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Abstract
PURPOSE One outcome of DNA damage from hydroxyl radical generated by ionizing radiation (IR) or by the Fenton reaction is oxidation of the nucleobases, especially guanine (G). While 8-oxo-7,8-dihydroguanine (OG) is a commonly studied oxidized lesion, several others are formed in high abundance, including 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), a prevalent product in in vitro chemistry that is challenging to study from cellular sources. In this short review, we have a goal of explaining new insights into hydroxyl radical-induced oxidation chemistry of G in DNA and comparing it to endogenous DNA damage, as well as commenting on the biological outcomes of DNA base damage. CONCLUSIONS Pathways of oxidation of G are discussed and a comparison is made between IR (hydroxyl radical chemistry) and endogenous oxidative stress that largely forms carbonate radical anion as a reactive intermediate. These pathways overlap with the formation of OG and 2Ih, but other guanine-derived lesions are more pathway specific. The biological consequences of guanine oxidation include both mutagenesis and epigenetics; a new mechanism of gene regulation via the base excision repair pathway is described for OG, whereas the impact of IR in forming guanine modifications may be to confound this process in addition to introduction of mutagenic sites.
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Shafirovich V, Geacintov NE. Excision of Oxidatively Generated Guanine Lesions by Competitive DNA Repair Pathways. Int J Mol Sci 2021; 22:2698. [PMID: 33800059 DOI: 10.3390/ijms22052698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/18/2022] Open
Abstract
The base and nucleotide excision repair pathways (BER and NER, respectively) are two major mechanisms that remove DNA lesions formed by the reactions of genotoxic intermediates with cellular DNA. It is generally believed that small non-bulky oxidatively generated DNA base modifications are removed by BER pathways, whereas DNA helix-distorting bulky lesions derived from the attack of chemical carcinogens or UV irradiation are repaired by the NER machinery. However, existing and growing experimental evidence indicates that oxidatively generated DNA lesions can be repaired by competitive BER and NER pathways in human cell extracts and intact human cells. Here, we focus on the interplay and competition of BER and NER pathways in excising oxidatively generated guanine lesions site-specifically positioned in plasmid DNA templates constructed by a gapped-vector technology. These experiments demonstrate a significant enhancement of the NER yields in covalently closed circular DNA plasmids (relative to the same, but linearized form of the same plasmid) harboring certain oxidatively generated guanine lesions. The interplay between the BER and NER pathways that remove oxidatively generated guanine lesions are reviewed and discussed in terms of competitive binding of the BER proteins and the DNA damage-sensing NER factor XPC-RAD23B to these lesions.
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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Zheng L, Dai X, Su H, Greenberg MM. Independent Generation and Time-Resolved Detection of 2'-Deoxyguanosin-N2-yl Radicals. Angew Chem Int Ed Engl 2020; 59:13406-13413. [PMID: 32365264 PMCID: PMC7395871 DOI: 10.1002/anie.202005300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/01/2020] [Indexed: 12/25/2022]
Abstract
Guanine radicals are important reactive intermediates in DNA damage. Hydroxyl radical (HO. ) has long been believed to react with 2'-deoxyguanosine (dG) generating 2'-deoxyguanosin-N1-yl radical (dG(N1-H). ) via addition to the nucleobase π-system and subsequent dehydration. This basic tenet was challenged by an alternative mechanism, in which the major reaction of HO. with dG was proposed to involve hydrogen atom abstraction from the N2-amine. The 2'-deoxyguanosin-N2-yl radical (dG(N2-H). ) formed was proposed to rapidly tautomerize to dG(N1-H). . We report the first independent generation of dG(N2-H). in high yield via photolysis of 1. dG(N2-H). is directly observed upon nanosecond laser flash photolysis (LFP) of 1. The absorption spectrum of dG(N2-H). is corroborated by DFT studies, and anti- and syn-dG(N2-H). are resolved for the first time. The LFP experiments showed no evidence for tautomerization of dG(N2-H). to dG(N1-H). within hundreds of microseconds. This observation suggests that the generation of dG(N1-H). via dG(N2-H). following hydrogen atom abstraction from dG is unlikely to be a major pathway when HO. reacts with dG.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Xiaojuan Dai
- Department of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Hongmei Su
- Department of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
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Lee YA, Cho HY, Kim SK. Neighboring base sequence effect on DNA damage. J Biomol Struct Dyn 2019; 38:3188-3195. [PMID: 31432766 DOI: 10.1080/07391102.2019.1659186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Guanine is the most strongly oxidized base in DNA; generation of a guanine radical cation as an intermediate in an oxidation reaction leads to migration through a resulting cationic hole in the DNA π-stack until it is trapped by irreversible reaction with water or other free radicals. In the case of normal sequences, the primary position of Guanine oxidations by one-electron oxidants such as carbonate radical anions, BPT(7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene), and riboflavin are 5'-G in GG doublets and the central G in a GGG triplet. According to results, the properties of guanine oxidation on abasic site containing sequences are independent from the position of AP(apurinic/apyrimidinic) site in the presence of carbonate radical anions under a short irradiation time, although this radical is exposed to solvent by the existence of an abasic site. The lack of abasic site effect on guanine oxidative damage by the carbonate radical may be due to a sequence-independent property of the initial electron transfer rate in the hole injection step, or may relate to an electron transfer mechanism with large reorganization energy dependency. Consequently, the carbonate radical anions may easily migrate to another single G in the charge re-distribution step. Meanwhile, there is a strong dependency on the presence of an AP(apurinic/apyrimidinic) site in the cleavage patterns of guanine oxidations by physically large oxidizing agents, such as BPT(7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene) and riboflavin. These radicals show strong AP(apurinic/apyrimidinic) site dependency and clear G-site selectivity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
