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CEBA: A new heterobifunctional reagent for plasmid DNA functionalization by click chemistry. Int J Pharm 2021; 601:120566. [PMID: 33812974 DOI: 10.1016/j.ijpharm.2021.120566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 11/20/2022]
Abstract
Here, we report the synthesis of 3,6,9-trioxaundecan-1-{4-[(2-Chloroethyl)Ethylamino)]-Benzylamino},11-Azide (CEBA). CEBA alkylates the N7 of guanine of DNA thanks its chloroethyl group and can be coupled by a strain-promoted azide-alkyne cycloaddition to an alkynylated molecule. The optimization of the alkylation level of pDNA reveals that the expression of the encoded gene is preserved when it is randomly modified with at most 1 CEBA molecule per 150 bp. We show that the azido group of CEBA allows the linkage via click chemistry of CEBA-pDNA with a fluorophore or a peptide containing a dibenzocyclooctyne (DBCO) function. This new heterobifunctional reagent opens new ways to equip pDNA easily with signal molecules including peptides and nucleic acids without side products providing great interest for non-viral gene therapy.
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2
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Storoniak P, Rak J, Ko YJ, Wang H, Bowen KH. Excess Electron Attachment to the Nucleoside Pair 2′-Deoxyadenosine (dA)–2′-Deoxythymidine (dT). J Phys Chem B 2016; 120:4955-62. [DOI: 10.1021/acs.jpcb.6b03450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Storoniak
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Janusz Rak
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Yeon Jae Ko
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Haopeng Wang
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kit H. Bowen
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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3
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Zhang J, Yang YI, Yang L, Gao YQ. Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations. J Phys Chem B 2015; 119:5518-30. [DOI: 10.1021/jp511057f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun Zhang
- Institute of Theoretical and Computational Chemistry,
College of
Chemistry and Molecular Engineering, and ‡Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Yi Isaac Yang
- Institute of Theoretical and Computational Chemistry,
College of
Chemistry and Molecular Engineering, and ‡Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Lijiang Yang
- Institute of Theoretical and Computational Chemistry,
College of
Chemistry and Molecular Engineering, and ‡Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry,
College of
Chemistry and Molecular Engineering, and ‡Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
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4
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Gu J, Wang J, Leszczynski J. Photoinduced Electron Detachment and Proton Transfer: The Proposal for Alternative Path of Formation of Triplet States of Guanine (G) and Cytosine (C) Pair. J Phys Chem B 2014; 119:2454-8. [DOI: 10.1021/jp507385r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Wang
- Interdisciplinary
Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary
Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, United States
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Jahangiri S, Cai L, Peslherbe GH. Performance of density-functional tight-binding models in describing hydrogen-bonded anionic-water clusters. J Comput Chem 2014; 35:1707-15. [DOI: 10.1002/jcc.23677] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Soran Jahangiri
- Department of Chemistry and Biochemistry; Centre for Research in Molecular Modeling (CERMM), Concordia University; 7141 Sherbrooke Street West Montréal Québec Canada H4B 1R6
| | - Lemin Cai
- Department of Chemistry and Biochemistry; Centre for Research in Molecular Modeling (CERMM), Concordia University; 7141 Sherbrooke Street West Montréal Québec Canada H4B 1R6
| | - Gilles H. Peslherbe
- Department of Chemistry and Biochemistry; Centre for Research in Molecular Modeling (CERMM), Concordia University; 7141 Sherbrooke Street West Montréal Québec Canada H4B 1R6
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6
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Scholz R, Luschtinetz R, Seifert G, Jägeler-Hoheisel T, Körner C, Leo K, Rapacioli M. Quantifying charge transfer energies at donor-acceptor interfaces in small-molecule solar cells with constrained DFTB and spectroscopic methods. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:473201. [PMID: 24135026 DOI: 10.1088/0953-8984/25/47/473201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Charge transfer states around the donor-acceptor interface in an organic solar cell determine the device performance in terms of the open circuit voltage. In the present work, we propose a computational scheme based on constrained density functional tight binding theory (c-DFTB) to assess the energy of the lowest charge transfer (CT) state in such systems. A comparison of the c-DFTB scheme with Hartree-Fock based configuration interaction of singles (CIS) and with time-dependent density functional theory (TD-DFT) using the hybrid functional B3LYP reveals that CIS and c-DFTB reproduce the correct Coulomb asymptotics between cationic donor and anionic acceptor configurations, whereas TD-DFT gives a qualitatively wrong excitation energy. Together with an embedding scheme accounting for the polarizable medium, this c-DFTB scheme is applied to several donor-acceptor combinations used in molecular solar cells. The external quantum efficiency of photovoltaic cells based on zinc phthalocyanine-C60 blends reveals a CT band remaining much narrower than the density of states of acceptor HOMO and donor LUMO, an observation which can be interpreted in a natural way in terms of Marcus transfer theory. A detailed comparison with c-DFTB calculations reveals an energy difference of 0.32 eV between calculated and observed absorption from the electronic ground state into the CT state. In a blend of a functionalized thiophene and C60, the photoluminescence spectra differ significantly from neat films, allowing again an assignment to CT states. The proposed computational scheme reproduces the observed trends of the observed open circuit voltages in photovoltaic devices relying on several donor-acceptor blends, finding an offset of 1.16 eV on average. This value is similar as in polymer-fullerene photovoltaic systems where it amounts to about 0.9 eV, indicating that the photophysics of CT states in molecular donor-acceptor blends and in polymer-fullerene blends are governed by the same mechanisms.
