1
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Wang Y, Demir B, Mohammad H, Oren EE, Anantram MP. Computational study of the role of counterions and solvent dielectric in determining the conductance of B-DNA. Phys Rev E 2023; 107:044404. [PMID: 37198817 DOI: 10.1103/physreve.107.044404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/01/2023] [Indexed: 05/19/2023]
Abstract
DNA naturally exists in a solvent environment, comprising water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the sodium ion (Na^{+}), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment in charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.
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Affiliation(s)
- Yiren Wang
- Deparment of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98105, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06510, Turkey
| | - Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06510, Turkey
| | - M P Anantram
- Deparment of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98105, USA
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2
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Mohammad H, Demir B, Akin C, Luan B, Hihath J, Oren EE, Anantram MP. Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics. NANOSCALE HORIZONS 2021; 6:651-660. [PMID: 34190284 DOI: 10.1039/d1nh00211b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Caglanaz Akin
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research, Yorktown Heights, NY 10598, USA
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
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3
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Ye Z, Du Y, Pan X, Zheng X, Xue J. Electron transfer from guanosine to the lowest triplet excited state of 4-nitroindole through hydrogen-bonded complex. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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4
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Onuchic JN, Rubtsov IV, Therien MJ. Tribute to David N. Beratan. J Phys Chem B 2020; 124:3437-3440. [DOI: 10.1021/acs.jpcb.0c02606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Jin Y, Ru X, Su NQ, Mei Y, Beratan DN, Zhang P, Yang W. Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections. J Phys Chem B 2020; 124:3428-3435. [PMID: 32272019 DOI: 10.1021/acs.jpcb.0c03112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier's wave function delocalization is regulated by the solvation induced localization and the quantum delocalization among the π stacked base pairs at any instant of time. Using a newly developed localized orbital scaling correction (LOSC) density functional theory method, we accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA. This approach can be used to diagnose the extent of delocalization in fluctuating DNA structures. Our studies indicate that the hole state tends to delocalize among 4 guanine-cytosine (GC) base pairs and among 3 adenine-thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. The relatively small delocalization in AT base pairs is caused by the weaker π-π interaction. This extent of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering coherent carrier transport in DNA.
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Affiliation(s)
- Ye Jin
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Neil Qiang Su
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yuncai Mei
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27705, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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6
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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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7
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Abstract
Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.
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8
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Suma A, Poppleton E, Matthies M, Šulc P, Romano F, Louis AA, Doye JPK, Micheletti C, Rovigatti L. TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami. J Comput Chem 2019; 40:2586-2595. [PMID: 31301183 DOI: 10.1002/jcc.26029] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/20/2019] [Accepted: 06/22/2019] [Indexed: 12/11/2022]
Abstract
Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122.,SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001, South McAllister Avenue, Tempe, Arizona 85281
| | - Michael Matthies
- Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062, Dresden, Germany
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001, South McAllister Avenue, Tempe, Arizona 85281
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca Foscari di Venezia, Via Torino, 155, 30172, Venezia Mestre, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Cristian Micheletti
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Universitá di Roma, Piazzale A. Moro, 2, 00185, Rome, Italy.,CNR-ISC, Uos Sapienza, Piazzale A. Moro, 2, 00185, Rome, Italy
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9
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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10
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Leveille MP, Tran T, Dingillo G, Cannon B. Detection of Mg 2+-dependent, coaxial stacking rearrangements in a bulged three-way DNA junction by single-molecule FRET. Biophys Chem 2018; 245:25-33. [PMID: 30551070 DOI: 10.1016/j.bpc.2018.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/15/2022]
Abstract
Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) approaches. The 3WJs varied according to the GC content and sequence of the junction core as well as the pyrimidine content of the internal bulge. Mg2+ titration experiments by ensemble FRET show that both stacking conformations have similar Mg2+ requirements for folding. Strikingly, smFRET experiments reveal that a specific junction sequence can populate both conformers and that this junction undergoes continual interconversion between the two stacked conformers. These findings will support the development of folding principles for the rational design of functional DNA nanostructures.
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Affiliation(s)
| | - Thao Tran
- Department of Physics, Loyola University Chicago, Chicago, IL, USA
| | - Gianna Dingillo
- Department of Physics, Loyola University Chicago, Chicago, IL, USA
| | - Brian Cannon
- Department of Physics, Loyola University Chicago, Chicago, IL, USA.
