1
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Bauer B, Sharma R, Chergui M, Oppermann M. Exciton decay mechanism in DNA single strands: back-electron transfer and ultrafast base motions. Chem Sci 2022; 13:5230-5242. [PMID: 35655577 PMCID: PMC9093102 DOI: 10.1039/d1sc06450a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/09/2022] [Indexed: 12/03/2022] Open
Abstract
The photochemistry of DNA systems is characterized by the ultraviolet (UV) absorption of π-stacked nucleobases, resulting in exciton states delocalized over several bases. As their relaxation sensitively depends on local stacking conformations, disentangling the ensuing electronic and structural dynamics has remained an experimental challenge, despite their fundamental role in protecting the genome from potentially harmful UV radiation. Here we use transient absorption and transient absorption anisotropy spectroscopy with broadband femtosecond deep-UV pulses (250–360 nm) to resolve the exciton dynamics of UV-excited adenosine single strands under physiological conditions. Due to the exceptional deep-UV bandwidth and polarization sensitivity of our experimental approach, we simultaneously resolve the population dynamics, charge-transfer (CT) character and conformational changes encoded in the UV transition dipoles of the π-stacked nucleotides. Whilst UV excitation forms fully charge-separated CT excitons in less than 0.3 ps, we find that most decay back to the ground state via a back-electron transfer. Based on the anisotropy measurements, we propose that this mechanism is accompanied by a structural relaxation of the photoexcited base-stack, involving an inter-base rotation of the nucleotides. Our results finally complete the exciton relaxation mechanism for adenosine single strands and offer a direct view into the coupling of electronic and structural dynamics in aggregated photochemical systems. Despite its key role in DNA photochemistry, the decay mechanism of excitons in stacked bases has remained difficult to resolve. Ultrafast polarization spectroscopy now reveals a back-electron transfer and ultrafast base motions in adenosine strands.![]()
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Affiliation(s)
- Benjamin Bauer
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
| | - Rahul Sharma
- Laboratory for Computation and Visualization in Mathematics and Mechanics, École Polytechnique Fédérale de Lausanne, MATH-FSB CH-1015 Lausanne Switzerland
| | - Majed Chergui
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
| | - Malte Oppermann
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
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2
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González-Olvera JC, Zamorano-Carrillo A, Arreola-Jardón G, Pless RC. Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods. J Mol Model 2022; 28:43. [DOI: 10.1007/s00894-022-05033-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/18/2022] [Indexed: 11/24/2022]
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3
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Ibele LM, Sánchez-Murcia PA, Mai S, Nogueira JJ, González L. Excimer Intermediates en Route to Long-Lived Charge-Transfer States in Single-Stranded Adenine DNA as Revealed by Nonadiabatic Dynamics. J Phys Chem Lett 2020; 11:7483-7488. [PMID: 32794719 PMCID: PMC7503858 DOI: 10.1021/acs.jpclett.0c02193] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/14/2020] [Indexed: 05/25/2023]
Abstract
The ultrafast time evolution of a single-stranded adenine DNA is studied using a hybrid multiscale quantum mechanics/molecular mechanics (QM/MM) scheme coupled to nonadiabatic surface hopping dynamics. As a model, we use (dA)20 where a stacked adenine tetramer is treated quantum chemically. The dynamical simulations combined with on-the-fly quantitative wave function analysis evidence the nature of the long-lived electronically excited states formed upon absorption of UV light. After a rapid decrease of the initially excited excitons, relaxation to monomer-like states and excimers occurs within 100 fs. The former monomeric states then relax into additional excimer states en route to forming stabilized charge-transfer states on a longer timescale of hundreds of femtoseconds. The different electronic-state characters is reflected on the spatial separation between the adenines: excimers and charge-transfer states show a much smaller spatial separation than the monomer-like states and the initially formed excitons.
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Affiliation(s)
- Lea M. Ibele
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Pedro A. Sánchez-Murcia
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Juan J. Nogueira
- Chemistry
Department, Universidad Autónoma
de Madridand IADCHEM, Institute for Advanced Research in Chemistry, Calle Francisco Tomás y Valiente
7, 28049 Madrid, Spain
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
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4
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Wohlgemuth M, Mitrić R. Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping. Phys Chem Chem Phys 2020; 22:16536-16551. [DOI: 10.1039/d0cp02255a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Revealing the extended excited state lifetime due to excitation energy transport in DNA by multi-chromophoric field-induced surface-hopping (McFISH).
