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Bag S, Maiti PK. Tuning molecular fluctuation to boost the conductance in DNA based molecular wires. Phys Chem Chem Phys 2019; 21:23514-23520. [PMID: 31617554 DOI: 10.1039/c9cp03589c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na+ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.
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Affiliation(s)
- Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, India.
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2
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Jiménez-Monroy KL, Renaud N, Drijkoningen J, Cortens D, Schouteden K, van Haesendonck C, Guedens WJ, Manca JV, Siebbeles LDA, Grozema FC, Wagner PH. High Electronic Conductance through Double-Helix DNA Molecules with Fullerene Anchoring Groups. J Phys Chem A 2017; 121:1182-1188. [PMID: 28094940 PMCID: PMC5330649 DOI: 10.1021/acs.jpca.7b00348] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Determining
the mechanism of charge transport through native DNA
remains a challenge as different factors such as measuring conditions,
molecule conformations, and choice of technique can significantly
affect the final results. In this contribution, we have used a new
approach to measure current flowing through isolated double-stranded
DNA molecules, using fullerene groups to anchor the DNA to a gold
substrate. Measurements were performed at room temperature in an inert
environment using a conductive AFM technique. It is shown that the
π-stacked B-DNA structure is conserved on depositing the DNA.
As a result, currents in the nanoampere range were obtained for voltages
ranging between ±1 V. These experimental results are supported
by a theoretical model that suggests that a multistep hopping mechanism
between delocalized domains is responsible for the long-range current
flow through this specific type of DNA.
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Affiliation(s)
- Kathia L Jiménez-Monroy
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Nicolas Renaud
- Department of Chemical Engineering, Delft University of Technology , Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Jeroen Drijkoningen
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium.,IMO & X-LaB, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - David Cortens
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | | | | | - Wanda J Guedens
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Jean V Manca
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium.,IMO & X-LaB, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Laurens D A Siebbeles
- Department of Chemical Engineering, Delft University of Technology , Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Ferdinand C Grozema
- Department of Chemical Engineering, Delft University of Technology , Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Patrick H Wagner
- IMO-IMOMEC, Hasselt University , Campus Diepenbeek, Wetenschapspark 1, 3590 Diepenbeek, Belgium
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Levine AD, Iv M, Peskin U. Length-independent transport rates in biomolecules by quantum mechanical unfurling. Chem Sci 2016; 7:1535-1542. [PMID: 28808530 PMCID: PMC5530864 DOI: 10.1039/c5sc03495g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/19/2015] [Indexed: 11/22/2022] Open
Abstract
Experiments on hole transfer in DNA between donor and acceptor moieties revealed transfer rates which are independent of the molecular bridge length (within experimental error). However, the physical origin of this intriguing observation is still unclear. The hopping model implies that the hole propagates in multiple steps along the bridge from one localized state to another, and therefore the longer the bridge, the slower the transfer. This can explain weak length-dependence but not a length-independent transfer rate. We show that the rigid molecular structure of a poly-A bridge supports single step transitions from a localized hole state to delocalized states, spread over the entire bridge. Since propagation to the bridge end is a single step process (termed quantum unfurling) the transfer rate becomes independent of the bridge length. This explanation is consistent with experimental results, and emphasizes the importance of structural order in charge transfer through bio-molecular systems.
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Affiliation(s)
- Ariel D Levine
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
| | - Michael Iv
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
| | - Uri Peskin
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
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Okubo T. Dissipative crystallization of aqueous mixtures of potassium salts of poly(riboguanylic acid) and poly(ribocytidylic acid). Colloid Polym Sci 2014. [DOI: 10.1007/s00396-014-3200-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Ramos P, Pavanello M. Quantifying Environmental Effects on the Decay of Hole Transfer Couplings in Biosystems. J Chem Theory Comput 2014; 10:2546-56. [DOI: 10.1021/ct400921r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Pablo Ramos
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
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6
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Renaud N, Berlin YA, Lewis FD, Ratner MA. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc 2013; 135:3953-63. [PMID: 23402652 DOI: 10.1021/ja3113998] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.
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Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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Osakada Y, Kawai K, Majima T. Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yasuko Osakada
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
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8
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Berlin YA, Voityuk AA, Ratner MA. DNA base pair stacks with high electric conductance: a systematic structural search. ACS NANO 2012; 6:8216-8225. [PMID: 22901272 DOI: 10.1021/nn3030139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.
