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Sedmidubská B, Kočišek J. Interaction of low-energy electrons with radiosensitizers. Phys Chem Chem Phys 2024; 26:9112-9136. [PMID: 38376461 DOI: 10.1039/d3cp06003a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
We provide an experimentalist's perspective on the present state-of-the-art in the studies of low-energy electron interactions with common radiosensitizers, including compounds used in combined chemo-radiation therapy and their model systems. Low-energy electrons are important secondary species formed during the interaction of ionizing radiation with matter. Their role in the radiation chemistry of living organisms has become an important topic for more than 20 years. With the increasing number of works and reviews in the field, we would like to focus here on a very narrow area of compounds that have been shown to have radio-sensitizing properties on the one hand, and high reactivity towards low-energy electrons on the other hand. Gas phase experiments studying electron attachment to isolated molecules and environmental effects on reaction dynamics are reviewed for modified DNA components, nitroimidazoles, and organometallics. In the end, we provide a perspective on the future directions that may be important for transferring the fundamental knowledge about the processes induced by low-energy electrons into practice in the field of rational design of agents for concomitant chemo-radiation therapy.
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Affiliation(s)
- Barbora Sedmidubská
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 182223 Prague, Czech Republic.
- Department of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering, Břehová 7, 11519 Prague, Czech Republic
- Institut de Chimie Physique, UMR 8000 CNRS and Faculté des sciences d'Orsay, Université Paris Saclay, F-91405 Orsay Cedex, France
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 182223 Prague, Czech Republic.
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2
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Saraswat M, Venkataramani S. Thermal unimolecular reactivity pathways in dehydro‐diazines radicals. J PHYS ORG CHEM 2021; 34. [DOI: 10.1002/poc.4152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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3
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Jagiello K, Makurat S, Pereć S, Rak J, Puzyn T. Molecular features of thymidine analogues governing the activity of human thymidine kinase. Struct Chem 2018. [DOI: 10.1007/s11224-018-1124-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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4
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Westphal K, Skotnicki K, Bobrowski K, Rak J. Radiation damage to single stranded oligonucleotide trimers labelled with 5-iodopyrimidines. Org Biomol Chem 2018; 14:9331-9337. [PMID: 27714271 DOI: 10.1039/c6ob01713d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radiolysis of deoxygenated aqueous solution containing trimeric oligonucleotides labelled with iodinated pyrimidines and Tris-HCl as the hydroxyl radical scavenger leads to electron attachment to the halogenated bases that mainly results in single strand breaks. The iodinated trimers are 2-fold more sensitive to solvated electrons than the brominated oligonucleotides, which is explained by the barrier-free dissociation of the iodinated base anions. The present study fills the literature gap concerning the chemistry triggered by ionizing radiation in the iodinated pyrimidines incorporated into DNA.
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Affiliation(s)
- Kinga Westphal
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Konrad Skotnicki
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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Abstract
This study targets the kinetics and product detection of the gas-phase oxidation reaction of the protonated 5-dehydrouracil (uracil-5-yl) distonic radical cation using ion-trap mass spectrometry. Protonated 5-dehydrouracil radical ions (5-dehydrouracilH+ radical ion, m/z 112) are produced within an ion trap by laser photolysis of protonated 5-iodouracil. Storage of the 5-dehydrouracilH+ radical ion in the presence of controlled concentration of O2 reveals two main products. The major reaction product pathway is assigned as the formation of protonated 2-hydroxypyrimidine-4,5-dione (m/z 127) + •OH. A second product ion (m/z 99), putatively assigned as a five-member-ring ketone structure, is tentatively explained as arising from the decarbonylation (-CO) of protonated 2-hydroxypyrimidine-4,5-dione. Because protonation of the 5-dehydrouracil radical likely forms a dienol structure, the O2 reaction at the 5 position is ortho to an -OH group. Following this addition of O2, the peroxyl-radical intermediate isomerizes by H atom transfer from the -OH group. The ensuing hydroperoxide then decomposes to eliminate •OH radical. It is shown that this elimination of •OH radical (-17 Da) is evidence for the presence of an -OH group ortho to the initial phenyl radical site, in good accord with calculations. The subsequent CO loss mechanism, to form the aforementioned five-member-ring structure, is unclear, but some pathways are discussed. By following the kinetics of the reaction, the room temperature second-order rate coefficient of the 5-dehydrouracilH+ distonic radical cation with molecular oxygen is measured at 7.2 × 10-11 cm3 molecule-1 s-1, Φ = 12% (with ±50% total accuracy). For aryl radical reactions with O2, the presence of the •OH elimination product pathway, following the peroxyl-radical formation, is an indicator of an -OH group ortho to the radical site.
