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Rooman M, Pucci F. Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules. J Chem Inf Model 2023; 63:1766-1775. [PMID: 36877828 DOI: 10.1021/acs.jcim.2c01525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The electronic properties of DNA molecules, defined by the sequence-dependent ionization potentials of nucleobases, enable long-range charge transport along the DNA stacks. This has been linked to a range of key physiological processes in the cells and to the triggering of nucleobase substitutions, some of which may cause diseases. To gain molecular-level understanding of the sequence dependence of these phenomena, we estimated the vertical ionization potential (vIP) of all possible nucleobase stacks in B-conformation, containing one to four Gua, Ade, Thy, Cyt, or methylated Cyt. To do this, we used quantum chemistry calculations and more precisely the second-order Møller-Plesset perturbation theory (MP2) and three double-hybrid density functional theory methods, combined with several basis sets for describing atomic orbitals. The calculated vIP of single nucleobases were compared to experimental data and those of nucleobase pairs, triplets, and quadruplets, to observed mutability frequencies in the human genome, reported to be correlated with vIP values. This comparison selected MP2 with the 6-31G* basis set as the best of the tested calculation levels. These results were exploited to set up a recursive model, called vIPer, which estimates the vIP of all possible single-stranded DNA sequences of any length based on the calculated vIPs of overlapping quadruplets. vIPer's vIP values correlate well with oxidation potentials measured by cyclic voltammetry and activities obtained through photoinduced DNA cleavage experiments, further validating our approach. vIPer is freely available on the github.com/3BioCompBio/vIPer repository.
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Affiliation(s)
- Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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Zhang J, Liu Z, Song S, Fang J, Wang L, Zhao L, Li C, Li W, Byun HM, Guo L, Li P. The exposure levels and health risk assessment of antibiotics in urine and its association with platelet mitochondrial DNA methylation in adults from Tianjin, China: A preliminary study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 231:113204. [PMID: 35065505 DOI: 10.1016/j.ecoenv.2022.113204] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
There has been extensive research on antibiotics exposure in adults by biomonitoring, but the biological mechanisms and potential risks to human health remain limited. In this study, 102 adults aged 26-44 years in Tianjin were studied and 23 common antibiotics in urine were analyzed by Liquid chromatography-mass spectrometry (LC-MS). All antibiotics were detected in urine, with an overall detection frequency of 40.4% (the detection frequencies of phenothiazines, quinolones, sulfonamides, tetracyclines, and chloramphenicol were 77%, 54%, 24%, 28%, and 49%, respectively.). Ofloxacin and enrofloxacin had the highest detection frequencies (85% and 81%), with median concentrations of 0.26 (IQR: 0.05-1.36) and 0.09 (IQR: 0.03-0.14) ng/mL, respectively. Based on health risk assessment, the predicted estimated daily exposures (EDEs) ranged from 0 μg/kg/day to 13.98 μg/kg/day. The hazard quotient (HQ) values of all the antibiotics except ofloxacin and ciprofloxacin were bellow one, which are considered safe. For all blood samples, the mitochondrial DNA (mtDNA) methylation levels in the MT-ATP6 (ranging between 3.86% and 34.18%) were slightly higher than MT-ATP8 and MT-ND5 (ranging between 0.57% and 9.32%, 1.08% and 19.62%, respectively). Furthermore, mtDNA methylation from MT-ATP6, MT-ATP8 and MT-ND5 were measured by bisulfite-PCR pyrosequencing. The association (P < 0.05) was found between mtDNA methylation level (MT-ATP8 and MT-ND5) and individual antibiotics including chlorpromazine, ciprofloxacin, enrofloxacin, norfloxacin, pefloxacin, sulfaquinoxaline, sulfachloropyridazine, chloramphenicol, and thiamphenicol, indicating that persistent exposure to low-dose multiple antibiotics may affect the mtDNA methylation level and in turn pose health risks.
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Affiliation(s)
- Jing Zhang
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China; Tianjin Key Laboratory of Hazardous Waste Safety Disposal and Recycling Technology, Tianjin 300384, China
| | - Ziquan Liu
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China; Wenzhou Safety (Emergency) Institute, Tianjin University, 325000, Wenzhou, China
| | - Shanjun Song
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China; National Institute of Metrology, Beijing 100029, China
| | - Junkai Fang
- Tianjin Institute of Medical & Pharmaceutical Sciences, Tianjin 300070, China
| | - Lei Wang
- Hebei Research Center for Geoanalysis, Hebei 071000, China
| | - Lei Zhao
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China; Wenzhou Safety (Emergency) Institute, Tianjin University, 325000, Wenzhou, China
| | - Chenguang Li
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China; Tianjin Key Laboratory of Hazardous Waste Safety Disposal and Recycling Technology, Tianjin 300384, China
| | - Weixia Li
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China; Tianjin Key Laboratory of Hazardous Waste Safety Disposal and Recycling Technology, Tianjin 300384, China
| | - Hyang-Min Byun
- Population Health Science Institute, Newcastle University, Campus for Ageing and Vitality, Newcastle Upon Tyne NE4 5PL, UK
| | - Liqiong Guo
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China; Wenzhou Safety (Emergency) Institute, Tianjin University, 325000, Wenzhou, China.