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Affiliation(s)
- Reinhard Scholz
- Institut für Angewandte Photophysik, Technische Universität Dresden, D-01062 Dresden, Germany
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7
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Storoniak P, Rak J, Ko YJ, Wang H, Bowen KH. Photoelectron spectroscopic and density functional theoretical studies of the 2′-deoxycytidine homodimer radical anion. J Chem Phys 2013; 139:075101. [DOI: 10.1063/1.4817779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ko YJ, Storoniak P, Wang H, Bowen KH, Rak J. Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions. J Chem Phys 2012. [PMID: 23206036 DOI: 10.1063/1.4767053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine, (rU)(2)(●-). It features a broad band consisting of an onset of ∼1.2 eV and a maximum at the electron binding energy (EBE) ranging from 2.0 to 2.5 eV. Calculations performed at the B3LYP∕6-31++G∗∗ level of theory suggest that the PES is dominated by dimeric radical anions in which one uridine nucleoside, hosting the excess charge on the base moiety, forms hydrogen bonds via its O8 atom with hydroxyl of the other neutral nucleoside's ribose. The calculated adiabatic electron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimers show an excellent agreement with the experimental values. The anionic complexes consisting of two intermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers. Despite the fact that uracil-uracil anionic homodimers are additionally stabilized by barrier-free electron-induced proton transfer, their relative thermodynamic stabilities and the calculated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)(2)(●-).
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Affiliation(s)
- Yeon Jae Ko
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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9
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Storoniak P, Rak J, Ko YJ, Wang H, Bowen KH. Photoelectron Spectroscopy and Computational Modeling of Thymidine Homodimer Anions. J Phys Chem B 2012; 116:13975-81. [DOI: 10.1021/jp307570p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Piotr Storoniak
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952
Gdańsk, Poland
| | - Janusz Rak
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952
Gdańsk, Poland
| | - Yeon Jae Ko
- Department
of Chemistry, Johns Hopkins University,
Baltimore, Maryland 21218,
United States
| | - Haopeng Wang
- Department
of Chemistry, Johns Hopkins University,
Baltimore, Maryland 21218,
United States
| | - Kit H. Bowen
- Department
of Chemistry, Johns Hopkins University,
Baltimore, Maryland 21218,
United States
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Gu J, Leszczynski J, Schaefer HF. Interactions of electrons with bare and hydrated biomolecules: from nucleic acid bases to DNA segments. Chem Rev 2012; 112:5603-40. [PMID: 22694487 DOI: 10.1021/cr3000219] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS, PR China.
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Gupta A, Jaeger HM, Compaan KR, Schaefer HF. Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer. J Phys Chem B 2012; 116:5579-87. [PMID: 22530702 DOI: 10.1021/jp211608b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.
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13
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Ko YJ, Wang H, Radisic D, Stokes ST, Eustis SN, Bowen KH, Mazurkiewicz K, Storoniak P, Kowalczyk A, Haranczyk M, Gutowski M, Rak J. Barrier-free proton transfer induced by electron attachment to the complexes between 1‐methylcytosine and formic acid. Mol Phys 2010. [DOI: 10.1080/00268976.2010.515623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yeon Jae Ko
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Haopeng Wang
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Dunja Radisic
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Sarah T. Stokes
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Soren N. Eustis
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Kit H. Bowen
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Kamil Mazurkiewicz
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
| | - Piotr Storoniak
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
| | - Arkadiusz Kowalczyk
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
| | - Maciej Haranczyk
- c Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
| | - Maciej Gutowski
- d Chemistry-School of Engineering and Physical Sciencs, Heriot-Watt University , Edinburgh EH14 4AS , UK
| | - Janusz Rak
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
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Villani G. Theoretical Investigation of Hydrogen Atom Transfer in the Cytosine-Guanine Base Pair and Its Coupling with Electronic Rearrangement. Concerted vs Stepwise Mechanism. J Phys Chem B 2010; 114:9653-62. [DOI: 10.1021/jp102457s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Giovanni Villani
- Istituto per i Processi Chimico-Fisici, IPCF-CNR, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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15
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Szyperska A, Rak J, Leszczynski J, Li X, Ko YJ, Wang H, Bowen KH. Low-Energy-Barrier Proton Transfer Induced by Electron Attachment to the Guanine⋅⋅⋅Cytosine Base Pair. Chemphyschem 2010; 11:880-8. [DOI: 10.1002/cphc.200900810] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Fox H, Newman KE, Schneider WF, Corcelli SA. Bulk and Surface Properties of Rutile TiO2 from Self-Consistent-Charge Density Functional Tight Binding. J Chem Theory Comput 2010; 6:499-507. [DOI: 10.1021/ct900665a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H. Fox
- Department of Chemistry and Biochemistry, Department of Physics, Department of Chemical and Biomolecular Engineering, and Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - K. E. Newman
