1
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Narayanan S J J, Bachhar A, Tripathi D, Dutta AK. Electron Attachment to Wobble Base Pairs. J Phys Chem A 2023; 127:457-467. [PMID: 36622294 DOI: 10.1021/acs.jpca.2c07469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have analyzed the low-energy electron attachment to wobble base pairs using the equation of motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.
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Affiliation(s)
- Jishnu Narayanan S J
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Arnab Bachhar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Divya Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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2
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Banerjee S, Sokolov AY. Efficient implementation of the single-reference algebraic diagrammatic construction theory for charged excitations: Applications to the TEMPO radical and DNA base pairs. J Chem Phys 2021; 154:074105. [PMID: 33607870 DOI: 10.1063/5.0040317] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We present an efficient implementation of the second- and third-order single-reference algebraic diagrammatic construction (ADC) theory for electron attachment and ionization energies and spectra [EA/IP-ADC(n), n = 2, 3]. Our new EA/IP-ADC program features spin adaptation for closed-shell systems, density fitting for efficient handling of the two-electron integral tensors, and vectorized and parallel implementation of tensor contractions. We demonstrate capabilities of our efficient implementation by applying the EA/IP-ADC(n) (n = 2, 3) methods to compute the photoelectron spectrum of the (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) radical, as well as the vertical and adiabatic electron affinities of TEMPO and two DNA base pairs (guanine-cytosine and adenine-thymine). The spectra and electron affinities computed using large diffuse basis sets with up to 1028 molecular orbitals are found to be in good agreement with the best available results from the experiment and theoretical simulations.
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Affiliation(s)
- Samragni Banerjee
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alexander Yu Sokolov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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3
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Crystallographic evidence of Watson-Crick connectivity in the base pair of anionic adenine with thymine. Proc Natl Acad Sci U S A 2020; 117:18224-18230. [PMID: 32680959 PMCID: PMC7414232 DOI: 10.1073/pnas.2008379117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N4444]+) or tetrabutylphosphonium ([P4444]+) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N4444][Ad]·2H2O, and thymine, [P4444][Thy]·2H2O, as well as the double salt cocrystal, [P4444]2[Ad][Thy]·3H2O·2HThy. The cocrystal includes the anionic [Ad-(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson-Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.
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4
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Tripathi D, Dutta AK. Electron Attachment to DNA Base Pairs: An Interplay of Dipole- and Valence-Bound States. J Phys Chem A 2019; 123:10131-10138. [DOI: 10.1021/acs.jpca.9b08974] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Divya Tripathi
- Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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5
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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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6
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Li M, Diao L, Liao X, Kou L, Lu W. DFT study on addition reaction mechanism of guanine-cytosine base pair with OH radical. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Minjie Li
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Ling Diao
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Xiaofei Liao
- School of Information Science and Technology; Donghua University; Shanghai 201620 China
| | - Li Kou
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Wencong Lu
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
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7
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Intriguing radical–radical interactions among double-electron oxidized adenine–thymine base pairs. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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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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9
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Dutta AK, Gupta J, Pathak H, Vaval N, Pal S. Partitioned EOMEA-MBPT(2): An Efficient N5 Scaling Method for Calculation of Electron Affinities. J Chem Theory Comput 2014; 10:1923-33. [DOI: 10.1021/ct4009409] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Achintya Kumar Dutta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India
| | - Jitendra Gupta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India
| | - Himadri Pathak
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India
| | - Nayana Vaval
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India
| | - Sourav Pal
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India
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10
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Gryn’ova G, Coote ML. Origin and Scope of Long-Range Stabilizing Interactions and Associated SOMO–HOMO Conversion in Distonic Radical Anions. J Am Chem Soc 2013; 135:15392-403. [DOI: 10.1021/ja404279f] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ganna Gryn’ova
- ARC Centre of Excellence
for Free Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence
for Free Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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11
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Wu Y, Wang H, Lin Y, Gao S, Zhang F. Hydrogen-bonded proton transfer in the hydrated adenine–thymine anion. CAN J CHEM 2013. [DOI: 10.1139/cjc-2013-0162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The proton transfer processes of microhydrated adenine–thymine anions are studied using density functional theory with the B3LYP method and DZP++ basis set. The microhydration effects on the geometrical structures, adsorption site, and the proton transfer reaction of the adenine–thymine anion are investigated. The site N10 atom of the adenine moiety has a larger proton affinity than the site O24 atom of thymine, which facilitates the proton H26 transfers from the N25 site of thymine to the N10 site of adenine. Therefore, the first single-proton transfer pathway (SPT1) is found for the all of the monohydrated adenine–thymine anions (AN4T)−·H2O, (AN13T)−·H2O, (ATO24)−·H2O, and (ATO28)−·H2O and tetrahydrated adenine–thymine anions (AT)−·4H2O. The proton H9 at the N7 site of adenine is also found to transfer to the O24 site of thymine for (AN4T)−·H2O and (AN13T)−·H2O in the gas phase. The double-proton transferred pathway is found when one water molecule interacts with the O28 atom of thymine. The reactant structures before the proton transfer are more stable than the product structures, and the structural changes mainly occur in thymine. The reaction energies of the microhydrated adenine–thymine anion in the gas phase and in the aqueous environment predict that the proton transfer process of the microhydrated adenine–thymine anion are more favorable in the gas phase than in aqueous solution.