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Affiliation(s)
- Matthias Wohlgemuth
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
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5
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Morrison AF, Epifanovsky E, Herbert JM. Double-buffered, heterogeneous CPU + GPU integral digestion algorithm for single-excitation calculations involving a large number of excited states. J Comput Chem 2018; 39:2173-2182. [PMID: 30368836 DOI: 10.1002/jcc.25531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/12/2018] [Accepted: 06/14/2018] [Indexed: 01/29/2023]
Abstract
The most widely used quantum-chemical models for excited states are single-excitation theories, a category that includes configuration interaction with single substitutions, time-dependent density functional theory, and also a recently developed ab initio exciton model. When a large number of excited states are desired, these calculations incur a significant bottleneck in the "digestion" step in which two-electron integrals are contracted with density or density-like matrices. We present an implementation that moves this step onto graphical processing units (GPUs), and introduce a double-buffer scheme that minimizes latency by computing integrals on the central processing units (CPUs) concurrently with their digestion on the GPUs. An automatic code generation scheme simplifies the implementation of high-performance GPU kernels. For the exciton model, which requires separate excited-state calculations on each electronically coupled chromophore, the heterogeneous implementation described here results in speedups of 2-6× versus a CPU-only implementation. For traditional time-dependent density functional theory calculations, we obtain speedups of up to 5× when a large number of excited states is computed. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Adrian F Morrison
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.,Q-Chem Inc., Pleasanton, California
| | | | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
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6
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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7
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Affiliation(s)
- Juan J. Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Wien, Austria;,
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Wien, Austria;,
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8
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Nogueira JJ, Plasser F, González L. Electronic delocalization, charge transfer and hypochromism in the UV absorption spectrum of polyadenine unravelled by multiscale computations and quantitative wavefunction analysis. Chem Sci 2017; 8:5682-5691. [PMID: 28989607 PMCID: PMC5621053 DOI: 10.1039/c7sc01600j] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/09/2017] [Indexed: 12/23/2022] Open
Abstract
The characterization of the electronically excited states of DNA strands populated upon solar UV light absorption is essential to unveil light-induced DNA damage and repair processes. We report a comprehensive analysis of the electronic properties of the UV spectrum of single-stranded polyadenine based on theoretical calculations that include excitations over eight nucleobases of the DNA strand and environmental effects by a multiscale quantum mechanics/molecular mechanics scheme, conformational sampling by molecular dynamics, and a meaningful interpretation of the electronic structure by quantitative wavefunction analysis. We show that electronic excitations are extended mainly over two nucleobases with additional important contributions of monomer-like excitations and excitons delocalized over three monomers. Half of the spectral intensity derives from locally excited and Frenkel exciton states, while states with partial charge-transfer character account for the other half and pure charge-transfer states represent only a minor contribution. The hypochromism observed when going from the isolated monomer to the strand occurs independently from delocalization and charge transfer and is instead explained by long-range environmental perturbations of the monomer states.
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Affiliation(s)
- Juan J Nogueira
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ; ;
| | - Felix Plasser
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ; ;
| | - Leticia González
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ; ;
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9
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Saha S, Quiney HM. Solvent effects on the excited state characteristics of adenine–thymine base pairs. RSC Adv 2017. [DOI: 10.1039/c7ra03244g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.
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Affiliation(s)
- S. Saha
- ARC Centre of Excellence for Advanced Molecular Imaging
- Theoretical Condensed Matter Physics Group
- School of Physics
- The University of Melbourne
- Australia
| | - H. M. Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging
- Theoretical Condensed Matter Physics Group
- School of Physics
- The University of Melbourne
- Australia
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10
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Padula D, Jurinovich S, Di Bari L, Mennucci B. Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum. Chemistry 2016; 22:17011-17019. [PMID: 27699878 DOI: 10.1002/chem.201602777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Indexed: 12/18/2022]
Abstract
We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.
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Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
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11
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 338] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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12
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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13
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Lech CJ, Phan AT, Michel-Beyerle ME, Voityuk AA. Influence of base stacking geometry on the nature of excited states in G-quadruplexes: a time-dependent DFT study. J Phys Chem B 2015; 119:3697-705. [PMID: 25654765 DOI: 10.1021/jp512767j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K(+) ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads.