- Department of Chemistry and Biochemistry, Department of Physics, Department of Chemical and Biomolecular Engineering, and Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - W. F. Schneider
- Department of Chemistry and Biochemistry, Department of Physics, Department of Chemical and Biomolecular Engineering, and Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - S. A. Corcelli
- Department of Chemistry and Biochemistry, Department of Physics, Department of Chemical and Biomolecular Engineering, and Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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Kobyłecka M, Leszczynski J, Rak J. Stability of the valence anion of cytosine is governed by nucleobases sequence in the double stranded DNA pi-stack: A computational study. J Chem Phys 2009; 131:085103. [PMID: 19725636 DOI: 10.1063/1.3204939] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The stabilities of the valence anion of cytosine (C(-)) in model trimers of complementary base pairs that possess the B-DNA geometry but differ in base sequence are reported. In order to estimate the energetics of electron attachment to the middle cytosine incorporated in the trimer, a thermodynamic cycle employing all possible two-body interaction energies in the neutral and anionic duplex as well as the adiabatic electron affinity of isolated cytosine were developed. All calculations were carried out at the MP2 level of theory with the aug-cc-pVDZ basis set. We have demonstrated that contrary to the literature reports, concerning single stranded DNA, the sequence of nucleic bases has a profound effect on the stability of the cytosine valence anion. The anionic 3(')-CCC-5(') complex is the most stable configuration (EA=0.399 eV) and the 3(')-GCG-5(') trimer anion is the most unstable species (EA=-0.193 eV). Moreover, with the energetic correction for the presence of sugar-phosphate backbone all possible double stranded DNA sequences lead to the stable C(-). The predicted electron affinities of the cytosine anion have been compared to the results of analogous studies on the thymine anion published recently [M. Kobyłecka et al., J. Am. Chem. Soc. 130, 15683 (2008)]. The consequences of low-energy barrier proton transfer in the GC anion have been discussed in the context of induced by electrons DNA single strand breaks. The DNA sequences that should dramatically differ in their vulnerability to be damaged by low energy electrons have been proposed.
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Affiliation(s)
- Monika Kobyłecka
- Faculty of Chemistry, University of Gdańsk, 80-952 Gdansk, Poland
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18
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Mishra D, Pal S. Ionization potential and structure relaxation of adenine, thymine, guanine and cytosine bases and their base pairs: A quantification of reactive sites. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.02.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Szyperska A, Rak J, Leszczynski J, Li X, Ko YJ, Wang H, Bowen KH. Valence Anions of 9-Methylguanine−1-Methylcytosine Complexes. Computational and Photoelectron Spectroscopy Studies. J Am Chem Soc 2009; 131:2663-9. [DOI: 10.1021/ja808313e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Anna Szyperska
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Janusz Rak
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Jerzy Leszczynski
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Xiang Li
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Yeon Jae Ko
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Haopeng Wang
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Kit H. Bowen
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
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20
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Villani G. Properties of the Thiobase Pairs Hydrogen Bridges: A Theoretical Study. J Phys Chem B 2009; 113:2128-34. [PMID: 19166279 DOI: 10.1021/jp807670f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giovanni Villani
- Istituto per i Processi Chimico-Fisici, IPCF-CNR, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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Kobyłecka M, Leszczynski J, Rak J. Valence anion of thymine in the DNA pi-stack. J Am Chem Soc 2008; 130:15683-7. [PMID: 18954049 DOI: 10.1021/ja806251h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Most of theoretical data on the stability of radical anions supported by nucleic acid bases have been obtained for anions of isolated nucleobases, their nucleosides, or nucleotides. This approach ignores the hallmark forces of DNA, namely, hydrogen bonding and pi-stacking interactions. Since these interactions might be crucial for the electron affinities of nucleobases bound in DNA, we report for the first time on the stability of the thymine valence anion in trimers of complementary bases possessing the regular B-DNA geometry but differing in base sequence. In order to estimate the energetics of electron attachment to a trimer, we developed a thermodynamic cycle employing all possible two-body interaction energies in the neutral and anionic duplex as well as the adiabatic electron affinity of isolated thymine. All calculations were carried out at the MP2 level of theory with the aug-cc-pVDZ basis set. The two-body interaction energies were corrected for the basis set superposition error, and in benchmark systems, they were extrapolated to the basis set limit and supplemented with correction for higher order correlation terms calculated at the CCSD(T) level. We have demonstrated that the sequence of nucleic bases has a profound effect on the stability of the thymine valence anion: the anionic 5'-CTC-3' (6.0 kcal/mol) sequence is the most stable configuration, and the 5'-GTG-3' (-8.0 kcal/mol) trimer anion is the most unstable species. On the basis of obtained results, one can propose DNA sequences that are different in their vulnerability to damage by low energy electron.