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Affiliation(s)
- Yingxi Wu
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Hongyan Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Yuexia Lin
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Simin Gao
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Feng Zhang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
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12
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Zhao J, Wang M, Yang H, Zhang M, Liu P, Bu Y. Radical–Radical Interactions among Oxidized Guanine Bases Including Guanine Radical Cation and Dehydrogenated Guanine Radicals. J Phys Chem B 2013; 117:10698-710. [DOI: 10.1021/jp4042149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Zhao
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Mei Wang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Hongfang Yang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Meng Zhang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Ping Liu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Yuxiang Bu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
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13
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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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14
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Jissy AK, Konar S, Datta A. Molecular Switching Behavior in Isosteric DNA Base Pairs. Chemphyschem 2013; 14:1219-26. [DOI: 10.1002/cphc.201201083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Indexed: 12/22/2022]
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15
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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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16
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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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17
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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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18
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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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19
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Gu J, Liang G, Xie Y, Schaefer HF. Electron attachment to solvated dGpdG: effects of stacking on base-centered and phosphate-centered valence-bound radical anions. Chemistry 2012; 18:5232-8. [PMID: 22431283 DOI: 10.1002/chem.201103850] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 01/30/2012] [Indexed: 11/06/2022]
Abstract
To explore the nature of electron attachment to guanine-centered DNA single strands in the presence of a polarizable medium, a theoretical investigation of the DNA oligomer dinucleoside phosphate deoxyguanylyl-3',5'-deoxyguanosine (dGpdG) was performed by using density functional theory. Four different electron-distribution patterns for the radical anions of dGpdG in aqueous solution have been located as local minima on the potential energy surface. The excess electron is found to reside on the proton of the phosphate group (dGp(H-)dG), or on the phosphate group (dGp(.-)dG), or on the nucleobase at the 5' position (dG(.-)pdG), or on the nucleobase at the 3' position (dGpdG(.-)), respectively. These four radical anions are all expected to be electronically viable species under the influence of the polarizable medium. The predicted energetics of the radical anions follows the order dGp(.-)dG>dG(.-)pdG>dGpdG(.-)>dGp(H-)dG. The base-base stacking pattern in DNA single strands seems unaffected by electron attachment. On the contrary, intrastrand H-bonding is greatly influenced by electron attachment, especially in the formation of base-centered radical anions. The intrastrand H-bonding patterns revealed in this study also suggest that intrastrand proton transfer might be possible between successive guanines due to electron attachment to DNA single strands.
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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, Chinese Academy of Sciences, Shanghai 201203, P. R. China.
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20
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Cheng Q, Gu J, Compaan KR, Schaefer HF. Isoguanine formation from adenine. Chemistry 2012; 18:4877-86. [PMID: 22411110 DOI: 10.1002/chem.201102415] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Indexed: 11/06/2022]
Abstract
Several possible mechanisms underlying isoguanine formation when OH radical attacks the C(2) position of adenine (A C 2) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A C 2⋅⋅⋅OH reactant complexes is formed, leading to C(2)-H(2) bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG 1 or isoG 2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20 kcal mol(-1) , indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH(⋅) →isoG+H(⋅) reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG 1 has the lowest energy. Our findings explain why only the N(1)H and O(2)H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.
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Affiliation(s)
- Qianyi Cheng
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA
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21
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Gu J, Wang J, Leszczynski J. Electron Attachment to the Cytosine-Centered DNA Single Strands: Does Base Stacking Matter? J Phys Chem B 2012; 116:1458-66. [DOI: 10.1021/jp211386x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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, P. R. 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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22
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Peng B, McNew SR, Li QS, Xie Y, Schaefer HF. Remarkable hydrogen bonding in the radical anions of guanine–cytosine and adenine–thymine. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Ivanova B, Spiteller M. Conformation, optical properties, and absolute configuration of 2′,3′-isopropylideneadenosines: Theoretical vs. experimental study. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.08.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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24
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Jena NR, Bansal M. Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair. Phys Biol 2011; 8:046007. [PMID: 21666294 DOI: 10.1088/1478-3975/8/4/046007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg128 into the DNA double helix and its interaction with the O6MG:C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.
