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Herb D, Rossini M, Ankerhold J. Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence. Phys Rev E 2024; 109:064413. [PMID: 39020927 DOI: 10.1103/physreve.109.064413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/21/2024] [Indexed: 07/20/2024]
Abstract
After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.
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2
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Siebert R, Ammerpohl O, Rossini M, Herb D, Rau S, Plenio MB, Jelezko F, Ankerhold J. A quantum physics layer of epigenetics: a hypothesis deduced from charge transfer and chirality-induced spin selectivity of DNA. Clin Epigenetics 2023; 15:145. [PMID: 37684676 PMCID: PMC10492394 DOI: 10.1186/s13148-023-01560-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Epigenetic mechanisms are informational cellular processes instructing normal and diseased phenotypes. They are associated with DNA but without altering the DNA sequence. Whereas chemical processes like DNA methylation or histone modifications are well-accepted epigenetic mechanisms, we herein propose the existence of an additional quantum physics layer of epigenetics. RESULTS We base our hypothesis on theoretical and experimental studies showing quantum phenomena to be active in double-stranded DNA, even under ambient conditions. These phenomena include coherent charge transfer along overlapping pi-orbitals of DNA bases and chirality-induced spin selectivity. Charge transfer via quantum tunneling mediated by overlapping orbitals results in charge delocalization along several neighboring bases, which can even be extended by classical (non-quantum) electron hopping. Such charge transfer is interrupted by flipping base(s) out of the double-strand e.g., by DNA modifying enzymes. Charge delocalization can directly alter DNA recognition by proteins or indirectly by DNA structural changes e.g., kinking. Regarding sequence dependency, charge localization, shown to favor guanines, could influence or even direct epigenetic changes, e.g., modification of cytosines in CpG dinucleotides. Chirality-induced spin selectivity filters electrons for their spin along DNA and, thus, is not only an indicator for quantum coherence but can potentially affect DNA binding properties. CONCLUSIONS Quantum effects in DNA are prone to triggering and manipulation by external means. By the hypothesis put forward here, we would like to foster research on "Quantum Epigenetics" at the interface of medicine, biology, biochemistry, and physics to investigate the potential epigenetic impact of quantum physical principles on (human) life.
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Affiliation(s)
- Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany.
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Mirko Rossini
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
| | - Dennis Herb
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
| | - Sven Rau
- Institute of Inorganic Chemistry I, Ulm University, 89081, Ulm, Germany
| | - Martin B Plenio
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute of Theoretical Physics, Ulm University, 89081, Ulm, Germany
| | - Fedor Jelezko
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Quantum Optics, Ulm University, 89081, Ulm, Germany
| | - Joachim Ankerhold
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
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3
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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Capobianco A, Landi A, Peluso A. Modeling DNA oxidation in water. Phys Chem Chem Phys 2018; 19:13571-13578. [PMID: 28513687 DOI: 10.1039/c7cp02029e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel set of hole-site energies and electronic coupling parameters to be used, in the framework of the simplest tight-binding approximation, for predicting DNA hole trapping efficiencies and rates of hole transport in oxidized DNA is proposed. The novel parameters, significantly different from those previously reported in the literature, have been inferred from reliable density functional calculations, including both the sugar-phosphate ionic backbone and the effects of the aqueous environment. It is shown that most of the experimental oxidation free energies of DNA tracts and of oligonucleotides available from photoelectron spectroscopy and voltammetric measurements are reproduced with great accuracy, without the need for introducing sequence dependent parameters.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, I-84084 Fisciano (SA), Italy.
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5
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Na S, Bauß A, Langenmaier M, Koslowski T. Thermodynamic integration network study of electron transfer: from proteins to aggregates. Phys Chem Chem Phys 2017; 19:18938-18947. [DOI: 10.1039/c7cp03030d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe electron transfer through the NrfHA nitrite reductase using a thermodynamic integration scheme. Driving forces are hardly affected by dimerization, but the transport mechanism only emerges simulating the dimer.
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Affiliation(s)
- Sehee Na
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Anna Bauß
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Michael Langenmaier
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
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6
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Burggraf F, Koslowski T. Charge transfer through a cytochrome multiheme chain: Theory and simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:186-92. [DOI: 10.1016/j.bbabio.2013.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/22/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
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7
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Schill M, Koslowski T. Sensing organic molecules by charge transfer through aptamer-target complexes: theory and simulation. J Phys Chem B 2013; 117:475-83. [PMID: 23227783 DOI: 10.1021/jp308042n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aptamers, i.e., short sequences of RNA and single-stranded DNA, are capable of specificilly binding objects ranging from small molecules over proteins to entire cells. Here, we focus on the structure, stability, dynamics, and electronic properties of oligonucleotides that interact with aromatic or heterocyclic targets. Large-scale molecular dynamics simulations indicate that aromatic rings such as dyes, metabolites, or alkaloides form stable adducts with their oligonucleotide host molecules at least on the simulation time scale. From molecular dynamics snapshots, the energy parameters relevant to Marcus' theory of charge transfer are computed using a modified Su-Schrieffer-Heeger Hamiltonian, permitting an estimate of the charge transfer rates. In many cases, aptamer binding seriously influences the charge transfer kinetics and the charge carrier mobility within the complex, with conductivities up to the nanoampere range for a single complex. We discuss the conductivity properties with reference to potential applications as biosensors.