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Affiliation(s)
- Monika Kobyłecka
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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22
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Yamagami R, Kobayashi K, Tagawa S. Formation of spectral intermediate G-C and A-T anion complex in duplex DNA studied by pulse radiolysis. J Am Chem Soc 2008; 130:14772-7. [PMID: 18841971 DOI: 10.1021/ja805127e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of electron adducts of 2'-deoxynucleotides and oligonucelotides (ODNs) were measured spectroscopically by nanosecond pulse radiolysis. The radical anions of the nucleotides were produced within 10 ns by the reaction of hydrated electrons (e(aq)(-)) and were protonated to form the corresponding neutral radicals. At pH 7.0, the radical anion of deoxythymidine (dT(*-)) was protonated to form the neutral radical dT(H)(*) in the time range of microseconds. The rate constant for the protonation was determined as 1.8 x 10(10) M(-1) s(-1). In contrast, the neutral radical of dC(H)(*) was formed immediately after the pulse, suggesting that the protonation occurs within 10 ns. The transient spectra of excess electrons of the double-stranded ODNs 5'-TAATTTAATAT-3' (AT) and 5'-CGGCCCGGCGC-3' (GC) differed from those of pyrimidine radicals (C and T) and their composite. In contrast, the spectra of the electron adducts of the single-stranded ODNs GC and AT exhibited characteristics of C and T, respectively. These results suggest that, in duplex ODNs, the spectral intermediates of G-C and A-T anions complex were formed. On the microsecond time scale, the subsequent changes in absorbance of the ODN AT had a first-order rate constant of 4 x 10(4) s(-1), reflecting the protonation of T.
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Affiliation(s)
- Ryuhei Yamagami
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan
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23
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Kim S, Lind MC, Schaefer HF. Structures and Energetics of the Deprotonated Adenine−Uracil Base Pair, Including Proton-Transferred Systems. J Phys Chem B 2008; 112:3545-51. [DOI: 10.1021/jp711518n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunghwan Kim
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Maria C. Lind
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
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Radiation Effects On DNA: Theoretical Investigations Of Electron, Hole And Excitation Pathways To DNA Damage. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Shukla MK, Leszczynski J. Electronic Spectra, Excited State Structures and Interactions of Nucleic Acid Bases and Base Assemblies: A Review. J Biomol Struct Dyn 2007; 25:93-118. [PMID: 17676942 DOI: 10.1080/07391102.2007.10507159] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A comprehensive review of recent theoretical and experimental advances in the singlet electronic transitions, excited state structures and dynamics of nucleic acid bases (NABs) and base assemblies are presented. It is well known that NABs absorb ultraviolet radiation, but the absorbed energy is efficiently dissipated in the form of ultrafast internal conversion processes believed to occur in the subpicosecond time scale and, therefore, enabling NABs highly photostable. It is not known how much evolutionary role was played in evolving these molecules and the ultimate selection by nature as genetic materials, but it is well accepted that survival-of-fittest prevails. Recently, significant efforts have been continuously paid to understand the mechanism of electronic excitation deactivation, but universally acceptable mechanism is still elusive. However, recent investigations reveal that electronic excited state geometries of DNA bases are usually nonplanar and this structural nonplanarity may facilitate nonradiative deactivation. Investigation of excited state structures is challenging and, therefore, it is not surprising that despite the impressive theoretical and computational advances, this research area is still hampered by the methodological and computational limitations. Further, stacking has significant influence on the emission properties of molecules. The 2-aminopurine, a fluorescent adenine derivative frequently used in studying DNA dynamics, shows significant attenuations in fluorescence quantum yield when incorporated in the DNA. Theoretical and computational bottlenecks limit a thorough theoretical understanding of effect of stacking interactions on the excited state dynamics of NABs. Despite these limitations the investigations of excited state properties are progressing in the right direction and our better understanding of excited state structure and dynamics of NABs and nucleic acids may help to design preventive strategy for radiation induced illness and photostable materials.
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Affiliation(s)
- M K Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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Bhattacharyya S, Stankovich MT, Truhlar DG, Gao J. Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase. J Phys Chem A 2007. [PMID: 17567113 DOI: 10.1021/jp071526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavin adenine dinucleotide (FAD) is a common cofactor in redox proteins, and its reduction potentials are controlled by the protein environment. This regulation is mainly responsible for the versatile catalytic functions of flavoenzymes. In this article, we report computations of the reduction potentials of FAD in medium-chain acyl-CoA dehydrogenase (MCAD) and cholesterol oxidase (CHOX). In addition, the reduction potentials of lumiflavin in aqueous solution have also been computed. Using molecular dynamics and free-energy perturbation techniques, we obtained the free-energy changes for two-electron/two-proton as well as one-electron/one-proton addition steps. We employed a combined quantum mechanical and molecular mechanical (QM/MM) potential, in which the flavin ring was represented by the self-consistent-charge density functional tight-binding (SCC-DFTB) method, while the rest of the enzyme-solvent system was treated by classical force fields. The computed two-electron/two-proton reduction potentials for lumiflavin and the two enzyme-bound FADs are in reasonable agreement with experimental data. The calculations also yielded the pKa values for the one-electron reduced semiquinone (FH*) and the fully reduced hydroquinone (FH2) forms. The pKa of the FAD semiquinone in CHOX was found to be around 4, which is 4 units lower than that in the enzyme-free state and 2 units lower than that in MCAD; this supports the notion that oxidases have a greater ability than dehydrogenases to stabilize anionic semiquinones. In MCAD, the flavin ring interacts with four hydrophobic residues and has a significantly bent structure, even in the oxidized state. The present study shows that this bending of the flavin imparts a significant destabilization (approximately 5 kcal/mol) to the oxidized state. The reduction potential of lumiflavin was also computed using DFT (M06-L and B3LYP functionals with 6-31+G(d,p) basis set) with the SM6 continuum solvation model, and the results are in good agreement with results from explicit free-energy simulations, which supports the conclusion that the SCC-DFTB/MM computation is reasonably accurate for both 1e(-)/1H+ and 2e(-)/2H+ reduction processes. These results suggest that the first coupled electron-proton addition is stepwise for both the free and the two enzyme-bound flavins. In contrast, the second coupled electron-proton addition is also stepwise for the free flavin but is likely to be concerted when the flavin is bound to either the dehydrogenase or the oxidase enzyme.