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Affiliation(s)
- James P Bezzina
- School of Chemistry, University of Wollongong , Wollongong, Australia 2522
| | | | - Stephen J Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology , Brisbane, Australia 4001
| | - Adam J Trevitt
- School of Chemistry, University of Wollongong , Wollongong, Australia 2522
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Westphal K, Zdrowowicz M, Zylicz-Stachula A, Rak J. Chemically–enzymatic synthesis of photosensitive DNA. Journal of Photochemistry and Photobiology B: Biology 2017; 167:228-235. [DOI: 10.1016/j.jphotobiol.2017.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/20/2016] [Accepted: 01/03/2017] [Indexed: 01/24/2023]
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Wang S, Zhao P, Zhang C, Bu Y. Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines. J Phys Chem B 2016; 120:2649-57. [PMID: 26913546 DOI: 10.1021/acs.jpcb.5b11432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental studies showed that high energy radiation induced base release and DNA backbone breaks mainly occur at the neighboring 5' nucleotide when a single-stranded DNA is modified by radiosensitizing 5-halogenated deoxyuridines. However, no mechanism can be used to interpret these experimental observations. To better understand the radiosensitivity of 5-halogenated deoxyuridines, mechanisms involving hydrogen abstraction by the uracil-5-yl radical from the C2' and C3' positions of an adjacent nucleotide separately followed by the C3'-O3' or N-glycosidic bond rupture and the P-O3' bond breakage are investigated in the DNA sequence 5'-TU(•)-3' employing density functional theory calculations in the present study. It is found that hydrogen abstractions from both positions are comparable with the one from the C2' site slightly more favorable. The N-glycosidic bond cleavage in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is estimated to have the lowest activation free energies, indicating that the adjacent 5' base release dominates electron induced damage to single-stranded DNA incorporated by 5-halogenated deoxyuridines. Relative to the P-O3' bond breakage after the internucleotide C3'-H abstraction, the C3'-O3' bond rupture in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is predicted to have a lower activation free energy, implying that single-stranded DNA backbone breaks are prone to occur at the C3'-O3' bond site. The 5'-TU(•)-3' species has substantial electron affinity and can even capture a hydrated electron, forming the 5'-TU(-)-3' anion. However, the electron induced C3'-O3' bond rupture in 5'-TU(-)-3' anion via a pathway of internucleotide proton abstraction is only minor in both the gas phase and aqueous solution. The present theoretical predictions can interpret rationally experimental observations, thereby demonstrating that the mechanisms proposed here are responsible for high energy radiation induced damage to single-stranded DNA incorporated by radiosensitizing 5-halogenated deoxyuridines. By comparing with previous results, our work proves that the radiosensitizing action of 5-bromo-2-deoxyuridine is not weaker but stronger than its isomer 6-bromo-2-deoxyuridine on the basis of the available data.
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Affiliation(s)
- Shoushan Wang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Peiwen Zhao
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Changzhe Zhang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
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Rak J, Chomicz L, Wiczk J, Westphal K, Zdrowowicz M, Wityk P, Żyndul M, Makurat S, Golon Ł. Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation. J Phys Chem B 2015; 119:8227-38. [PMID: 26061614 DOI: 10.1021/acs.jpcb.5b03948] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hypoxia--a hallmark of solid tumors--makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet radiation. While incorporated into genomic DNA, modified nucleosides, 5-bromo-2'-deoxyuridine in particular, sensitize cells to both near-ultraviolet photons and γ rays. It is believed that, in both sensitization modes, the reactive nucleobase radical is formed as a primary product which swiftly stabilizes, leading to serious DNA damage, like strand breaks or cross-links. However, despite the apparent similarity, such radio- and photosensitization of DNA seems to be ruled by fundamentally different mechanisms. In this review, we demonstrate that the most important factors deciding on radiodamage to the labeled DNA are (i) the electron affinity (EA) of modified nucleoside (mNZ), (ii) the local surroundings of the label that significantly influences the EA of mNZ, and (iii) the strength of the chemical bond holding together the substituent and a nucleobase. On the other hand, we show that the UV damage to sensitized DNA is governed by long-range photoinduced electron transfer, the efficiency of which is controlled by local DNA sequences. A critical review of the literature mechanisms concerning both types of damage to the labeled biopolymer is presented. Ultimately, the perspectives of studies on DNA sensitization in the context of cancer therapy are discussed.
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Affiliation(s)
- Janusz Rak
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Lidia Chomicz
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Justyna Wiczk
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Kinga Westphal
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Magdalena Zdrowowicz
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Paweł Wityk
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Michał Żyndul
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Samanta Makurat
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Łukasz Golon
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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Chomicz L, Golon Ł, Rak J. The radiosensitivity of 5- and 6-bromocytidine derivatives--electron induced DNA degradation. Phys Chem Chem Phys 2015; 16:19424-8. [PMID: 25102433 DOI: 10.1039/c4cp03139c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Halogenated nucleotides belong to the group of radiosensitizers that sensitize solid tumors when incorporated into genomic DNA. Here, we consider the propensity of two isomeric bromocytidine derivatives, 3',5'-diphosphates of 5-bromo-2'-deoxycytidine (5BrdCDP) and 6-bromo-2'-deoxycytidine (6BrdCDP), to be damaged by electrons - one of the most abundant products formed during radiotherapy. An intranucleotide degradation mechanism leading to phosphodiester bond breakage (a model of single strand breakage in labeled DNA) and a ketone derivative formation was found for 6BrdCDP, while for 5BrdCDP a similar mechanism is sterically hindered. 5BrdCDP is, therefore, suggested to undergo electron induced degradation involving hydrogen transfer from a neighboring nucleotide or environment.