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Affiliation(s)
- Christopher J Lech
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University , 637371, Singapore
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14
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Blancafort L, Voityuk AA. Exciton delocalization, charge transfer, and electronic coupling for singlet excitation energy transfer between stacked nucleobases in DNA: An MS-CASPT2 study. J Chem Phys 2014; 140:095102. [DOI: 10.1063/1.4867118] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Nielsen LM, Hoffmann SV, Nielsen SB. Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated. Photochem Photobiol Sci 2014; 12:1273-85. [PMID: 23545881 DOI: 10.1039/c3pp25438k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In biology the interplay between multiple light-absorbers gives rise to complex quantum effects such as superposition states that are of extreme importance for life, both for harvesting solar energy and likely protecting nucleic acids from radiation damage. Still the characteristics of these states and their quantum dynamics are a much debated issue. While the electronic properties of single bases are fairly well understood, the situation for strands is complicated by the fact that stacked bases electronically couple when photoexcited. These newly arising states are denoted as exciton states and are simply linear combinations of localised wavefunctions that involve N - 1 ground-state bases and one base in its excited state (cf. the Frenkel exciton model). There is disagreement over the number of bases, N, that coherently couple, i.e., the spatial extent of the exciton, and how electronic deexcitation back to the ground state occurs. The importance of dark charge-transfer states has been inferred both from time-resolved fluorescence and transient absorption experiments. These states were suggested to be responsible for long deexcitation times but it is unclear whether 'long' is tens of picoseconds or nanoseconds. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see the beast in different, correct but incomplete ways.
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Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:1-37. [DOI: 10.1007/128_2013_517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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17
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Chen J, Zhang Y, Kohler B. Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:39-87. [DOI: 10.1007/128_2014_570] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Brancolini G, Migliore A, Corni S, Fuentes-Cabrera M, Luque FJ, Di Felice R. Dynamical treatment of charge transfer through duplex nucleic acids containing modified adenines. ACS NANO 2013; 7:9396-406. [PMID: 24060008 PMCID: PMC3903158 DOI: 10.1021/nn404165y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We address the issue of whether chemical alterations of nucleobases are an effective tool to modulate charge transfer through DNA molecules. Our investigation uses a multilevel computational approach based on classical molecular dynamics and quantum chemistry. We find yet another piece of evidence that structural fluctuations are a key factor to determine the electronic structure of double-stranded DNA. We argue that the electronic structure and charge transfer ability of flexible polymers is the result of a complex intertwining of various structural, dynamical and chemical factors. Chemical intuition may be used to design molecular wires, but this is not the sole component in the complex charge transfer mechanism through DNA.
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Affiliation(s)
- Giorgia Brancolini
- CNR Institute of Nanoscience, S3 Center, Via Campi 213/A, 41125 Modena, Italy
- (GB); (RDF). Phone: +39-059-205-5320. Fax: +39-059-205-5651
| | - Agostino Migliore
- School of Chemistry, Tel Aviv University, 69978 Tel Aviv, Israel
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Stefano Corni
- CNR Institute of Nanoscience, S3 Center, Via Campi 213/A, 41125 Modena, Italy
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, Tennessee 37831 6494, USA
| | - F. Javier Luque
- Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avenida Diagonal 643, Barcelona 08028, Spain
| | - Rosa Di Felice
- CNR Institute of Nanoscience, S3 Center, Via Campi 213/A, 41125 Modena, Italy
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089 USA
- (GB); (RDF). Phone: +39-059-205-5320. Fax: +39-059-205-5651
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19
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Coletta A, Castelli S, Chillemi G, Sanna N, Cushman M, Pommier Y, Desideri A. Solvent dependency of the UV-Vis spectrum of indenoisoquinolines: role of keto-oxygens as polarity interaction probes. PLoS One 2013; 8:e73881. [PMID: 24086299 PMCID: PMC3784438 DOI: 10.1371/journal.pone.0073881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 07/23/2013] [Indexed: 01/15/2023] Open
Abstract
Indenoisoquinolines are the most promising non-campthotecins topoisomerase IB inhibitors. We present an integrated experimental/computational investigation of the UV-Vis spectra of the IQNs parental compound (NSC314622) and two of its derivatives (NSC724998 and NSC725776) currently undergoing Phase I clinical trials. In all the three compounds a similar dependence of the relative absorption intensities at 270 nm and 290 nm on solvent polarity is found. The keto-oxygens in positions 5 and 11 of the molecular scaffold of the molecule are the principal chromophores involved in this dependence. Protic interactions on these sites are also found to give rise to absorptions at wavelength <250 nm observed in water solution, due to the stabilization of highly polarized tautomers of the molecule. These results suggest that the keto-oxygens are important polarizable groups that can act as useful interactors with the molecular receptor, providing at the same time an useful fingerprint for the monitoring of the drug binding to topoisomerase IB.
