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D'Agostino L. Native DNA electronics: is it a matter of nanoscale assembly? NANOSCALE 2018; 10:12268-12275. [PMID: 29946628 DOI: 10.1039/c8nr03153c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The genomic DNA is enveloped by nanotubes formed by the nuclear aggregates of polyamines (NAPs) that induce DNA conformational changes and provide protection and increased interaction abilities for the double strands. In a physiological environment, the nanotube arrangement is initiated by spontaneous interaction among the terminal amino groups of the polyamines and the phosphate ions, with the consequent formation of cyclic monomers that hook at the DNA grooves. The polymer thus formed has the morphological features of an organic semiconductor and therefore, it can be considered to be able to conduct electric charges. Phosphate ions positioned on the NAP external surface could regulate, as in a physical electric circuit, both linear and rotational (histones) protein motion, in accordance with the basilar principles of the electronics. A model of a carrier system for protein motion along the polymer wrapping the DNA strands, based on the phosphate-phosphate complexation, is proposed.
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Abu-Khudir R, Habieb ME, Mohamed MA, Hawas AM, Mohamed TM. Anti-apoptotic role of spermine against lead and/or gamma irradiation-induced hepatotoxicity in male rats. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:24272-24283. [PMID: 28889190 DOI: 10.1007/s11356-017-0069-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
Exposure to either lead (Pb) or γ-irradiation (IR) results in oxidative stress in biological systems. Herein, we explored the potential anti-apoptotic effect of spermine (Spm) against lead and/or γ-irradiation-induced hepatotoxicity in male albino rats. Rats were divided into eight experimental groups of ten rats each: groups including negative control, whole body γ-irradiated (6 Gray (Gy)), lead acetate (PbAct) trihydrate orally administered (75 mg/kg bw ≡ 40 mg/kg bw Pb for 14 consecutive days), and Spm intraperitoneally dosed (10 mg/kg bw for 14 consecutive days) rats and groups subjected to combinations of Pb + IR, Spm + IR, Spm + Pb, and Spm + Pb followed by IR on day 14 (Spm + Pb + IR). A significant decrease in arginase activity as well as mRNA and protein levels of Bcl-2 and p21 was observed in rats intoxicated with Pb and/or γ-irradiation compared to controls, whereas Bax mRNA and protein levels were significantly increased. Also, an increased level of nitric oxide (NO) with a reduced arginase activity was observed in liver tissues of intoxicated rats. Spm co-treatment with lead and/or γ-irradiation attenuated the increase in Bax mRNA and protein expression, while it restored those of Bcl-2 and p21 together with NO levels and arginase activity to control values. Altogether, we suggest that Spm may be useful in combating free radical-induced apoptosis in Pb-intoxicated and/or γ-irradiated rats.
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Affiliation(s)
- Rasha Abu-Khudir
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, P.O. 31527, Tanta, Egypt.
| | - Mahmoud E Habieb
- Drug Radiation Research Department, National Centre for Radiation Research and Technology (NCRRT), Atomic Energy Authority, P.O. Box; 29, Nasr City, Cairo, Egypt
| | - Marwa A Mohamed
- Drug Radiation Research Department, National Centre for Radiation Research and Technology (NCRRT), Atomic Energy Authority, P.O. Box; 29, Nasr City, Cairo, Egypt
| | - Asrar M Hawas
- Drug Radiation Research Department, National Centre for Radiation Research and Technology (NCRRT), Atomic Energy Authority, P.O. Box; 29, Nasr City, Cairo, Egypt
| | - Tarek M Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, P.O. 31527, Tanta, Egypt
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An R, Dong P, Komiyama M, Pan X, Liang X. Inhibition of nonenzymatic depurination of nucleic acids by polycations. FEBS Open Bio 2017; 7:1707-1714. [PMID: 29123979 PMCID: PMC5666391 DOI: 10.1002/2211-5463.12308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/08/2017] [Accepted: 08/24/2017] [Indexed: 11/11/2022] Open
Abstract
DNA base depurination is one of the most common forms of DNA damage in vivo and in vitro, and the suppression of depurination is very important for versatile applications of DNA in biotechnology and medicine. In this work, it was shown that the polycations chitosan (Cho) and spermine (Spm) strongly inhibit DNA depurination through the formation of polyion complexes with DNA molecules. The intramolecular electrostatic interaction of positively charged polycations with DNA efficiently suppresses the protonation of purine groups, which is the key step of depurination. Importantly, the optimal pH for Cho's inhibition of depurination is significantly different from that of Spm. Cho is very effective in the inhibition of depurination in highly acidic media (pH: 1.5–3), whereas Spm is found to suppress the chemical reaction near neutral pH, as well as in acidic solutions. This remarkable pH specificity of the two biorelevant polycations is attributed to the difference in the pKa values of the amino groups. The relevance of our results with the biological roles of biogenic polycations is also discussed.