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Affiliation(s)
- Sudeep Bhattacharyya
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Smith Hall, Minneapolis, Minnesota 55455-0431, USA
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Bhattacharyya S, Stankovich MT, Truhlar DG, Gao J. Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase. J Phys Chem A 2007; 111:5729-42. [PMID: 17567113 PMCID: PMC4480342 DOI: 10.1021/jp071526+] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flavin adenine dinucleotide (FAD) is a common cofactor in redox proteins, and its reduction potentials are controlled by the protein environment. This regulation is mainly responsible for the versatile catalytic functions of flavoenzymes. In this article, we report computations of the reduction potentials of FAD in medium-chain acyl-CoA dehydrogenase (MCAD) and cholesterol oxidase (CHOX). In addition, the reduction potentials of lumiflavin in aqueous solution have also been computed. Using molecular dynamics and free-energy perturbation techniques, we obtained the free-energy changes for two-electron/two-proton as well as one-electron/one-proton addition steps. We employed a combined quantum mechanical and molecular mechanical (QM/MM) potential, in which the flavin ring was represented by the self-consistent-charge density functional tight-binding (SCC-DFTB) method, while the rest of the enzyme-solvent system was treated by classical force fields. The computed two-electron/two-proton reduction potentials for lumiflavin and the two enzyme-bound FADs are in reasonable agreement with experimental data. The calculations also yielded the pKa values for the one-electron reduced semiquinone (FH*) and the fully reduced hydroquinone (FH2) forms. The pKa of the FAD semiquinone in CHOX was found to be around 4, which is 4 units lower than that in the enzyme-free state and 2 units lower than that in MCAD; this supports the notion that oxidases have a greater ability than dehydrogenases to stabilize anionic semiquinones. In MCAD, the flavin ring interacts with four hydrophobic residues and has a significantly bent structure, even in the oxidized state. The present study shows that this bending of the flavin imparts a significant destabilization (approximately 5 kcal/mol) to the oxidized state. The reduction potential of lumiflavin was also computed using DFT (M06-L and B3LYP functionals with 6-31+G(d,p) basis set) with the SM6 continuum solvation model, and the results are in good agreement with results from explicit free-energy simulations, which supports the conclusion that the SCC-DFTB/MM computation is reasonably accurate for both 1e(-)/1H+ and 2e(-)/2H+ reduction processes. These results suggest that the first coupled electron-proton addition is stepwise for both the free and the two enzyme-bound flavins. In contrast, the second coupled electron-proton addition is also stepwise for the free flavin but is likely to be concerted when the flavin is bound to either the dehydrogenase or the oxidase enzyme.
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Affiliation(s)
| | | | - Donald G. Truhlar
- To whom correspondence should be addressed (M.T.S); (D.G.T.); (J.G.)
| | - Jiali Gao
- To whom correspondence should be addressed (M.T.S); (D.G.T.); (J.G.)
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28
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Xie H, Xia F, Cao Z. Density Functional Study toward Understanding Dehydrogenation of the Adenine−Thymine Base Pair and Its Anion. J Phys Chem A 2007; 111:4384-90. [PMID: 17474725 DOI: 10.1021/jp0686137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The dehydrogenated radicals and anions of Watson-Crick adenine-thymine (A-T) base pair have been investigated by the B3LYP/DZP++ approach. Calculations show that the dehydrogenated radicals and anions have relatively high stabilities compared with the single base adenine and thymine. The electron attachment to the A-T base pair and its derivatives significantly modifies the hydrogen bond interactions and results in remarkable structural changes. As for the dehydrogenated A-T radicals, they have relatively high electron affinities and different dehydrogenation properties with respect to their constituent elements. The relatively low-cost hydrogen eliminations correspond to the (N9)-H (adenine) and (N1)-H (thymine) bonds cleavage. Both dehydrogenation processes have Gibbs free energies of reaction DeltaG degrees of 13.4 and 17.2 kcal mol-1, respectively. The solvent water exhibits significant effect on electron attachment and dehydrogenation properties of the A-T base pair and its derivatives. In the dehydrogenating process, the anionic A-T fragment gradually changes its electronic configuration from pi* to sigma* state, like the single bases adenine and thymine.
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Affiliation(s)
- Hujun Xie
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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29
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Jena NR, Mishra PC. Interaction of Guanine, Its Anions, and Radicals with Lysine in Different Charge States. J Phys Chem B 2007; 111:5418-24. [PMID: 17432899 DOI: 10.1021/jp0703004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Modification in DNA or protein structure can severely affect DNA-protein interactions and the functioning of biological systems. Some new insights into radiation-induced effects of guanine-lysine interactions have been obtained here by theoretical investigations. Geometries of zwitterionic and non-zwitterionic lysine in different charge states (neutral, radical cation, and protonated cation) were optimized employing the B3LYP/6-31G** and B3LYP/AUG-cc-pVDZ levels of hybrid density functional theory (DFT) and using the second-order Møller-Plesset perturbation theory along with the 6-31G** basis set. In the case of neutral lysine in the gas phase, no zwitterionic structure was obtained. The non-zwitterionic structures of lysine in radical and protonated cationic forms are appreciably more stable than the corresponding zwitterionic structures in the gas phase as obtained at all levels of theory employed here. Binding of guanine and different dehydrogenated guanine radicals with lysine in different charge states was studied at the B3LYP/6-31G** level of DFT. When guanine makes a complex with the lysine radical cation, large amounts of spin and positive charge densities are transferred from the lysine radical cation to guanine and the guanine is thus converted from its normal form to the radical cationic form. Complexation of the lysine radical cation with the H1-hydrogen-abstracted guanine radical leads to CO2 liberation and proton transfer from lysine. These results are compared with the available experimental ones.
