. 88, Issue 9
Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics
journal, January 2006
- Wagenknecht, Hans-Achim
- Natural Product Reports, Vol. 23, Issue 6
Long-Distance Charge Transport in DNA: The Hopping Mechanism
journal, September 2000
- Giese, Bernd
- Accounts of Chemical Research, Vol. 33, Issue 9
Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions
journal, April 2007
- Mahapatro, Ajit K.; Jeong, Kyung J.; Lee, Gil U.
- Nanotechnology, Vol. 18, Issue 19
Mechanism of Charge Transport in DNA: Internally-Linked Anthraquinone Conjugates Support Phonon-Assisted Polaron Hopping
journal, October 1999
- Ly, Danith; Sanii, Laurie; Schuster, Gary B.
- Journal of the American Chemical Society, Vol. 121, Issue 40
An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids
journal, August 2000
- Feller, Scott E.; MacKerell, Alexander D.
- The Journal of Physical Chemistry B, Vol. 104, Issue 31
Solvent Effects on Charge Spatial Extent in DNA and Implications for Transfer
journal, August 2007
- Mantz, Yves A.; Gervasio, Francesco Luigi; Laino, Teodoro
- Physical Review Letters, Vol. 99, Issue 5
Electrical Conduction through Poly(dA)-Poly(dT) and Poly(dG)-Poly(dC) DNA Molecules
journal, October 2001
- Yoo, K. -H.; Ha, D. H.; Lee, J. -O.
- Physical Review Letters, Vol. 87, Issue 19
Between Superexchange and Hopping: An Intermediate Charge-Transfer Mechanism in Poly(A)-Poly(T) DNA Hairpins
journal, February 2013
- Renaud, Nicolas; Berlin, Yuri A.; Lewis, Frederick D.
- Journal of the American Chemical Society, Vol. 135, Issue 10
Hole Migration in DNA: a Theoretical Analysis of the Role of Structural Fluctuations
journal, February 2002
- Troisi, Alessandro; Orlandi, Giorgio
- The Journal of Physical Chemistry B, Vol. 106, Issue 8
DNA Charge Transport: Conformationally Gated Hopping through Stacked Domains
journal, September 2004
- O'Neil, Melanie A.; Barton, Jacqueline K.
- Journal of the American Chemical Society, Vol. 126, Issue 37
DNA-Mediated Charge Transport Requires Conformational Motion of the DNA Bases: Elimination of Charge Transport in Rigid Glasses at 77 K
journal, October 2004
- O‘Neill, Melanie A.; Barton, Jacqueline K.
- Journal of the American Chemical Society, Vol. 126, Issue 41
Insulating Behavior of -DNA on the Micron Scale
journal, October 2002
- Zhang, Y.; Austin, R. H.; Kraeft, J.
- Physical Review Letters, Vol. 89, Issue 19
Oxidative DNA damage through long-range electron transfer
journal, August 1996
- Hall, Daniel B.; Holmlin, R. Erik; Barton, Jacqueline K.
- Nature, Vol. 382, Issue 6593
real-space method for ab initio quantum transport calculations: Application to carbon nanotube–metal contacts
journal, December 2001
- Nardelli, Marco Buongiorno; Fattebert, J. -L.; Bernholc, J.
- Physical Review B, Vol. 64, Issue 24
Electron Transfer Between Bases in Double Helical DNA
journal, January 1999
- Kelley, S. O.
- Science, Vol. 283, Issue 5400
Conductance, curves, and negative differential resistance of carbon atomic wires
journal, July 2001
- Larade, Brian; Taylor, Jeremy; Mehrez, H.
- Physical Review B, Vol. 64, Issue 7
Soft self-consistent pseudopotentials in a generalized eigenvalue formalism
journal, April 1990
- Vanderbilt, David
- Physical Review B, Vol. 41, Issue 11, p. 7892-7895
Long-range oxidative damage to DNA: Effects of distance and sequence
journal, February 1999
- Núñez, Megan E.; Hall, Daniel B.; Barton, Jacqueline K.
- Chemistry & Biology, Vol. 6, Issue 2
Sequence Dependent Electron Transport in Wet DNA: Ab initio and Molecular Dynamics Studies
journal, October 2008
- Mallajosyula, Sairam S.; Lin, J. C.; Cox, D. L.
- Physical Review Letters, Vol. 101, Issue 17
Proximity-Induced Superconductivity in DNA
journal, January 2001
- Kasumov, A. Yu.
- Science, Vol. 291, Issue 5502
Charge Migration along the DNA Duplex: Hole versus Electron Transport
journal, January 2008
- Elias, Benjamin; Shao, Fangwei; Barton, Jacqueline K.
- Journal of the American Chemical Society, Vol. 130, Issue 4
A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation
journal, November 1997
- Young, M. A.; Ravishanker, G.; Beveridge, D. L.
- Biophysical Journal, Vol. 73, Issue 5
Sequence Dependent Long Range Hole Transport in DNA
journal, December 1998
- Meggers, Eric; Michel-Beyerle, Maria E.; Giese, Bernd
- Journal of the American Chemical Society, Vol. 120, Issue 49
Long-distance charge transport in duplex DNA: The phonon-assisted polaron-like hopping mechanism
journal, July 1999
- Henderson, P. T.; Jones, D.; Hampikian, G.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 15
Single-Step Charge Transport through DNA over Long Distances
journal, March 2011
- Genereux, Joseph C.; Wuerth, Stephanie M.; Barton, Jacqueline K.
- Journal of the American Chemical Society, Vol. 133, Issue 11
Charge Migration in DNA: Ion-Gated Transport
journal, October 2001
- Barnett, R. N.
- Science, Vol. 294, Issue 5542
Charge transport in DNA in solution: The role of polarons
journal, June 2005
- Conwell, E. M.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 25
Sequence Dependence of Charge Transport through DNA Domains
journal, December 2005
- Shao, Fangwei; Augustyn, Katherine; Barton, Jacqueline K.
- Journal of the American Chemical Society, Vol. 127, Issue 49
Nonequilibrium Quantum Transport Properties of Organic Molecules on Silicon
journal, November 2005
- Lu, Wenchang; Meunier, Vincent; Bernholc, J.
- Physical Review Letters, Vol. 95, Issue 20
Works referencing / citing this record:
Molecular rectifier composed of DNA with high rectification ratio enabled by intercalation
journal, April 2016
- Guo, Cunlan; Wang, Kun; Zerah-Harush, Elinor
- Nature Chemistry, Vol. 8, Issue 5
Effect of interstitial palladium on plasmon-driven charge transfer in nanoparticle dimers
journal, April 2018
- Lerch, Sarah; Reinhard, Björn M.
- Nature Communications, Vol. 9, Issue 1