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Affiliation(s)
- Andrea Coletta
- Dipartimento di Biologia, Università degli Studi di Roma “Tor Vergata”, Roma, Italy
| | - Silvia Castelli
- Dipartimento di Biologia, Università degli Studi di Roma “Tor Vergata”, Roma, Italy
| | - Giovanni Chillemi
- Consorzio interuniversitario per le Applicazioni del Supercalcolo Per Università e Ricerca, Roma, Italy
| | - Nico Sanna
- Consorzio interuniversitario per le Applicazioni del Supercalcolo Per Università e Ricerca, Roma, Italy
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, United States of America
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Alessandro Desideri
- Dipartimento di Biologia, Università degli Studi di Roma “Tor Vergata”, Roma, Italy
- * E-mail:
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D'Abramo M, Castellazzi CL, Orozco M, Amadei A. On the nature of DNA hyperchromic effect. J Phys Chem B 2013; 117:8697-704. [PMID: 23799235 DOI: 10.1021/jp403369k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A combined theoretical-experimental study of the hyperchromic effect as occurring in the denaturation of a double stranded polyA-polyT is presented. Our theoretical/computational procedure allows us to reproduce the essential features of the experimental spectra and to characterize those molecular interactions responsible for the changes in the UV absorbance. We found that although excitonic intrastrand interactions strongly affect the absorbance, they are almost fully maintained in the single-stranded DNA. Our data indicate that hyperchromic effect originates from the higher delocalization of the excitonic states in the denaturated DNA with respect to the double-stranded conformation.
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21
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Santoro F, Improta R, Avila F, Segado M, Lami A. The interplay between neutral exciton and charge transfer states in single-strand polyadenine: a quantum dynamical investigation. Photochem Photobiol Sci 2013; 12:1527-43. [DOI: 10.1039/c3pp50111f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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22
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Dou Y, Liu Z, Yuan S, Zhang W, Tang H, Zhao J, Fang W, Lo GV. Dynamics of laser-excited stacked adenines: Semiclassical simulations. Int J Biol Macromol 2013; 52:358-67. [DOI: 10.1016/j.ijbiomac.2012.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/01/2012] [Accepted: 10/06/2012] [Indexed: 11/16/2022]
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23
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Weber JM, Marcum J, Nielsen SB. UV Photophysics of DNA and RNA Nucleotides In Vacuo: Dissociation Channels, Time Scales, and Electronic Spectra. PHOTOPHYSICS OF IONIC BIOCHROMOPHORES 2013. [DOI: 10.1007/978-3-642-40190-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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24
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Miyahara T, Nakatsuji H, Sugiyama H. Helical Structure and Circular Dichroism Spectra of DNA: A Theoretical Study. J Phys Chem A 2012; 117:42-55. [DOI: 10.1021/jp3085556] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute,
JST, CREST, Kyodai Katsura Venture Plaza,
North Building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto 615-8245,
Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute,
JST, CREST, Kyodai Katsura Venture Plaza,
North Building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto 615-8245,
Japan
| | - Hiroshi Sugiyama
- Department of Chemistry,
Graduate
School of Science, Kyoto University, Kitashirakawa-Oiwakecho,
Sakyo-Ku, Kyoto 606-8502, Japan
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25
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Edens LE, Brozik JA, Keller DJ. Coarse-grained model DNA: structure, sequences, stems, circles, hairpins. J Phys Chem B 2012; 116:14735-43. [PMID: 23157455 DOI: 10.1021/jp3009095] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A coarse-grained model for DNA that is intended to function realistically at the level of individual bases is reported. The model is composed of residues with up to eight coarse-grained beads each, which is sufficient for DNA-like base stacking and base-base recognition by hydrogen bonding. The beads interact by means of short-ranged pair potentials and a simple implicit solvent model. Movement is simulated by Brownian dynamics without hydrodynamic coupling. The main stabilizing forces are base stacking and hydrogen bonding, as modified by the effects of solvation. Complementary double-stranded chains of such residues form stable double helices over long runs (~10 μs) at or near room temperature, with structural parameters close to those of B-form DNA. Most mismatched chains or mismatched regions within a complementary molecule melt and become disordered. Long-range fluctuations and elastic properties, as measured by bending and twisting persistence lengths, are close to experimental values. Single-stranded chains are flexible, with transient stretches of free bases in equilibrium with globules stabilized by intrastrand stacking and hydrogen bonding. Model DNAs in covalently closed loops form right- or left-handed supercoils, depending on the sign of overtwist or undertwist. Short stem-loop structures melt at elevated temperatures and reanneal when the temperature is carefully lowered. Overall, most qualitative properties of real DNA arise naturally in the model from local interactions at the base-pair level.