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Affiliation(s)
- Ran An
- College of Food Science and Engineering Ocean University of China Qingdao China.,Laboratory for Marine Drugs and Bioproducts Qingdao National Laboratory for Marine Science and Technology China
| | - Ping Dong
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Makoto Komiyama
- College of Food Science and Engineering Ocean University of China Qingdao China.,National Institute for Materials Science (NIMS) Tsukuba Japan
| | - Xiaoming Pan
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Xingguo Liang
- College of Food Science and Engineering Ocean University of China Qingdao China.,Laboratory for Marine Drugs and Bioproducts Qingdao National Laboratory for Marine Science and Technology China
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Iacomino G, Picariello G, Sbrana F, Raiteri R, D'Agostino L. DNA-HMGB1 interaction: The nuclear aggregates of polyamine mediation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1402-10. [PMID: 27451951 DOI: 10.1016/j.bbapap.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/13/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022]
Abstract
Nuclear aggregates of polyamines (NAPs) are supramolecular compounds generated by the self-assembly of protonated nuclear polyamines (spermine, spermidine and putrescine) and phosphate ions. In the presence of genomic DNA, the hierarchical process of self-structuring ultimately produces nanotube-like polymers that envelop the double helix. Because of their modular nature and their aggregation-disaggregation dynamics, NAPs confer plasticity and flexibility to DNA. Through the disposition of charges, NAPs also enable a bidirectional stream of information between the genome and interacting moieties. High mobility group (HMG) B1 is a non-histone chromosomal protein that binds to DNA and that influences multiple nuclear processes. Because genomic DNA binds to either NAPs or HMGB1 protein, we explored the ability of in vitro self-assembled NAPs (ivNAPs) to mediate the DNA-HMGB1 interaction. To this end, we structured DNA-NAPs-HMGB1 and DNA-HMGB1-NAPs ternary complexes in vitro through opportune sequential incubations. Mobility shift electrophoresis and atomic force microscopy showed that the DNA-ivNAPs-HGMB1 complex had conformational assets supposedly more suitable those of the DNA-HGMB1-ivNAPs to comply with the physiological and functional requirements of DNA. Our findings indicated that ivNAPs act as mediators of the DNA-HMGB1 interaction.
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Affiliation(s)
- Giuseppe Iacomino
- Istituto di Scienze dell'Alimentazione - CNR, Via Roma 64 - 83100, Avellino, Italy
| | - Gianluca Picariello
- Istituto di Scienze dell'Alimentazione - CNR, Via Roma 64 - 83100, Avellino, Italy
| | - Francesca Sbrana
- Istituto di Biofisica - CNR, Via De Marini 6 - 16149, Genova, Italy
| | - Roberto Raiteri
- Istituto di Biofisica - CNR, Via De Marini 6 - 16149, Genova, Italy; Dipartimento di Informatica, Bioingegneria, Robotica ed Ingegneria dei Sistemi - Università degli Studi di Genova, Via All'Opera Pia 13 - 16145, Genova, Italy
| | - Luciano D'Agostino
- Istituto di Scienze dell'Alimentazione - CNR, Via Roma 64 - 83100, Avellino, Italy.
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Satpathi S, Sengupta A, Hridya VM, Gavvala K, Koninti RK, Roy B, Hazra P. A Green Solvent Induced DNA Package. Sci Rep 2015. [PMCID: PMC5378943 DOI: 10.1038/srep09137] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mechanistic details of DNA compaction is essential blue print for gene regulation in living organisms. Many in vitro studies have been implemented using several compaction agents. However, these compacting agents may have some kinds of cytotoxic effects to the cells. To minimize this aspect, several research works had been performed, but people have never focused green solvent, i.e. room temperature ionic liquid as DNA compaction agent. To the best of our knowledge, this is the first ever report where we have shown that guanidinium tris(pentafluoroethyl)trifluorophosphate (Gua-IL) acts as a DNA compacting agent. The compaction ability of Gua-IL has been verified by different spectroscopic techniques, like steady state emission, circular dichroism, dynamic light scattering and UV melting. Notably, we have extensively probed this compaction by Gua-IL through field emission scanning electron microscopy (FE-SEM) and fluorescence microscopy images. We also have discussed the plausible compaction mechanism process of DNA by Gua-IL. Our results suggest that Gua-IL forms a micellar kind of self aggregation above a certain concentration (≥1 mM), which instigates this compaction process. This study divulges the specific details of DNA compaction mechanism by a new class of compaction agent, which is highly biodegradable and eco friendly in nature.