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Affiliation(s)
- N R Jena
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India.
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25
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Li X, Chen J, Bowen KH. Photoelectron spectroscopic study of the negative ions of 4-thiouracil and 2,4-dithiouracil. J Chem Phys 2011; 134:074304. [DOI: 10.1063/1.3555177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gu J, Wong NB, Xie Y, Schaefer FH. Electron attachment to a hydrated DNA duplex: the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine. Chemistry 2011; 16:13155-62. [PMID: 20922718 DOI: 10.1002/chem.201001306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.
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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, P. R. China.
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Kim S, Schaefer HF. Vertical detachment energies of anionic thymidine: Microhydration effects. J Chem Phys 2010; 133:144305. [DOI: 10.1063/1.3488105] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cheng Q, Gu J, Compaan KR, Schaefer HF. Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes. Chemistry 2010; 16:11848-58. [DOI: 10.1002/chem.201001236] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Qianyi Cheng
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
| | - Jiande Gu
- Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203 (P. R. China)
| | - Katherine R. Compaan
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
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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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Storoniak P, Mazurkiewicz K, Haranczyk M, Gutowski M, Rak J, Eustis SN, Ko YJ, Wang H, Bowen KH. The Anionic (9-Methyladenine)−(1-Methylthymine) Base Pair Solvated by Formic Acid. A Computational and Photoelectron Spectroscopy Study. J Phys Chem B 2010; 114:11353-62. [DOI: 10.1021/jp104668h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Piotr Storoniak
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Kamil Mazurkiewicz
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Maciej Haranczyk
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Maciej Gutowski
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Janusz Rak
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Soren N. Eustis
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., 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, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - Haopeng Wang
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., 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, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50F-1650, Berkeley, California 94720-8139, Chemistry-School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K., and Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
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Gu J, Xie Y, Schaefer HF. Electron attachment to hydrated oligonucleotide dimers: guanylyl-3',5'-cytidine and cytidylyl-3',5'-guanosine. Chemistry 2010; 16:5089-96. [PMID: 20349466 DOI: 10.1002/chem.200902977] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The dinucleoside phosphate deoxycytidylyl-3',5'-deoxyguanosine (dCpdG) and deoxyguanylyl-3',5'-deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5' end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3' end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine-containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The pi-stacking interaction between nucleobases G and C seems unlikely to improve the electron-capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron-capturing ability of cytosine should be attributed to the intensified proton accepting-donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O-C sigma bond and N-glycosidic bond breakage, might be expected for the radical anions of the guanosine-cytosine mixed oligonucleotides.
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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, P. R. China.
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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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Sevilla MD. Comment on "Excited states of DNA base pairs using long-range corrected time-dependent density functional theory". J Phys Chem A 2009; 113:11093-4; discussion 11095. [PMID: 19764792 PMCID: PMC4679139 DOI: 10.1021/jp908098a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Michael D Sevilla
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA.
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34
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Voityuk AA. Stabilization of radical anion states of nucleobases in DNA. Phys Chem Chem Phys 2009; 11:10608-13. [PMID: 20145805 DOI: 10.1039/b910690a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trapping of an electron by DNA leads to the formation of radical anion states of pyrimidine bases. Because these states play an important role in biological and chemical processes, their computational treatment is of particular interest. We show that simple electrostatic and quantum chemical models can accurately reproduce the adiabatic electron affinities (EAs) of short DNA stacks recently derived from high-level ab initio calculations (M. Kobylecka, J. Leszczynski, and J. Rak, J. Am. Chem. Soc., 2008, 130, 15683). The electrostatic interaction of an excess electron localized on cytosine or thymine with intra- and inter-strand adjacent nucleobases is found to strongly affect the energy of the radical anions. This interaction is the main origin of the dependence of EA of nucleobases on the nature of neighboring base pairs. In particular, the states XT(-)Y and XC(-)Y, where X and Y = C, T, are, by ca. 0.7 eV, more stable than radical anions GT(-)G and GC(-)G. We find that second-neighbor effects can also significantly modulate EAs, although being smaller than the effects of adjacent bases. The strongest destabilizing effect is found for 5'-GC and 3'-GC, while the 5'-AT base pair stabilizes the radical anion states. Using a combined QM/MD approach, we consider how structural fluctuations of DNA influence the stability of the radical anion states. Despite large dispersions of the stabilization energies due to conformational dynamics of DNA, there are only few thermally accessible structures where GT(-)G and GC(-)G are energetically more favorable than the corresponding pyrimidine triplets. Although stabilization energies calculated for stacks of regular structure are in qualitative agreement with the QM/MD results, structural fluctuations of pi stacks should be taken into account for more accurate description of the excess electron trapped by DNA. The results obtained in this study suggest that simple electrostatic models, in combination with MD simulations, can be very helpful to explore the long time scale behavior of radical anions in DNA.