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Affiliation(s)
- Lance E Edens
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, United States
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26
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Ghane T, Brancolini G, Varsano D, Di Felice R. Optical Properties of Triplex DNA from Time-Dependent Density Functional Theory. J Phys Chem B 2012; 116:10693-702. [DOI: 10.1021/jp304818s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Tahereh Ghane
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
- Department of Physics, University of Modena and Reggio Emilia, Via Campi 213/A,
41125 Modena, Italy
| | - Giorgia Brancolini
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
| | - Daniele Varsano
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
- Department
of Physics, University of Rome “La Sapienza”, Piazzale
Aldo Moro 5, 00185 Rome, Italy
| | - Rosa Di Felice
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
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27
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Su C, Middleton CT, Kohler B. Base-Stacking Disorder and Excited-State Dynamics in Single-Stranded Adenine Homo-oligonucleotides. J Phys Chem B 2012; 116:10266-74. [DOI: 10.1021/jp305350t] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Charlene Su
- Department
of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
| | - Chris T. Middleton
- Department
of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
| | - Bern Kohler
- Department of Chemistry and
Biochemistry, Montana State University,
Bozeman, Montana 59717-3400, United States
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28
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Zelený T, Ruckenbauer M, Aquino AJ, Müller T, Lankaš F, Dršata T, Hase WL, Nachtigallova D, Lischka H. Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine. J Am Chem Soc 2012; 134:13662-9. [DOI: 10.1021/ja3028845] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomáš Zelený
- Regional Centre of
Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University Olomouc,
17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Matthias Ruckenbauer
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
| | - Adelia J.A. Aquino
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
- Institute of Soil
Research, University of Natural Resources and Life Sciences,
Peter-Jordan-Straße 82, A-1190 Vienna, Austria
| | - Thomas Müller
- Institute of Advanced Simulation, Jülich Supercomuter Centre, Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Filip Lankaš
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Tomáš Dršata
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
| | - Dana Nachtigallova
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Hans Lischka
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
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29
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Plasser F, Aquino AJA, Hase WL, Lischka H. UV Absorption Spectrum of Alternating DNA Duplexes. Analysis of Excitonic and Charge Transfer Interactions. J Phys Chem A 2012; 116:11151-60. [DOI: 10.1021/jp304725r] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Felix Plasser
- Institute of Theoretical
Chemistry, University of Vienna, Währingerstrasse
17, A-1090,
Vienna, Austria
| | - Adelia J. A. Aquino
- Institute
of Soil Research, University of Natural Resources and Life Sciences,
Peter-Jordan-Strasse 82, A-1190, Vienna, Austria
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - William L. Hase
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Hans Lischka
- Institute of Theoretical
Chemistry, University of Vienna, Währingerstrasse
17, A-1090,
Vienna, Austria
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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30
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Dou Y, Yuan S, Zhang W, Tang H, Lo GV. Bonded exciplex formation from stacked thymine and adenine: semiclassical simulations. Mol Phys 2012. [DOI: 10.1080/00268976.2012.663944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Rosu F, Gabelica V, De Pauw E, Antoine R, Broyer M, Dugourd P. UV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase. J Phys Chem A 2012; 116:5383-91. [DOI: 10.1021/jp302468x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Frédéric Rosu
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Valérie Gabelica
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Edwin De Pauw
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Rodolphe Antoine
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Michel Broyer
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Philippe Dugourd
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
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32
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33
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Lu Y, Lan Z, Thiel W. Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem 2012; 33:1225-35. [DOI: 10.1002/jcc.22952] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/09/2012] [Accepted: 01/16/2012] [Indexed: 01/25/2023]
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34
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Improta R, Barone V. Interplay between “Neutral” and “Charge-Transfer” Excimers Rules the Excited State Decay in Adenine-Rich Polynucleotides. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104382] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Improta R, Barone V. Interplay between "neutral" and "charge-transfer" excimers rules the excited state decay in adenine-rich polynucleotides. Angew Chem Int Ed Engl 2011; 50:12016-9. [PMID: 22012744 DOI: 10.1002/anie.201104382] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/23/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini (IBB-CNR), Via Mezzocannone 16, 80136, Napoli, Italy.