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11
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Martínez‐Fernández L, Banyasz A, Markovitsi D, Improta R. Topology Controls the Electronic Absorption and Delocalization of Electron Holes in Guanine Quadruplexes. Chemistry 2018; 24:15185-15189. [DOI: 10.1002/chem.201803222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/21/2022]
Affiliation(s)
| | - Akos Banyasz
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | | | - Roberto Improta
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
- Istituto di Biostrutture e BioimmaginiCNR Via Mezzocannone 16 80134 Napoli Italy
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12
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Sha R, Xiang L, Liu C, Balaeff A, Zhang Y, Zhang P, Li Y, Beratan DN, Tao N, Seeman NC. Charge splitters and charge transport junctions based on guanine quadruplexes. NATURE NANOTECHNOLOGY 2018; 13:316-321. [PMID: 29483600 DOI: 10.1038/s41565-018-0070-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions, and nucleobase stacks can transport charge over long distances. However, nucleobase stacking is often disrupted at junction points, hindering electric charge transport between the two terminals of the junction. Here, we show that a guanine-quadruplex (G4) motif can be used as a connector element for a multi-ended DNA junction. By attaching specific terminal groups to the motif, we demonstrate that charges can enter the structure from one terminal at one end of a three-way G4 motif, and can exit from one of two terminals at the other end with minimal carrier transport attenuation. Moreover, we study four-way G4 junction structures by performing theoretical calculations to assist in the design and optimization of these connectors.
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Affiliation(s)
- Ruojie Sha
- Department of Chemistry, New York University, New York, NY, USA
| | - Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Chaoren Liu
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Alexander Balaeff
- Departments of Chemistry, Duke University, Durham, NC, USA
- Nanoscience Technology Center & Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Yuqi Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Peng Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - David N Beratan
- Departments of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University, Durham, NC, USA.
- Department of Physics, Duke University, Durham, NC, USA.
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, USA.
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13
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Toulmin A, Baltierra-Jasso LE, Morten MJ, Sabir T, McGlynn P, Schröder GF, Smith BO, Magennis SW. Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint. Biochemistry 2017; 56:4985-4991. [PMID: 28820590 DOI: 10.1021/acs.biochem.7b00677] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully complementary 3WJ and found that it contained unpaired bases at the branchpoint, which is consistent with previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule Förster resonance energy transfer, molecular modeling, time-resolved ensemble fluorescence spectroscopy, and the first 19F nuclear magnetic resonance observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint. A 3WJ with a GC-rich branchpoint adopts an open conformation with unpaired bases at the branch and at least one additional conformation with an increased number of base interactions at the branchpoint. This structural diversity has implications for branch interactions and processing in vivo and for technological applications.
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Affiliation(s)
- Anita Toulmin
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Laura E Baltierra-Jasso
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K.,School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Michael J Morten
- School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Tara Sabir
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Peter McGlynn
- Department of Biology, University of York , Wentworth Way, York YO10 5DD, U.K
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich , 52425 Jülich, Germany.,Physics Department, Heinrich-Heine Universität Düsseldorf , Düsseldorf, Germany
| | - Brian O Smith
- Institute of Molecular, Cell and Systems Biology, University of Glasgow , Glasgow G12 8QQ, U.K
| | - Steven W Magennis
- School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
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14
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Mishra AK, Harris MA, Young RM, Wasielewski MR, Lewis FD. Dynamics of Charge Injection and Charge Recombination in DNA Mini-Hairpins. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b03084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ashutosh Kumar Mishra
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michelle A. Harris
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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15
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Kolář MH, Kubař T. Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer. J Phys Chem B 2017; 121:1520-1532. [PMID: 28121443 DOI: 10.1021/acs.jpcb.6b12109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.
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Affiliation(s)
- Michal H Kolář
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich , 52428 Jülich, Germany.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , 16610 Praha, Czech Republic
| | - Tomáš Kubař
- Institute of Physical Chemistry & Center for Functional Nanostructures, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
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16
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Thazhathveetil AK, Harris MA, Young RM, Wasielewski MR, Lewis FD. Efficient Charge Transport via DNA G-Quadruplexes. J Am Chem Soc 2017; 139:1730-1733. [DOI: 10.1021/jacs.6b10265] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Arun K. Thazhathveetil
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michelle A. Harris
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
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17
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Hole transport in DNA hairpins via base mismatches and strand crossings: Efficiency and dynamics. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Liu C, Beratan DN, Zhang P. Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise. J Phys Chem B 2016; 120:3624-33. [DOI: 10.1021/acs.jpcb.6b01018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chaoren Liu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Departments
of Biochemistry and Physics, Duke University, Durham, North Carolina 27708, United States
| | - Peng Zhang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
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