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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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Gu J, Xie Y, Schaefer HF. Electron attachment to oligonucleotide dimers in water: Microsolvation-assisted base-stacking forms. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Duncan Lyngdoh RH, Schaefer HF. Elementary lesions in DNA subunits: electron, hydrogen atom, proton, and hydride transfers. Acc Chem Res 2009; 42:563-72. [PMID: 19231845 DOI: 10.1021/ar800077q] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
When DNA is damaged by ionizing radiation, the genes in a cell may acquire mutations or the cell could die. The smallest known DNA-damaging unit is an electron, often low-energy secondary electrons. Additional electrons and transfers involving hydrogen atoms, protons, and hydride anions can damage DNA subunits, including individual nucleobases and nucleoside pairs. Researchers would like to better understand the molecular mechanisms involved in DNA damage from ionizing radiation. In this Account, we highlight our theoretical investigations of the molecular mechanisms of DNA damage using quantum mechanical models. Our investigations use robust theoretical methods with computations conducted in the gas phase and with solution models. We calculate adiabatic electron affinities (AEAs), which describe the energetics of electronic attachment to closed-shell DNA subunits, for the free bases, nucleosides, nucleotides, base pairs, and single and double DNA strand units. Electron affinities for free nucleobases yield the order uracil > thymine > cytosine > guanine > adenine and the same order for the DNA nucleosides, mononucleotides, and nucleoside 3',5'-diphosphates. AEA values increase steadily with the size and complexity of the system because of greater hydration, glycosylation, nucleotide formation, and base pairing. We predict and experimental results partially confirm that most of the more complex and hydrated species are observable as radical anions. Our modeling studies indicate that depyrimidination reactions of radical anion nucleosides release cytosine more often than thymine. Recent experimental results support those findings. Our theoretical studies of DNA base-pair radical anions predict increases in electron affinity accompanying H bonding and solvation. Electron addition facilitates some proton transfers in these pairs, which results in strongly perturbed pairing configurations. Of all nucleobase moieties within the more complex radical anion systems, thymine is best able to retain a negative charge. Charge and spin are well-separated in some of these systems. Radical species derived via hydrogen abstraction from DNA subunits yield large AEA values because they form closed-shell anions. Our studies predict single-strand breaks following H abstraction from nucleotides. Some H-abstraction processes in the DNA base pairs lead to severe distortions in pairing configuration based on our calculations. This body of systematic theoretical studies provides realistic descriptions of some events that lead to elementary DNA lesions, while providing rationalizations for many observed phenomena. Such approaches can lead to the design of new experiments, which would contribute to our understanding of the chemical physics of nucleic acids.
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Affiliation(s)
| | - Henry F. Schaefer
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
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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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Roca-Sanjuán D, Merchán M, Serrano-Andrés L, Rubio M. Ab initio determination of the electron affinities of DNA and RNA nucleobases. J Chem Phys 2009; 129:095104. [PMID: 19044892 DOI: 10.1063/1.2958286] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the accurate determination of the intrinsic electron acceptor properties of the isolated nucleic acid bases as described by their electron affinities, establishing an overall set of theoretical reference values at a level not reported before and helping to rule out less reliable theoretical and experimental data and to calibrate theoretical strategies.