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36
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González L, Escudero D, Serrano-Andrés L. Progress and Challenges in the Calculation of Electronic Excited States. Chemphyschem 2011; 13:28-51. [DOI: 10.1002/cphc.201100200] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 08/05/2011] [Indexed: 11/09/2022]
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37
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Lu Y, Lan Z, Thiel W. Hydrogen bonding regulates the monomeric nonradiative decay of adenine in DNA strands. Angew Chem Int Ed Engl 2011; 50:6864-7. [PMID: 21661082 DOI: 10.1002/anie.201008146] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 05/12/2011] [Indexed: 11/07/2022]
Affiliation(s)
- You Lu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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38
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Lu Y, Lan Z, Thiel W. Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Kumar A, Sevilla MD. Density functional theory studies of the extent of hole delocalization in one-electron oxidized adenine and guanine base stacks. J Phys Chem B 2011; 115:4990-5000. [PMID: 21417208 PMCID: PMC3084348 DOI: 10.1021/jp200537t] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study investigates the extent of hole delocalization in one-electron oxidized adenine (A) and guanine (G) stacks and shows that new IR vibrational bands are predicted that are characteristic of hole delocalization within A-stacks. The geometries of A-stacks (A(i); i = 2-8) and G-stacks (GG and GGG) in their neutral and one-electron oxidized states were optimized with the bases in a B-DNA conformation using the M06-2X/6-31G* method. The highest occupied molecular orbital (HOMO) is localized on a single adenine in A-stacks and on a single guanine in GG and GGG stacks located at the 5'-site of the stack. On one-electron oxidation (removal of an electron from the HOMO of the neutral A- and G-stacks) a "hole" is created. Mulliken charge analysis shows that these "holes" are delocalized over two to three adenine bases in the A-stack. The calculated spin density distribution of A(i)(•+) (i = 2-8) also showed delocalization of the hole predominantly on two adenine bases, with some delocalization on a neighboring base. For GG and GGG radical cations, the hole was found to be localized on a single G in the stack. The calculated HFCCs of GG and GGG are in good agreement with the experiment. Further, from the vibrational frequency analysis, it was found that IR spectra of neutral and the corresponding one-electron oxidized adenine stacks are quite different. The IR spectra of A(2)(•+) has intense IR peaks between 900 and 1500 cm(-1) that are not present in the neutral A(2) stack. The presence of A(2)(•+) in the adenine stack has a characteristic intense peak at ~1100 cm(-1). Thus, IR and Raman spectroscopy has potential for monitoring the extent of hole delocalization in A stacks.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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40
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Zelený T, Hobza P, Nachtigallová D, Ruckenbauer M, Lischka H. Photodynamics of the adenine model 4-aminopyrimidine embedded within double strand of DNA. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
On-the-fly surface hopping nonadiabatic photodynamical simulations using hybrid quantum mechanical/molecular mechanical approach of 4-aminopyrimidine were performed to model the relaxation mechanism of adenine within DNA double strand. The surrounding bases do not affect the overall ring-puckering relaxation mechanisms significantly, however, interesting hydrogen-bond dynamics is observed. First, formation of intra-strand hydrogen bonds is found. It is shown that this effect speeds up the decay process. In addition, the Watson–Crick structure is altered by breaking one of the inter-strand hydrogen bonds also leading to a decrease of the life time.