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Affiliation(s)
- Lidia Chomicz
- Department of Chemistry, University of Gdansk, 80-308 Gdansk, Poland.
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10
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Lepczyńska J, Komodziński K, Milecki J, Kierzek R, Gdaniec Z, Franzen S, Skalski B. Photoaddition of 5-bromouracil to uracil in oligonucleotides leading to 5,5'-bipyrimidine-type adducts: mechanism of the photoreaction. J Org Chem 2012. [PMID: 23186224 DOI: 10.1021/jo3021067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Bromouracil ((Br)U) modified di- and hexanucleotides having (Br)U flanked on the 5' or the 3' side by uracil (U) have been synthesized, and their photochemical reactivity was examined under the conditions of irradiation with near UV light. The results indicate that the primary photochemical process in all of these compounds involves the formation of an intermediate cyclobutane phodoadduct composed of (Br)U and U, which undergoes further photochemically and thermally induced transformations to 5,5'-bipyrimidine type adducts.
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Affiliation(s)
- Jolanta Lepczyńska
- Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland
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Samanta PK, Manna AK, Pati SK. Structural, Electronic, and Optical Properties of Metallo Base Pairs in Duplex DNA: A Theoretical Insight. Chem Asian J 2012; 7:2718-28. [DOI: 10.1002/asia.201200630] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Indexed: 12/23/2022]
Affiliation(s)
- Pralok K. Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
| | - Arun K. Manna
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
| | - Swapan K. Pati
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
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Samanta PK, Periyasamy G, Manna AK, Pati SK. Computational studies on structural and optical properties of single-stranded DNA encapsulated silver/gold clusters. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16068d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Abstract
The reaction of low-energy electrons (LEEs; 10 eV) with 5'-TpXpT-3' (TXT), where X is uracil (U), thymine (T), and 5-bromouracil (5BrU), was examined by HPLC-UV analysis. The presence of 5BrU increased total damage by >50%. The radiation products of T5BrUT included TUT (40%), free U, T, 5BrU (23%), and fragments (13%). These products may be explained by initial capture of LEEs by the nucleobase to form a transient anion, followed by transfer of the electron within the molecule and cleavage of susceptible bonds by dissociative electron attachment (C-Br, C-N, or C-O bonds). In addition, these products may arise from the uracilyl-5-yl (U-5-yl) radicals that undergo H-atom abstraction from the sugar moiety. Interestingly, several products contained two sites of cleavage (U, pUT, and TUp). The formation of these products was linear with dose, and thus, they arise from the single-electron reactions. To explain these products, we propose that the reaction of LEEs (10 eV) involves the coupling of two dissociative processes in the same molecule (for example, dissociative excitation and dissociative electron attachment). The latter reactions may contribute to the formation of clustered damage, which is the most deleterious damage induced by ionizing radiation.
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Affiliation(s)
- Zejun Li
- Center for Radiobiology and Radiotherapy, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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14
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Abstract
The formation and structure of the 5'-G[8-5]U-3' intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine-pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5'-G[8-5]U-3' within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5'-G[8-5]U-3', may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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Churchill CDM, Wetmore SD. Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA. Phys Chem Chem Phys 2011; 13:16373-83. [PMID: 21842033 DOI: 10.1039/c1cp21689a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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Affiliation(s)
- Patric Schyman
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden, and Örebro Life Science Center, School of Science and Technology, Örebro University, Fakultetsgatan 1, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden, and Örebro Life Science Center, School of Science and Technology, Örebro University, Fakultetsgatan 1, 701 82 Örebro, Sweden
| | - Aatto Laaksonen
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden, and Örebro Life Science Center, School of Science and Technology, Örebro University, Fakultetsgatan 1, 701 82 Örebro, Sweden
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Schyman P, Laaksonen A, Hugosson HW. Phosphodiester bond rupture in 5′ and 3′ cytosine monophosphate in aqueous environment and the effect of low-energy electron attachment: A Car–Parrinello QM/MM molecular dynamics study. Chem Phys Lett 2008; 462:289-94. [DOI: 10.1016/j.cplett.2008.07.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Kumar A, Sevilla MD, Suhai S. Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: a density functional study. J Phys Chem B 2008; 112:5189-98. [PMID: 18380501 DOI: 10.1021/jp710957p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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