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Affiliation(s)
- Maria Schill
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
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8
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Lampe B, Koslowski T. Theory and simulation of organic solar cell model compounds: How packing and morphology determine the electronic conductivity. J Chem Phys 2012; 137:094903. [DOI: 10.1063/1.4748816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Krapf S, Weber S, Koslowski T. The road not taken: a theoretical view of an unexpected cryptochrome charge transfer path. Phys Chem Chem Phys 2012; 14:11518-24. [DOI: 10.1039/c2cp40793k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Semiempirical configuration interaction calculations in biochemical environments. Biophys Chem 2011; 153:173-8. [DOI: 10.1016/j.bpc.2010.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/11/2010] [Accepted: 11/12/2010] [Indexed: 11/21/2022]
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11
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Burggraf F, Koslowski T. The simulation of interquinone charge transfer in a bacterial photoreaction center highlights the central role of a hydrogen-bonded non-heme iron complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:53-8. [DOI: 10.1016/j.bbabio.2010.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/02/2010] [Accepted: 08/05/2010] [Indexed: 11/30/2022]
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12
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Wang XF, Chakraborty T, Berashevich J. Quantum transport anomalies in DNA containing mispairs. NANOTECHNOLOGY 2010; 21:485101. [PMID: 21051800 DOI: 10.1088/0957-4484/21/48/485101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The effect of mispairs on charge transport in DNA of sequence (GC)(TA)(N)(GC)(3) connected to platinum electrodes is studied using the tight-binding model. With parameters derived from an ab initio density functional result, we calculate the current versus bias voltage for DNA with and without a mispair and for different numbers of (TA) basepairs N between the single and triple (GC) basepairs. The current decays exponentially with N under low bias but reaches a minimum under high bias when a multichannel transport mechanism is established. A (GA) mispair substituting a (TA) basepair near the middle of the (TA)(N) sequence usually enhances the current by one order due to its low ionization energy but may decrease the current significantly when an established multichannel mechanism is broken.
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Affiliation(s)
- Xue-Feng Wang
- Department of Physics, Soochow University, 1 Shizi Street, Suzhou 215006, People's Republic of China.
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13
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Hawke LGD, Kalosakas G, Simserides C. Electronic parameters for charge transfer along DNA. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2010; 32:291-305. [PMID: 20680380 DOI: 10.1140/epje/i2010-10650-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 06/08/2010] [Indexed: 05/26/2023]
Abstract
We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The pi molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wave functions and energies of DNA bases are discussed and then used for calculating the corresponding wave functions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the pi molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons. Our findings are also compared with existing calculations from first principles.
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Affiliation(s)
- L G D Hawke
- Materials Science Department, University of Patras, GR-26504, Rio, Greece
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14
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A combined Kirchhoff–Master equation approach to electronic transport in one-dimensional molecular conductors. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Krapf S, Koslowski T, Steinbrecher T. The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions. Phys Chem Chem Phys 2010; 12:9516-25. [DOI: 10.1039/c000876a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Koslowski T, Steinbrecher T. A Direct Simulation of Adiabatic Charge Transfer Through Bridged Organic Molecules. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.2009.5416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
We approach the dynamics of adiabatic charge transfer through bridged triarylamine cations by a direct molecular dynamics simulation involving classical and quantum mechanical degrees of freedom. Within a simple yet chemically specific model, the quantum mechanical subsystem is described by a tight-binding Hamiltonian, which is coupled to a classical force field. From a population analysis of the quantum part, the charge transfer rate can be readily extracted, including the influence of memory effects. The direct computation of the associated thermodynamic potential establishes a close link to analytical rate concepts. The theoretical data are compared to experiments, and the limits and possible extensions of our approach are discussed.
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17
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Hawke L, Kalosakas G, Simserides C. Empirical LCAO parameters forπmolecular orbitals in planar organic molecules. Mol Phys 2009. [DOI: 10.1080/00268970903049089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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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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19
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Abstract
We present an application of a molecular-dynamics-based scheme to evaluate the solvent reorganization energy of hole transfer in DNA. The obtained parameters can be used for simulations of hole transfer in DNA by means of Marcus' theory. Also, we perform an analysis of the reorganization energies, including the case of transfer of a delocalized hole.