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41
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Aquino AJA, Nachtigallova D, Hobza P, Truhlar DG, Hättig C, Lischka H. The charge-transfer states in a stacked nucleobase dimer complex: A benchmark study. J Comput Chem 2010; 32:1217-27. [DOI: 10.1002/jcc.21702] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 09/27/2010] [Accepted: 10/01/2010] [Indexed: 02/06/2023]
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42
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Singh A, Snyder S, Lee L, Johnston APR, Caruso F, Yingling YG. Effect of oligonucleotide length on the assembly of DNA materials: molecular dynamics simulations of layer-by-layer DNA films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:17339-17347. [PMID: 20939494 DOI: 10.1021/la102762t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA strand length has been found to be an important factor in many DNA-based nanoscale systems. Here, we apply molecular dynamics simulations in a synergistic effort with layer-by-layer experimental data to understand the effect of DNA strand length on the assembly of DNA films. The results indicate that short (less than 10 bases) and long (more than 30 bases) single-stranded DNAs do not exhibit optimal film growth, and this can be associated with the limited accessibility of the bases on the surface due to formation of self-protected interactions that prevent efficient hybridization. Interestingly, the presence of a duplex attached to a single strand significantly alters the persistence length of the polyT strands. Our study suggests that restrained polyT, compared to labile suspensions of free polyT, are more capable of hybridization and hence DNA-based assembly.
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Affiliation(s)
- Abhishek Singh
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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43
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Shukla MK, Leszczynski J. Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study. Mol Phys 2010. [DOI: 10.1080/00268976.2010.496741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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44
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Holm AIS, Nielsen LM, Hoffmann SV, Nielsen SB. Vacuum-ultraviolet circular dichroism spectroscopy of DNA: a valuable tool to elucidate topology and electronic coupling in DNA. Phys Chem Chem Phys 2010; 12:9581-96. [PMID: 20607185 DOI: 10.1039/c003446k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circular dichroism (CD) is a powerful technique to obtain information on electronic transitions and has been used extensively for studies on DNA. Most experiments are done in the UV region but new information is often revealed from extending the wavelength region down into the vacuum ultraviolet (VUV) region. Such experiments are most easily carried out with synchrotron radiation (SR) light sources that provide large photon fluxes. Here we provide a summary of the SRCD data taken on different DNA strands with emphasis on results from our own laboratory within the last five years.(1-3) Signal intensities in the VUV are often significantly larger than those in the UV, and the electronic coupling between bases may increase with excitation energy. CD spectroscopy is particularly useful for investigating the extent of electronic coupling within a strand, i.e., the degree of delocalisation of the excited-state electronic wavefunction. The spatial extent of the wavefunction may be limited to just one base or it extends over two or more bases in a stack or between bases on different strands.(4,5) The actual character of the electronically excited state is linked to base composition and sequence as well as DNA folding motif (A-, B-, Z-DNA, triplexes, quadruplexes, etc.). The latter depends on experimental conditions such as solution acidity, temperature, ionic strength, and solvent.
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Affiliation(s)
- Anne Ivalu Sander Holm
- Department of Physics, Stockholm University, AlbaNova University Center, S-10691 Stockholm, Sweden.