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Affiliation(s)
- Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de Valencia, Apartado 22085, ES-46071 Valencia, Spain
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Puiatti M, Vera DMA, Pierini AB. In search for an optimal methodology to calculate the valence electron affinities of temporary anions. Phys Chem Chem Phys 2009; 11:9013-24. [DOI: 10.1039/b908870a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Wyer JA, Cederquist H, Haag N, Huber BA, Hvelplund P, Johansson HAB, Maisonny R, Brøndsted Nielsen S, Rangama J, Rousseau P, Schmidt HT. On the hydrogen loss from protonated nucleobases after electronic excitation or collisional electron capture. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:681-688. [PMID: 19940334 DOI: 10.1255/ejms.1039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this work, we have subjected protonated nucleobases MH(+) (M = guanine, adenine, thymine, uracil and cytosine) to a range of experiments that involve high-energy (50 keV) collision induced dissociation and electron capture induced dissociation. In the latter case, both neutralisation reionisation and charge reversal were done. For the collision induced dissociation experiments, the ions interacted with O(2). In neutral reionisation, caesium atoms were used as the target gas and the protonated nucleobases captured electrons to give neutrals. These were reionised to cations a microsecond later in collisions with O(2). In choosing Cs as the target gas, we have assured that the first electron transfer process is favourable (by about 0.1-0.8 eV depending on the base). In the case of protonated adenine, charge reversal experiments (two Cs collisions) were also carried out, with the results corroborating those from the neutralisation reionisation experiments. We find that while collisional excitation of protonated nucleobases in O(2) may lead to hydrogen loss with limited probabilities, this channel becomes dominant for electron capture events. Indeed, when sampling reionised neutrals on a microsecond timescale, we see that the ratio between MH(+) and M(+) is 0.2-0.4 when one electron is captured from Cs. There are differences in these ratios between the bases but no obvious correlation with recombination energies was found.
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Affiliation(s)
- Jean Ann Wyer
- Department of Physics and Astronomy, Aarhus University, Ny Munkegade, DK-8000 Aarhus C, Denmark.
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42
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Seal P, Jha PC, Ågren H, Chakrabarti S. Magnetic interactions in dehydrogenated Guanine–Cytosine base pair. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.09.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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Sarmah P, Deka RC. Density functional studies on the electron affinities of DNA and RNA bases. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020802235664] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Pubalee Sarmah
- a Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
| | - Ramesh C. Deka
- a Department of Chemical Sciences, Tezpur University, Tezpur, 784028, Assam, India
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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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Félix M, Voityuk AA. Parameters For Excess Electron Transfer in DNA. Estimation Using Unoccupied Kohn−Sham Orbitals and TD DFT. J Phys Chem A 2008; 112:9043-9. [DOI: 10.1021/jp803636x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Martín Félix
- Institut de Química Computational, Departament de Química, Universitat de Girona, 17071 Girona, Spain, and Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
| | - Alexander A. Voityuk
- Institut de Química Computational, Departament de Química, Universitat de Girona, 17071 Girona, Spain, and Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
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Zhang JD, Chen Z, Schaefer HF. Electron attachment to the hydrogenated Watson-Crick guanine cytosine base pair (GC+H): conventional and proton-transferred structures. J Phys Chem A 2008; 112:6217-26. [PMID: 18557604 DOI: 10.1021/jp711958p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The anionic species resulting from hydride addition to the Watson-Crick guanine-cytosine (GC) DNA base pair are investigated theoretically. Proton-transferred structures of GC hydride, in which proton H1 of guanine or proton H4 of cytosine migrates to the complementary base-pair side, have been studied also. All optimized geometrical structures are confirmed to be minima via vibrational frequency analyses. The lowest energy structure places the additional hydride on the C6 position of cytosine coupled with proton transfer, resulting in the closed-shell anion designated 1T (G(-)C(C6)). Energetically, the major groove side of the GC pair has a greater propensity toward hydride/hydrogen addition than does the minor grove side. The pairing (dissociation) energy and electron-attracting ability of each anionic structure are predicted and compared with those of the neutral GC and the hydrogenated GC base pairs. Anion 8T (G(O6)C(-)) is a water-extracting complex and has the largest dissociation energy. Anion 2 (GC(C4)(-)) and the corresponding open-shell radical GC(C4) have the largest vertical electron detachment energy and adiabatic electron affinity, respectively. From the difference between the dissociation energy and electron-removal ability of the normal GC anion and the most favorable structure of GC hydride, it is clear that one may dissociate the GC anion and maintain the integrity of the GC hydride.
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Affiliation(s)
- J David Zhang
- Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, GA 30602-2525, USA
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Affiliation(s)
- Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea.
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49
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Puiatti M, Vera DMA, Pierini AB. Species with negative electron affinity and standard DFT methods. Finding the valence anions. Phys Chem Chem Phys 2008; 10:1394-9. [PMID: 18309394 DOI: 10.1039/b716625g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, we have shown that traditional bound-electron DFT models are reliable enough to reproduce negative electron affinities (EA) within a few meV, as long as the valence anion state is found, but they seem to fail in predicting the lowest EA when the ground anion state obtained is non-valence, which holds the extra electron in a diffuse orbital around the molecule; here we propose an alternative approach for finding the valence anion state, based on the stabilization exerted by a polar solvent; the methodology yields correct EA values (i.e. beyond the Koopman's theorem approximation) by gradually decreasing the dielectric constant of the medium.
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Affiliation(s)
- Marcelo Puiatti
- INFIQC, Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000 Córdoba, Argentina
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50
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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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