| | - Penghui Li
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China; Tianjin Key Laboratory of Hazardous Waste Safety Disposal and Recycling Technology, Tianjin 300384, China.
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Atilano SR, Udar N, Satalich TA, Udar V, Chwa M, Kenney MC. Low frequency mitochondrial DNA heteroplasmy SNPs in blood, retina, and [RPE+choroid] of age-related macular degeneration subjects. PLoS One 2021; 16:e0246114. [PMID: 33513185 PMCID: PMC7846006 DOI: 10.1371/journal.pone.0246114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 01/13/2021] [Indexed: 01/07/2023] Open
Abstract
Purpose Mitochondrial (mt) DNA damage is associated with age-related macular degeneration (AMD) and other human aging diseases. This study was designed to quantify and characterize mtDNA low-frequency heteroplasmy single nucleotide polymorphisms (SNPs) of three different tissues isolated from AMD subjects using Next Generation Sequencing (NGS) technology. Methods DNA was extracted from neural retina, [RPE+choroid] and blood from three deceased age-related macular degeneration (AMD) subjects. Entire mitochondrial genomes were analyzed for low-frequency heteroplasmy SNPs using NGS technology that independently sequenced both mtDNA strands. This deep sequencing method (average sequencing depth of 30,000; range 1,000–100,000) can accurately differentiate low-frequency heteroplasmy SNPs from DNA modification artifacts. Twenty-three ‘hot-spot’ heteroplasmy mtDNA SNPs were analyzed in 222 additional blood samples. Results Germline homoplasmy SNPs that defined mtDNA haplogroups were consistent in the three tissues of each subject. Analyses of SNPs with <40% heteroplasmy revealed the blood had significantly greater numbers of heteroplasmy SNPs than retina alone (p≤0.05) or retina+choroid combined (p = 0.008). Twenty-three ‘hot-spot’ mtDNA heteroplasmy SNPs were present, with three being non-synonymous (amino acid change). Four ‘hot-spot’ heteroplasmy SNPs (m.1120C>T, m.1284T>C, m.1556C>T, m.7256C>T) were found in additional samples (n = 222). Five heteroplasmy SNPs (m.4104A>G, m.5320C>T, m.5471G>A, m.5474A>G, m.5498A>G) declined with age. Two heteroplasmy SNPs (m.13095T>C, m.13105A>G) increased in AMD compared to Normal samples. In the heteroplasmy SNPs, very few transversion mutations (purine to pyrimidine or vice versa, associated with oxidative damage) were found and the majority were transition changes (purine to purine or pyrimidine to pyrimidine, associated with replication errors). Conclusion Within an individual, the blood, retina and [RPE+choroid] contained identical homoplasmy SNPs representing inherited germline mtDNA haplogroup. NGS methodology showed significantly more mtDNA heteroplasmy SNPs in blood compared to retina and [RPE+choroid], suggesting the latter tissues have substantial protection. Significantly higher heteroplasmy levels of m.13095T>C and m.13105A>G may represent potential AMD biomarkers. Finally, high levels of transition mutations suggest that accumulation of heteroplasmic SNPs may occur through replication errors rather than oxidative damage.