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Affiliation(s)
- Tomás Kubar
- Institute of Physical Chemistry, Technische Universitat Braunschweig, D-38106 Braunschweig, Germany
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20
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Wittekindt C, Schwarz M, Friedrich T, Koslowski T. Aromatic Amino Acids as Stepping Stones in Charge Transfer in Respiratory Complex I: An Unusual Mechanism Deduced from Atomistic Theory and Bioinformatics. J Am Chem Soc 2009; 131:8134-40. [PMID: 19507904 DOI: 10.1021/ja900352t] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Wittekindt
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany, and Institut für Organische Chemie und Biochemie, Universität Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany
| | - Michael Schwarz
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany, and Institut für Organische Chemie und Biochemie, Universität Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany
| | - Thorsten Friedrich
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany, and Institut für Organische Chemie und Biochemie, Universität Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany, and Institut für Organische Chemie und Biochemie, Universität Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany
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21
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Steinbrecher T, Koslowski T, Case DA. Direct simulation of electron transfer reactions in DNA radical cations. J Phys Chem B 2009; 112:16935-44. [PMID: 19049302 DOI: 10.1021/jp8076134] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electron transfer properties of DNA radical cations are important in DNA damage and repair processes. Fast long-range charge transfer has been demonstrated experimentally, but the subtle influences that experimental conditions as well as DNA sequences and geometries have on the details of electron transfer parameters are still poorly understood. In this work, we employ an atomistic QM/MM approach, based on a one-electron tight binding Hamiltonian and a classical molecular mechanics forcefield, to conduct nanosecond length MD simulations of electron holes in DNA oligomers. Multiple spontaneous electron transfer events were observed in 100 ns simulations with neighboring adenine or guanine bases. Marcus parameters of charge transfer could be extracted directly from the simulations. The reorganization energy lambda for hopping between neighboring bases was found to be ca. 25 kcal/mol and charge transfer rates of 4.1 x 10(9) s(-1) for AA hopping and 1.3 x 10(9) s(-1) for GG hopping were obtained.
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Affiliation(s)
- Thomas Steinbrecher
- The Scripps Research Institute, 10550 North Torrey Pines Road, San Diego, CA 92037, USA
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22
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Kubař T, Woiczikowski PB, Cuniberti G, Elstner M. Efficient Calculation of Charge-Transfer Matrix Elements for Hole Transfer in DNA. J Phys Chem B 2008; 112:7937-47. [DOI: 10.1021/jp801486d] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tomáš Kubař
- Department of Physical and Theoretical Chemistry, Technische Universität Braunschweig, D-38106 Braunschweig, Germany, Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, D-01062 Dresden, Germany, and Department of Molecular Biophysics, German Cancer Research Center, D-69115 Heidelberg, Germany
| | - P. Benjamin Woiczikowski
- Department of Physical and Theoretical Chemistry, Technische Universität Braunschweig, D-38106 Braunschweig, Germany, Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, D-01062 Dresden, Germany, and Department of Molecular Biophysics, German Cancer Research Center, D-69115 Heidelberg, Germany
| | - Gianaurelio Cuniberti
- Department of Physical and Theoretical Chemistry, Technische Universität Braunschweig, D-38106 Braunschweig, Germany, Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, D-01062 Dresden, Germany, and Department of Molecular Biophysics, German Cancer Research Center, D-69115 Heidelberg, Germany
| | - Marcus Elstner
- Department of Physical and Theoretical Chemistry, Technische Universität Braunschweig, D-38106 Braunschweig, Germany, Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, D-01062 Dresden, Germany, and Department of Molecular Biophysics, German Cancer Research Center, D-69115 Heidelberg, Germany
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23
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Physics Aspects of Charge Migration Through DNA. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/978-3-540-72494-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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24
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Huertas O, Poater J, Fuentes-Cabrera M, Orozco M, Solà M, Luque FJ. Local Aromaticity in Natural Nucleobases and Their Size-Expanded Benzo-Fused Derivatives. J Phys Chem A 2006; 110:12249-58. [PMID: 17078622 DOI: 10.1021/jp063790t] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The influence of the insertion/addition of a benzene ring to the natural nucleic acid bases on the local aromaticity of the so-called size-expanded (xN, with N being adenine, guanine, cytosine, and thymine) bases is examined. To this end, the local aromaticity of the six- and five-membered rings in both the natural bases and their benzoderivatives is determined using HOMA, NICS, aromatic fluctuation index (FLU), and para-delocalization index (PDI) descriptors. In general, there is a good correspondence between the different indices, so that ring moieties with more negative NICS values also have larger HOMA and PDI measures and lower FLU indices. The results also point out notable differences in the aromatic character of the natural and size-expanded bases, which generally are hardly affected upon hydrogen bonding. The differences in the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap determined for the size-expanded nucleobases show an inverse correlation with the aromaticity of the fused benzene ring, so that the larger the HOMO-LUMO gap is, the lower the destabilization experienced by the benzene upon insertion/addition to the natural bases. This finding suggests that the introduction of suitable chemical modifications in the benzene ring might be useful to modulate the HOMO-LUMO gap while enabling the design of modified DNA duplexes that are able to act as molecular wires.