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Affiliation(s)
- Yuri A Berlin
- Department of Chemistry, Northwestern University, 1145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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Wu J, Walker VEJ, Boyd RJ. Theoretical study of polaron formation in poly(G)-poly(C) cations. J Phys Chem B 2011; 115:3136-45. [PMID: 21384938 DOI: 10.1021/jp108818u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polaron formation in poly(G)-poly(C) cations is investigated with density functional theory (DFT) and molecular mechanics (MM) employing a two-layer ONIOM method. In these calculations, the high layer, composed of all complementary base pairs, is treated by a DFT method, while the low layer, which includes the sugar-phosphate backbone, counterions and water molecules, is described by the AMBER force field. The high layer is the model system in which the charge transfer takes place. According to our calculations, three or four guanines move in a paddle-like fashion when an electron is removed from the neutral model system. In the cation model system, about 80% of the charge is delocalized onto the guanine residues, and the remaining charge is delocalized onto the cytosine residues. This happens because guanine has a lower ionization potential (IP) than cytosine. The counterions and water molecules in the low layer are important in the geometry optimization. The optimized geometry of the model system is closer to the standard B-form structure when counterions and water molecules are included than when they are omitted. Comparison of the optimized neutral and cationic model systems reveals a polaron in poly(G)-poly(C) cations extending from the first to the third guanine. It is demonstrated that the position of counterions and the number of surrounding water molecules can affect polaron formation.
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Affiliation(s)
- Jian Wu
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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de la Harpe K, Crespo-Hernández CE, Kohler B. The excited-state lifetimes in a G x C DNA duplex are nearly independent of helix conformation and base-pairing motif. Chemphyschem 2009; 10:1421-5. [PMID: 19301308 DOI: 10.1002/cphc.200900004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA photophysics: Femtosecond transient absorption experiments reveal that excited states produced by UV light in a duplex DNA oligonucleotide decay at essentially the same rate in B and Z helix conformers (see figure).
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Affiliation(s)
- Kimberly de la Harpe
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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12
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Abstract
Abstract
Aperiodic order plays a very significant role in biology, as it determines most informative content of genomes. Amongst the various physical, chemical or biological phenomena that might be inferred from sequence correlations, charge transfer properties deserve particular attention. Indeed, the nature of DNA-mediated charge migration has been related to the understanding of damage recognition process, protein binding, or with the task of engineering biological processes (e.g. designing nanoscale sensing of genomic mutations), opening new challenges for emerging nanobiotechnologies. Nevertheless, the solution of Schrödinger´s equation with a potential that is given by a one-dimensional array of the double-stranded DNA remains as a main open theme in solid state physics of biological macromolecules. In this contribution, I will shortly review several approaches introduced during the last few years in order to describe charge transfer migration in DNA in terms of tight-binding effective Hamiltonians.
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Kubař T, Kleinekathöfer U, Elstner M. Solvent Fluctuations Drive the Hole Transfer in DNA: A Mixed Quantum−Classical Study. J Phys Chem B 2009; 113:13107-17. [DOI: 10.1021/jp9073587] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Tomáš Kubař
- Institute of Physical Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany, and School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Institute of Physical Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany, and School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany, and School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany
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Cauët E, Liévin J. Ab Initio Study of the Electron Transfer in an Ionized Stacked Complex of Guanines. J Phys Chem A 2009; 113:9881-90. [DOI: 10.1021/jp902426p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Emilie Cauët
- Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles, CP 160/09, 50 Avenue F.D. Roosevelt, B-1050 Bruxelles, Belgium
| | - Jacques Liévin
- Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles, CP 160/09, 50 Avenue F.D. Roosevelt, B-1050 Bruxelles, Belgium
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Starikov E, Quintilla A, Nganou C, Lee K, Cuniberti G, Wenzel W. Single-molecule DNA conductance in water solutions: Role of DNA low-frequency dynamics. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Burin AL, Uskov DB. Strong localization of positive charge in DNA induced by its interaction with environment. J Chem Phys 2008; 129:025101. [PMID: 18624560 DOI: 10.1063/1.2953693] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate a quantum state of positive charge in DNA. A quantum state of electron hole is determined by the competition of the pi-stacking interaction b sharing a charge between different base pairs and the interaction lambda with the local environment which attempts to trap charge. To determine which interaction dominates, we investigate charge quantum states in various (GC)(n) sequences choosing DNA parameters that satisfy experimental data for the balance of charge transfer rates G(+) <--> G(n)(+), n = 2, 3. We show that experimental data can be consistent with theory only assuming b<<lambda, meaning that charge is typically localized within the single G site. Consequently, as follows from our modeling consideration, any DNA duplex including the one consisting of identical base pairs cannot be considered as a molecular conductor. Our theory can be verified experimentally, measuring balance of charge transfer reactions G(+) <--> G(n)(+), n > or = 4 and comparing the experimental results with our predictions.
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Affiliation(s)
- A L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA.
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Siriwong K, Voityuk AA. π Stack Structure and Hole Transfer Couplings in DNA Hairpins and DNA. A Combined QM/MD Study. J Phys Chem B 2008; 112:8181-7. [DOI: 10.1021/jp802222e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Khatcharin Siriwong
- Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Alexander A. Voityuk
- Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
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