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45
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Nachtigallová D, Zelený T, Ruckenbauer M, Müller T, Barbatti M, Hobza P, Lischka H. Does Stacking Restrain the Photodynamics of Individual Nucleobases? J Am Chem Soc 2010; 132:8261-3. [DOI: 10.1021/ja1029705] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic, Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria, and Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany
| | - Tomáš Zelený
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic, Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria, and Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany
| | - Matthias Ruckenbauer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic, Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria, and Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany
| | - Thomas Müller
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic, Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria, and Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany
| | - Mario Barbatti
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic, Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria, and Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic, Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria, and Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany
| | - Hans Lischka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic, Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria, and Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany
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46
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Improta R, Santoro F, Barone V, Lami A. Vibronic model for the quantum dynamical study of the competition between bright and charge-transfer excited states in single-strand polynucleotides: the adenine dimer case. J Phys Chem A 2010; 113:15346-54. [PMID: 19821596 DOI: 10.1021/jp906278t] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A simple vibronic model aimed at investigating the interplay between bright excitonic states and dark charge-transfer (CT) states in stacked adenine (Ade) nucleobases is presented. Two orbitals (the HOMO and the LUMO) for each Ade site have been included in the electronic Hamiltonian, whose parameters have been fitted to reproduce the main features of the absorption spectra of two stacked 9-methyladenine (9Me-A) molecules, computed in aqueous solution at the PCM/TD-PBE0 level. Three modes for each adenine unit have been included in the Hamiltonian, to describe the main structural changes among the different excited state minima of the adenine stacked dimer, as described at the TD-DFT level. The developed vibronic Hamiltonian (four electronic states and six nuclear coordinates) has been adopted to perform quantum dynamical calculations of a photoexcited Ade stacked dimer, utilizing the multiconfigurational time-dependent Hartree method. The obtained results indicate that the transfer between the bright excitonic state and the CT state is fast and effective.
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Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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Santoro F, Barone V, Lami A, Improta R. The excited electronic states of adenine-guanine stacked dimers in aqueous solution: a PCM/TD-DFT study. Phys Chem Chem Phys 2010; 12:4934-48. [DOI: 10.1039/b925108a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Voityuk AA. Conformational dependence of the electronic coupling for singlet excitation energy transfer in DNA. An INDO/S study. Phys Chem Chem Phys 2010; 12:7403-8. [DOI: 10.1039/c003131c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Santoro F, Barone V, Improta R. Excited States Decay of the A−T DNA: A PCM/TD-DFT Study in Aqueous Solution of the (9-Methyl-adenine)2·(1-methyl-thymine)2 Stacked Tetramer. J Am Chem Soc 2009; 131:15232-45. [DOI: 10.1021/ja904777h] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Santoro
- Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - V. Barone
- Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - R. Improta
- Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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Munksgaard Nielsen L, Holm AIS, Varsano D, Kadhane U, Hoffmann SV, Di Felice R, Rubio A, Brøndsted Nielsen S. Fingerprints of bonding motifs in DNA duplexes of adenine and thymine revealed from circular dichroism: synchrotron radiation experiments and TDDFT calculations. J Phys Chem B 2009; 113:9614-9. [PMID: 19537699 DOI: 10.1021/jp9032029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synchrotron radiation circular dichroism (SRCD) spectra were recorded for a family of 12 DNA duplexes that all contain nine adenines (A) and nine thymines (T) in each strand but in different combinations. The total number of AT Watson-Crick (WC) base pairs is constant (18), but the number of cross-strand (CS) hydrogen bonds between A and T varies between 0 and 16, the maximum possible. Eleven of the duplexes have one or more A tracts, and one duplex has T tracts. The signals due to hybridization were found from subtraction of spectra of single strands from spectra of the duplexes. The residual spectrum of the T-tract duplex T(9)A(9):A(9)T(9) (5'-3':3'-5') significantly differs from that of the A-tract duplex A(9)T(9):T(9)A(9), but only below 210 nm, which suggests that the signal in this region depends on the superhelicity of the duplex. A principal component analysis of all residual spectra reveals that spectra of A-tract duplexes can be obtained to a good approximation as a linear combination of just two basis spectra. The first component is assigned to the spectrum of 18 WC and 8 CS pairs, whereas the second component is that of 8 CS pairs. This interpretation is supported by separate experiments on duplexes of varying lengths but with similar arrangements of the A and T's and by experiments on two other duplex families of 14 and 30 base pairs. The best correlation is obtained by the assumption that cross-strand interactions occur as long as there are two adenine neighbors in a strand. Our data indicate that a circular dichroism spectrum of a duplex containing only A and T can simply be inferred from the number of WC base pairs and the number of CS interactions, and we provide reference spectra for these two interactions. Finally, time dependent density functional theory calculations of the circular dichroism spectra for an isolated WC base pair and two different CS base pairs (between adenine N-6 amine and thymine O-4 or between adenine C-2-H and thymine O-2) were performed to provide some additional support for the interpretation of the experimental spectra. We find large differences between the two calculated CS spectra. However, there is a reasonable qualitative agreement between the calculated WC and the C-2-H...O-2 CS spectra and those deduced from the experimental data.
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