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Affiliation(s)
- N R Jena
- Department of Physics, Banaras Hindu University, Varanasi-221005, India
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30
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Quinn JR, Zimmerman SC, Del Bene JE, Shavitt I. Does the A·T or G·C Base-Pair Possess Enhanced Stability? Quantifying the Effects of CH···O Interactions and Secondary Interactions on Base-Pair Stability Using a Phenomenological Analysis and ab Initio Calculations. J Am Chem Soc 2007; 129:934-41. [PMID: 17243830 DOI: 10.1021/ja066341f] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An empirically based relationship between overall complex stability (-DeltaG degrees ) and various possible component interactions is developed to probe the question of whether the A.T/U and G.C base-pairs exhibit enhanced stability relative to similarly hydrogen-bonded complexes. This phenomenological approach suggests ca. 2-2.5 kcal mol-1 in additional stability for A.T owing to a group interaction containing a CH...O contact. Pairing geometry and the role of the CH...O interaction in the A.T base-pair were also probed using MP2/6-31+G(d,p) calculations and a double mutant cycle. The ab initio studies indicated that Hoogsteen geometry is preferred over Watson-Crick geometry in A.T by ca. 1 kcal mol-1. Factors that might contribute to the preference for Hoogsteen geometry are a shorter CH...O contact, a favorable alignment of dipoles, and greater distances between secondary repulsive sites. The CH...O interaction was also investigated in model complexes of adenine with ketene and isocyanic acid. The ab initio calculations support the result of the phenomenological approach that the A.T base-pair does have enhanced stability relative to hydrogen-bonded complexes with just N-H...N and N-H...O hydrogen bonds.
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Affiliation(s)
- Jordan R Quinn
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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31
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Adhikary A, Kumar A, Becker D, Sevilla MD. The guanine cation radical: investigation of deprotonation states by ESR and DFT. J Phys Chem B 2006; 110:24171-80. [PMID: 17125389 PMCID: PMC2526163 DOI: 10.1021/jp064361y] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work reports ESR studies that identify the favored site of deprotonation of the guanine cation radical (G*+) in an aqueous medium at 77 K. Using ESR and UV-visible spectroscopy, one-electron oxidized guanine is investigated in frozen aqueous D2O solutions of 2'-deoxyguanosine (dGuo) at low temperatures at various pHs at which the guanine cation radical, G*+ (pH 3-5), singly deprotonated species, G(-H)* (pH 7-9), and doubly deprotonated species, G(-2H)*- (pH > 11), are found. C-8-deuteration of dGuo to give 8-D-dGuo removes the major proton hyperfine coupling at C-8. This isolates the anisotropic nitrogen couplings for each of the three species and aids our analyses. These anisotropic nitrogen couplings were assigned to specific nitrogen sites by use of 15N-substituted derivatives at N1, N2, and N3 atoms in dGuo. Both ESR and UV-visible spectra are reported for each of the species: G*+, G(-H)*, and G(-2H)*-. The experimental anisotropic ESR hyperfine couplings are compared to those obtained from DFT calculations for the various tautomers of G(-H)*. Using the B3LYP/6-31G(d) method, the geometries and energies of G*+ and its singly deprotonated state in its two tautomeric forms, G(N1-H)* and G(N2-H)*, were investigated. In a nonhydrated state, G(N2-H)* is found to be more stable than G(N1-H)*, but on hydration with seven water molecules G(N1-H)* is found to be more stable than G(N2-H)*. The theoretically calculated hyperfine coupling constants (HFCCs) of G*+, G(N1-H)*, and G(-2H)*- match the experimentally observed HFCCs best on hydration with seven or more waters. For G(-2H)*-, the hyperfine coupling constant (HFCC) at the exocyclic nitrogen atom (N2) is especially sensitive to the number of hydrating water molecules; good agreement with experiment is not obtained until nine or 10 waters of hydration are included.