| | - Ha Young Cho
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
| | - Seog K Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
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Abstract
The α-hemolysin nanopore has been studied for applications in DNA sequencing, various single-molecule detections, biomolecular interactions, and biochips. The detection of single molecules in a clinical setting could dramatically improve cancer detection and diagnosis as well as develop personalized medicine practices for patients. This brief review shortly presents the current solid state and protein nanopore platforms and their applications like biosensing and sequencing. We then elaborate on various epigenetic detections (like microRNA, G-quadruplex, DNA damages, DNA modifications) with the most widely used alpha-hemolysin pore from a biomedical diagnosis perspective. In these detections, a nanopore electrical current signature was generated by the interaction of a target with the pore. The signature often was evidenced by the difference in the event duration, current level, or both of them. An ideal signature would provide obvious differences in the nanopore signals between the target and the background molecules. The development of cancer biomarker detection techniques and nanopore devices have the potential to advance clinical research and resolve health problems. However, several challenges arise in applying nanopore devices to clinical studies, including super low physiological concentrations of biomarkers resulting in low sensitivity, complex biological sample contents resulting in false signals, and fast translocating speed through the pore resulting in poor detections. These issues and possible solutions are discussed.
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Affiliation(s)
- Yong Wang
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Li-qun Gu
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
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Oliveira N, Souza E, Ferreira D, Zanforlin D, Bezerra W, Borba MA, Arruda M, Lopes K, Nascimento G, Martins D, Cordeiro M, Lima-Filho J. A Sensitive and Selective Label-Free Electrochemical DNA Biosensor for the Detection of Specific Dengue Virus Serotype 3 Sequences. Sensors (Basel) 2015; 15:15562-77. [PMID: 26140346 PMCID: PMC4541844 DOI: 10.3390/s150715562] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/13/2015] [Accepted: 06/23/2015] [Indexed: 11/16/2022]
Abstract
Dengue fever is the most prevalent vector-borne disease in the world, with nearly 100 million people infected every year. Early diagnosis and identification of the pathogen are crucial steps for the treatment and for prevention of the disease, mainly in areas where the co-circulation of different serotypes is common, increasing the outcome of dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Due to the lack of fast and inexpensive methods available for the identification of dengue serotypes, herein we report the development of an electrochemical DNA biosensor for the detection of sequences of dengue virus serotype 3 (DENV-3). DENV-3 probe was designed using bioinformatics software and differential pulse voltammetry (DPV) was used for electrochemical analysis. The results showed that a 22-m sequence was the best DNA probe for the identification of DENV-3. The optimum concentration of the DNA probe immobilized onto the electrode surface is 500 nM and a low detection limit of the system (3.09 nM). Moreover, this system allows selective detection of DENV-3 sequences in buffer and human serum solutions. Therefore, the application of DNA biosensors for diagnostics at the molecular level may contribute to future advances in the implementation of specific, effective and rapid detection methods for the diagnosis dengue viruses.
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Affiliation(s)
- Natália Oliveira
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Elaine Souza
- Universidade Federal de Alagoas (UFAL), Campus Arapiraca, Av. Manoel Severino Barbosa, s/n, Bom Sucesso, 57.309-005 Arapiraca, AL, Brazil.
| | - Danielly Ferreira
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Deborah Zanforlin
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Wessulla Bezerra
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Maria Amélia Borba
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Mariana Arruda
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Kennya Lopes
- Departamento de Virologia e Terapia Experimental (LAVITE), Centro de Pesquisas Aggeu Magalhães (CPqAM), Fundação Oswaldo Cruz (Fiocruz)-Pernambuco, Av. Professor Moraes Rego, s/n, Campus da UFPE, 50.670-420 Recife, PE, Brazil.
| | - Gustavo Nascimento
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Danyelly Martins
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
- Departamento de Bioquímica, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego, s/n, Campus da UFPE, CEP: 50670-901 Recife, PE, Brazil.
| | - Marli Cordeiro
- Departamento de Bioquímica, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego, s/n, Campus da UFPE, CEP: 50670-901 Recife, PE, Brazil.
| | - José Lima-Filho
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
- Departamento de Bioquímica, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego, s/n, Campus da UFPE, CEP: 50670-901 Recife, PE, Brazil.