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Lozano P, Bernal JM, Nieto S, Gomez C, Garcia-Verdugo E, Luis SV. Active biopolymers in green non-conventional media: a sustainable tool for developing clean chemical processes. Chem Commun (Camb) 2015; 51:17361-74. [DOI: 10.1039/c5cc07600e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
By understanding structure–function relationships of active biopolymers (e.g. enzymes and nucleic acids) in green non-conventional media, sustainable chemical processes may be developed.
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Affiliation(s)
- Pedro Lozano
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | - Juana M. Bernal
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | - Susana Nieto
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | - Celia Gomez
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | | | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universidad Jaume I
- Castellón
- Spain
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Mata I, Molins E, Alkorta I, Espinosa E. The paradox of hydrogen-bonded anion-anion aggregates in oxoanions: a fundamental electrostatic problem explained in terms of electrophilic···nucleophilic interactions. J Phys Chem A 2014; 119:183-94. [PMID: 25495236 DOI: 10.1021/jp510198g] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A theoretical study of anionic complexes formed by two partly deprotonated oxoacids joined by hydrogen bonds has been carried out at the MP2 computational level. In spite of the ionic repulsion, local energy minima are found both in the gas phase and in aqueous solution. Electrostatic potential and electron density topologies, and the comparison with neutral complexes formed by oxoacids, reveal that the ionization has no significant effect on the properties of the hydrogen bonds. The stability of the complexes in the gas phase is explained by attractive forces localized in a volume situated in the hydrogen bond and defined as the electrostatic attraction region (EAR) and determined by the topological analyses of the electron density and the electrostatic potential, and by the electric field lines. In solution, the strong anionic repulsion is mostly screened by the effect of the surrounding polar solvent, which only leads to a weak destabilizing interaction in the hydrogen bond region and finally favors the overall stability of the complexes. The anion-anion complexes have been compared with the corresponding neutral ones (as salts or protonated forms), showing that EAR remains unchanged along the series.
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Affiliation(s)
- Ignasi Mata
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC) , Campus UAB, 08193 Bellaterra, Spain
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Kouass Sahbani S, Sanche L, Cloutier P, Bass AD, Hunting DJ. Loss of cellular transformation efficiency induced by DNA irradiation with low-energy (10 eV) electrons. J Phys Chem B 2014; 118:13123-31. [PMID: 25325149 DOI: 10.1021/jp508170c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Low energy electrons (LEEs) of energies less than 20 eV are generated in large quantities by ionizing radiation in biological matter. While LEEs are known to induce single (SSBs) and double strand breaks (DSBs) in DNA, their ability to inactivate cells by inducing nonreparable lethal damage has not yet been demonstrated. Here we observe the effect of LEEs on the functionality of DNA, by measuring the efficiency of transforming Escherichia coli with a [pGEM-3Zf (-)] plasmid irradiated with 10 eV electrons. Highly ordered DNA films were prepared on pyrolitic graphite by molecular self-assembly using 1,3-diaminopropane ions (Dap(2+)). The uniformity of these films permits the inactivation of approximately 50% of the plasmids compared to <10% using previous methods, which is sufficient for the subsequent determination of their functionality. Upon LEE irradiation, the fraction of functional plasmids decreased exponentially with increasing electron fluence, while LEE-induced isolated base damage, frank DSB, and non DSB-cluster damage increased linearly with fluence. While DSBs can be toxic, their levels were too low to explain the loss of plasmid functionality observed upon LEE irradiation. Similarly, non-DSB cluster damage, revealed by transforming cluster damage into DSBs by digestion with repair enzymes, also occurred relatively infrequently. The exact nature of the lethal damage remains unknown, but it is probably a form of compact cluster damage in which the lesions are too close to be revealed by purified repair enzymes. In addition, this damage is either not repaired or is misrepaired by E. coli, since it results in plasmid inactivation, when they contain an average of three lesions. Comparison with previous results from a similar experiment performed with γ-irradiated plasmids indicates that the type of clustered DNA lesions, created directly on cellular DNA by LEEs, may be more difficult to repair than those produced by other species from radiolysis.
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Affiliation(s)
- Saloua Kouass Sahbani
- Department of Nuclear Medicine & Radiobiology, Faculty of Medicine, Université de Sherbrooke , Sherbrooke, Quebec, Canada J1H 5N4
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