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Affiliation(s)
| | - Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309
| | - David Becker
- Department of Chemistry, Oakland University, Rochester, MI 48309
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33
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Kumar A, Mishra PC, Suhai S. Binding of Gold Clusters with DNA Base Pairs: A Density Functional Study of Neutral and Anionic GC−Aun and AT−Aun (n = 4, 8) Complexes. J Phys Chem A 2006; 110:7719-27. [PMID: 16774220 DOI: 10.1021/jp060932a] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Binding of clusters of gold atoms (Au) with the guanine-cytosine (GC) and adenine-thymine (AT) Watson-Crick DNA base pairs was studied using the density functional theory (DFT). Geometries of the neutral GC-Au(n) and AT-Au(n) and the corresponding anionic (GC-Au(n))(-1) and (AT-Au(n))(-1) (n = 4, 8) complexes were fully optimized in different electronic states, that is, singlet and triplet states for the neutral complexes and doublet and quartet states for the anionic complexes, using the B3LYP density functional method. The 6-31+G basis set was used for all atoms except gold. For gold atoms, the Los Alamos effective core potential (ECP) basis set LanL2DZ was employed. Vibrational frequency calculations were performed to ensure that the optimized structures corresponded to potential energy surface minima. The gold clusters around the neutral GC and AT base pairs have a T-shaped structure, which satisfactorily resemble those observed experimentally and in other theoretical studies. However, in anionic GC and AT base pairs, the gold clusters have extended zigzag and T-shaped structures. We found that guanine and adenine have high affinity for Au clusters, with their N3 and N7 sites being preferentially involved in binding with the same. The calculated adiabatic electron affinities (AEAs) of the GC-Au(n)complexes (n = 4, 8) were found to be much larger than those of the isolated base pairs.
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Affiliation(s)
- Anil Kumar
- Department of Physics, Banaras Hindu University, Varanasi-221 005, India
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34
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Lind MC, Bera PP, Richardson NA, Wheeler SE, Schaefer HF. The deprotonated guanine-cytosine base pair. Proc Natl Acad Sci U S A 2006; 103:7554-9. [PMID: 16684882 PMCID: PMC1472485 DOI: 10.1073/pnas.0600654103] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Indexed: 11/18/2022] Open
Abstract
Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26-27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine-cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal x mol(-1), vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal x mol(-1) lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H...O2 distance dramatically reduced from 1.88 to 1.58 A, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a "reverse wobble" incorporating two N-H...N hydrogen bonds. Three different types of relaxation energies (4.3-54 kcal x mol(-1)) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.
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Affiliation(s)
- Maria C Lind
- Center for Computational Chemistry, University of Georgia, Athens, GA 30602, USA.
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35
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Villani G. Theoretical investigation of hydrogen transfer mechanism in the guanine–cytosine base pair. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.11.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bao X, Sun H, Wong NB, Gu J. Microsolvation Effect, Hydrogen-Bonding Pattern, and Electron Affinity of the Uracil−Water Complexes U−(H2O)n (n = 1, 2, 3). J Phys Chem B 2006; 110:5865-74. [PMID: 16553392 DOI: 10.1021/jp055329r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To achieve a systematic understanding of the influence of microsolvation on the electron accepting behaviors of nucleobases, the reliable theoretical method (B3LYP/DZP++) has been applied to a comprehensive conformational investigation on the uracil-water complexes U-(H(2)O)(n) (n = 1, 2, 3) in both neutral and anionic forms. For the neutral complexes, the conformers of hydration on the O2 of uracil are energetically favored. However, hydration on the O4 atom of uracil is more stable for the radical anions. The electron structure analysis for the H-bonding patterns reveal that the CH...OH(2) type H-bond exists only for di- and trihydrated uracil complexes in which a water dimer or trimer is involved. The electron density structure analysis and the atoms-in-molecules (AIM) analysis for U-(H(2)O)(n) suggest a threshold value of the bond critical point (BCP) density to justify the CH...OH(2) type H-bond; that is, CH...OH(2) could be considered to be a H-bond only when its BCP density value is equal to or larger than 0.010 au. The positive adiabatic electron affinity (AEA) and vertical detachment energy (VDE) values for the uracil-water complexes suggest that these hydrated uracil anions are stable. Moreover, the average AEA and VDE of U-(H(2)O)(n) increase as the number of the hydration waters increases.
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Affiliation(s)
- Xiaoguang Bao
- Drug Design & Discovery Center, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China
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Villani G. Theoretical investigation of hydrogen transfer mechanism in the adenine–thymine base pair. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.04.030] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gu J, Xie Y, Schaefer HF. Structural and Energetic Characterization of a DNA Nucleoside Pair and Its Anion: Deoxyriboadenosine (dA) − Deoxyribothymidine (dT). J Phys Chem B 2005; 109:13067-75. [PMID: 16852625 DOI: 10.1021/jp0515535] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometries of the DNA nucleoside pairs between 2'-deoxyriboadenosine (dA) and 2'-deoxyribothymidine (dT) and its anion (dAdT-) were fully optimized using carefully calibrated density functional methods. The addition of an electron to dAdT results in remarkable changes to the two hydrogen bonding distances, the H...O distance decreasing by 0.303 angstroms and the N...H distance increasing by 0.229 angstroms. The electron affinity of the dAdT pair was studied to reveal the correct trends of adiabatic electron affinity (EA(ad)) under the influence of the additional components to the individual bases. The consequence of negative charge in terms of structural variations, energetic changes, and charge distribution were explored. The EA(ad) of dAdT is predicted to be positive (0.60 eV), and it exhibits a substantial increase compared with those of the corresponding bases A and T and the nucleic acid base pair AT. The effects of pairing and the addition of the sugar moiety on the EA(ad) are well described as the summation of the individual influences. The influence of the pairing on the EA is comparable to that of the addition of 2-deoxyribose. The excess charge is mainly located on the thyminyl moiety in the anionic dAdT pair. The positive vertical electron affinity (VEA = 0.20 eV) for dAdT suggests that it is able to form a stable anion through electron attachment. A large vertical detachment energy (VDE = 1.14 eV) has been determined for the anionic dAdT nucleoside pair. Therefore, one may expect that the stable anionic dAdT nucleoside pair should be able to undergo the subsequent glycosidic bond cleavage process.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203 PR China.