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Zhao Y, Farrer NJ, Li H, Butler JS, McQuitty RJ, Habtemariam A, Wang F, Sadler PJ. De novo generation of singlet oxygen and ammine ligands by photoactivation of a platinum anticancer complex. Angew Chem Int Ed Engl 2013; 52:13633-7. [PMID: 24167018 PMCID: PMC4230391 DOI: 10.1002/anie.201307505] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Indexed: 11/10/2022]
Abstract
Worth the excitement: Highly reactive oxygen and nitrogen species are generated by photoactivation of the anticancer platinum(IV) complex trans,trans,trans-[Pt(N3 )2 (OH)2 (MA)(Py)] (MA=methylamine, Py=pyridine). Singlet oxygen is formed from the hydroxido ligands and not from dissolved oxygen, and ammine ligands are products from the conversion of azido ligands to nitrenes. Both processes can induce oxidation of guanine.
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Affiliation(s)
- Yao Zhao
- Department of Chemistry, University of Warwick,CV4 7AL (United Kingdom)
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems,Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Nicola J Farrer
- Department of Chemistry, University of Warwick,CV4 7AL (United Kingdom)
| | - Huilin Li
- Department of Chemistry, University of Warwick,CV4 7AL (United Kingdom)
| | - Jennifer S Butler
- Department of Chemistry, University of Warwick,CV4 7AL (United Kingdom)
| | - Ruth J McQuitty
- Department of Chemistry, University of Warwick,CV4 7AL (United Kingdom)
| | | | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems,Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Peter J Sadler
- Department of Chemistry, University of Warwick,CV4 7AL (United Kingdom)
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Souza E, Nascimento G, Santana N, Ferreira D, Lima M, Natividade E, Martins D, Lima-Filho J. Label-free electrochemical detection of the specific oligonucleotide sequence of dengue virus type 1 on pencil graphite electrodes. Sensors (Basel) 2011; 11:5616-29. [PMID: 22163916 PMCID: PMC3231433 DOI: 10.3390/s110605616] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 05/13/2011] [Accepted: 05/18/2011] [Indexed: 11/21/2022]
Abstract
A biosensor that relies on the adsorption immobilization of the 18-mer single-stranded nucleic acid related to dengue virus gene 1 on activated pencil graphite was developed. Hybridization between the probe and its complementary oligonucleotides (the target) was investigated by monitoring guanine oxidation by differential pulse voltammetry (DPV). The pencil graphite electrode was made of ordinary pencil lead (type 4B). The polished surface of the working electrode was activated by applying a potential of 1.8 V for 5 min. Afterward, the dengue oligonucleotides probe was immobilized on the activated electrode by applying 0.5 V to the electrode in 0.5 M acetate buffer (pH 5.0) for 5 min. The hybridization process was carried out by incubating at the annealing temperature of the oligonucleotides. A time of five minutes and concentration of 1 μM were found to be the optimal conditions for probe immobilization. The electrochemical detection of annealing between the DNA probe (TS-1P) immobilized on the modified electrode, and the target (TS-1T) was achieved. The target could be quantified in a range from 1 to 40 nM with good linearity and a detection limit of 0.92 nM. The specificity of the electrochemical biosensor was tested using non-complementary sequences of dengue virus 2 and 3.
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Affiliation(s)
- Elaine Souza
- Laboratory of Immunopathology Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (G.N.); (N.S.); (D.F.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +55-81-2126-8484; Fax: +55-81-2126-8485
| | - Gustavo Nascimento
- Laboratory of Immunopathology Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (G.N.); (N.S.); (D.F.)
| | - Nataly Santana
- Laboratory of Immunopathology Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (G.N.); (N.S.); (D.F.)
| | - Danielly Ferreira
- Laboratory of Immunopathology Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (G.N.); (N.S.); (D.F.)
| | - Manoel Lima
- Computer Science Institute, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (M.L.); (E.N.)
| | - Edna Natividade
- Computer Science Institute, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (M.L.); (E.N.)
| | - Danyelly Martins
- Laboratory of Immunopathology Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (G.N.); (N.S.); (D.F.)
- Department of Biochemistry, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego s/n, 50670-901 Recife, PE, Brazil; E-Mails: (D.M.); (J.L.-F.)
| | - José Lima-Filho
- Laboratory of Immunopathology Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes s/n, 50670-901 Recife, PE, Brazil; E-Mails: (G.N.); (N.S.); (D.F.)
- Department of Biochemistry, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego s/n, 50670-901 Recife, PE, Brazil; E-Mails: (D.M.); (J.L.-F.)
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