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Affiliation(s)
- Oscar Huertas
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avenida Diagonal 643, 08028, Barcelona, Spain
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25
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Rink G, Kong Y, Koslowski T. Theory and simulation of charge transfer through DNA – nanotube contacts. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.03.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Ganzenmüller G, Koslowski T. Electronic conductivity in polyaromatic hydrocarbon glasses: A theoretical perspective. J Chem Phys 2006; 125:014707. [PMID: 16863324 DOI: 10.1063/1.2212410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Based upon Monte Carlo simulations of amorphous molecular glasses, we have computed the electronic structure of five prototypical polyaromatic hydrocarbons using an extended Su-Schrieffer-Heeger model [J. R. Schrieffer, W. P. Su, and A. J. Heeger, Phys. Rev. Lett. 42, 1698 (1979)]. In the presence of excess charges, the resulting potential energy surfaces have been analyzed using Marcus' [Annu. Rev. Phys. Chem. 15, 155 (1964)] theory of charge transfer to yield reaction coefficients and--via the application of linear response theory--local conductivities. Applying Kirchhoff's rules, the emerging random resistor network problem leads to global conductivities of the order of 10(-1)-1 Scm, which correlate with the structural characteristics of the underlying geometry.
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Affiliation(s)
- Georg Ganzenmüller
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
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27
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Kim H, Sim E. Environmental Effect on the Relative Contribution of the Charge-Transfer Mechanisms within a Short DNA Sequence. J Phys Chem B 2005; 110:631-6. [PMID: 16471576 DOI: 10.1021/jp053893w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time evolution of the charge-transfer site population is studied in a short DNA sequence to determine the type of governing charge-transfer mechanism. The system consists of a 5'-GAGGG-3' nucleobase sequence coupled with a dissipative bath that represents the DNA phosphate backbone and solvents. Relative contribution of transfer mechanisms to the whole charge-transfer process has been obtained using the on-the-fly filtered propagator functional path integral method with the density matrix decomposition. Partial density matrixes of the incoherent hopping and coherent superexchange pathways as well as the full reduced density matrix have been evaluated and discussed for both debye and ohmic baths. It was found that the relative contribution of the transfer mechanisms is rather sensitive to the frequency-dependent environmental description.
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Affiliation(s)
- Heeyoung Kim
- Department of Chemistry, Yonsei University, 134 Sinchondong Seodaemungu, Seoul 120-749, South Korea
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Cramer T, Steinbrecher T, Labahn A, Koslowski T. Static and dynamic aspects of DNA charge transfer: a theoretical perspective. Phys Chem Chem Phys 2005; 7:4039-50. [PMID: 16474867 DOI: 10.1039/b507454a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we approach the impact of dynamic and static disorder on DNA charge transfer from a theoretical and numerical perspective. Disordered or defect geometries are either realized via molecular dynamics simulations using a classical force field or by experimentally determined DNA bulge structures. We apply a chemically specific, atomically resolved extended Su-Schrieffer-Heeger model to compute the energy parameters relevant to DNA charge transfer. For both models studied here, the effective donor-acceptor couplings--and hence the charge transfer rates--significantly depend upon the geometry. Dynamic disorder leads to a correlation time in this quantity of the order of 30 fs, and the transfer rates universally exhibit a broad, yet well-defined, exponential distribution. For DNA bulges, the angle characterizing the defect controls the charge transfer efficiency. The results are discussed and extensively compared to experimental findings and other calculations.
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Affiliation(s)
- Tobias Cramer
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
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Cramer T, Volta A, Blumen A, Koslowski T. Theory and Simulation of DNA Charge Transfer: From Junctions to Networks. J Phys Chem B 2004. [DOI: 10.1021/jp047232v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tobias Cramer
- Theoretische Polymerphysik and Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
| | - Antonio Volta
- Theoretische Polymerphysik and Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
| | - Alexander Blumen
- Theoretische Polymerphysik and Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Theoretische Polymerphysik and Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
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