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Tian SX. Marked Influences on the Adenine−Cytosine Base Pairs by Electron Attachment and Ionization. J Phys Chem A 2005; 109:5153-9. [PMID: 16833870 DOI: 10.1021/jp050137h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reverse wobble and the reverse Hoogsteen adenine-cytosine mispairs regarding their radical cations and anions are studied with the hybrid three-parameter B3LYP density functional method and 6-31+G(d), 6-311+G(2df,2p) basis sets. Hydrogen bonding mispairs are remarkably influenced by electron attachment and ionization. Only one stronger hydrogen bond N6-H (in adenine)...N3 (in cytosine) exists in the radical pair, while the strengths of two N-H...N hydrogen bonds in the neutral pair are comparable. Geometrical coplanarity is found for the neutral and cationic pairs, in contrast to the anionic pairs in which the cytosine moiety exhibits significant deformation due to electron attachment. Dissociation energies for the neutral and radical pairs are slightly higher than those of the adenine-thymine pairs but much smaller than those of the guanine-cytosine pairs. Valence-bound anions of these two adenine-cytosine pairs are thermodynamically stable by 0.1-0.2 eV with respect to the neutral pairs. On the basis of the comparison between the experimental data of the solvated clusters and the calculated values, these two pairs can be quantitatively equivalent to the clusters in which each base is solvated by five water molecules.
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Affiliation(s)
- Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Bond Selective Chemistry, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.
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Kumar A, Mishra PC, Suhai S. Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study. J Phys Chem A 2005; 109:3971-9. [PMID: 16833718 DOI: 10.1021/jp0456178] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.
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Affiliation(s)
- Anil Kumar
- Department of Physics, Banaras Hindu University, Varanasi-221 005, India
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Radisic D, Bowen KH, Dabkowska I, Storoniak P, Rak J, Gutowski M. AT Base Pair Anions versus (9-Methyl-A)(1-Methyl-T) Base Pair Anions. J Am Chem Soc 2005; 127:6443-50. [PMID: 15853352 DOI: 10.1021/ja050724g] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The anionic base pairs of adenine and thymine, (AT)(-), and 9-methyladenine and 1-methylthymine, (MAMT)(-), have been investigated both theoretically and experimentally in a complementary, synergistic study. Calculations on (AT)(-) found that it had undergone a barrier-free proton transfer (BFPT) similar to that seen in other dimer anion systems and that its structural configuration was neither Watson-Crick (WC) nor Hoogsteen (HS). The vertical detachment energy (VDE) of (AT)(-) was determined by anion photoelectron spectroscopy and found to be in agreement with the VDE value predicted by theory for the BFPT mechanism. An AT pair in DNA is structurally immobilized into the WC configuration, in part, by being bonded to the sugars of the double helix. This circumstance was mimicked by methylating the sites on both A and T where these sugars would have been tied, viz., 9-methyladenine and 1-methylthymine. Calculations found no BFPT in (MAMT)(-) and a resulting (MAMT)(-) configuration that was either HS or WC, with the configurations differing in stability by ca. 2 kcal/mol. The photoelectron spectrum of (MAMT)(-) occurred at a completely different electron binding energy than had (AT)(-). Moreover, the VDE value of (MAMT)(-) was in agreement with that predicted by theory. The configuration of (MAMT)(-) and its lack of electron-induced proton transfer are inter-related. While there may be other pathways for electron-induced DNA alterations, BFPT in the WC/HS configurations of (AT)(-) is not feasible.
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Affiliation(s)
- Dunja Radisic
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Tsolakidis A, Kaxiras E. A TDDFT Study of the Optical Response of DNA Bases, Base Pairs, and Their Tautomers in the Gas Phase. J Phys Chem A 2005; 109:2373-80. [PMID: 16839008 DOI: 10.1021/jp044729w] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present calculations of the optical response of the DNA bases and base pairs both in their normal and tautomeric forms in the gas phase, using time-dependent density functional theory (TDDFT). These calculations are performed in real time within the adiabatic approximation with a basis of local orbitals. Our results for the individual bases are in good agreement with experiment and computationally more demanding calculations of chemical accuracy. The optical response of base pairs indicates that the differences between normal and tautomeric forms in certain cases are significant enough to provide a means of identification.
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Affiliation(s)
- Argyrios Tsolakidis
- Department of Physics and Division of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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Svozil D, Jungwirth P, Havlas Z. Electron Binding to Nucleic Acid Bases. Experimental and Theoretical Studies. A Review. ACTA ACUST UNITED AC 2004. [DOI: 10.1135/cccc20041395] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
An in-depth knowledge of an excess electron binding mechanism to DNA and RNA nucleobases is important for our understanding of radiation damage influence on the biological functions of nucleic acids, as well as for the possible use of DNA molecules as wires in molecular electronic circuits. The of anions created by electron attachment to individual nucleic acid bases is discussed in detail. The principles of the experimental and theoretical approaches to the description of these anions are outlined, and the available results concerning valence- and dipole-bound anions of nucleic acid bases are reviewed. A review with 167 references.
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