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Affiliation(s)
- Shari R. Atilano
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, United States of America
| | - Nitin Udar
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, United States of America
| | - Timothy A. Satalich
- Institute for Mathematical Behavioral Science, University of California Irvine, Irvine, CA, United States of America
| | - Viraat Udar
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, United States of America
| | - Marilyn Chwa
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, United States of America
| | - M. Cristina Kenney
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, United States of America
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, United States of America
- * E-mail:
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Pucci F, Rooman M. Relation between DNA ionization potentials, single base substitutions and pathogenic variants. BMC Genomics 2019; 20:551. [PMID: 31307386 PMCID: PMC6631442 DOI: 10.1186/s12864-019-5867-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background It is nowadays clear that single base substitutions that occur in the human genome, of which some lead to pathogenic conditions, are non-random and influenced by their flanking nucleobase sequences. However, despite recent progress, the understanding of these "non-local" effects is still far from being achieved. Results To advance this problem, we analyzed the relationship between the base mutability in specific gene regions and the electron hole transport along the DNA base stacks, as it is one of the mechanisms that have been suggested to contribute to these effects. More precisely, we studied the connection between the normalized frequency of single base substitutions and the vertical ionization potential of the base and its flanking sequence, estimated using MP2/6-31G* ab initio quantum chemistry calculations. We found a statistically significant overall anticorrelation between these two quantities: the lower the vIP value, the more probable the substitution. Moreover, the slope of the regression lines varies. It is larger for introns than for exons and untranslated regions, and for synonymous than for missense substitutions. Interestingly, the correlation appears to be more pronounced when considering the flanking sequence of the substituted base in the 3’ rather than in the 5’ direction, which corresponds to the preferred direction of charge migration. A weaker but still statistically significant correlation is found between the ionization potentials and the pathogenicity of the base substitutions. Moreover, pathogenicity is also preferentially associated with larger changes in ionization potentials upon base substitution. Conclusions With this analysis we gained new insights into the complex biophysical mechanisms that are at the basis of mutagenesis and pathogenicity, and supported the role of electron-hole transport in these matters. Electronic supplementary material The online version of this article (10.1186/s12864-019-5867-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave. 50, Bruxelles, 1050, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave. 50, Bruxelles, 1050, Belgium.
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Singh V, Jolly B, Rajput NK, Pramanik S, Bhardwaj A. MtBrowse: An integrative genomics browser for human mitochondrial DNA. Mitochondrion 2019; 48:31-36. [PMID: 30738202 DOI: 10.1016/j.mito.2019.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/10/2018] [Accepted: 02/06/2019] [Indexed: 12/18/2022]
Abstract
The human mitochondrion is a unique semi-autonomous organelle with a genome of its own and also requires nuclear encoded components to carry out its functions. In addition to being the powerhouse of the cell, mitochondria plays a central role in several metabolic pathways. It is therefore challenging to delineate the cause-effect relationship in context of mitochondrial dysfunction. Several studies implicate mutations in mitochondrial DNA (mtDNA) in various complex diseases. The human mitochondrial DNA (mtDNA) encodes a set of 37 genes, 13 protein coding, 22 tRNAs and two ribosomal RNAs, which are essential structural and functional components of the electron transport chain. As mentioned above, variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. A large number of databases and prediction methods have been published to elucidate the role of human mitochondrial DNA in various disease phenotypes. However, there is no centralized resource to visualize this genotype-phenotype data. Towards this, we have developed MtBrowse: an integrative genomics browser for human mtDNA. As of now, MtBrowse has four categories - Gene, Disease, Reported variation and Variation prediction. These categories have 105 tracks and house data on mitochondrial reference genes, around 600 variants reported in literature with respect to various disease phenotypes and predictions for potential pathogenic variations in protein-coding genes. MtBrowse also hosts genomic variation data from over 5000 individuals on 22 disease phenotypes. MtBrowse may be accessed at http://ab-openlab.csir.res.in/cgi-bin/gb2/gbrowse.
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Affiliation(s)
- Vipin Singh
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Bani Jolly
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Neeraj K Rajput
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sayan Pramanik
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Anshu Bhardwaj
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India.
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Suárez-Villagrán MY, Azevedo RBR, Miller JH. Influence of Electron-Holes on DNA Sequence-Specific Mutation Rates. Genome Biol Evol 2018; 10:1039-1047. [PMID: 29617801 PMCID: PMC5887664 DOI: 10.1093/gbe/evy060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2018] [Indexed: 12/22/2022] Open
Abstract
Biases in mutation rate can influence molecular evolution, yielding rates of evolution that vary widely in different parts of the genome and even among neighboring nucleotides. Here, we explore one possible mechanism of influence on sequence-specific mutation rates, the electron–hole, which can localize and potentially trigger a replication mismatch. A hole is a mobile site of positive charge created during one-electron oxidation by, for example, radiation, contact with a mutagenic agent, or oxidative stress. Its quantum wavelike properties cause it to localize at various sites with probabilities that vary widely, by orders of magnitude, and depend strongly on the local sequence. We find significant correlations between hole probabilities and mutation rates within base triplets, observed in published mutation accumulation experiments on four species of bacteria. We have also computed hole probability spectra for hypervariable segment I of the human mtDNA control region, which contains several mutational hotspots, and for heptanucleotides in noncoding regions of the human genome, whose polymorphism levels have recently been reported. We observe significant correlations between hole probabilities, and context-specific mutation and substitution rates. The correlation with hole probability cannot be explained entirely by CpG methylation in the heptanucleotide data. Peaks in hole probability tend to coincide with mutational hotspots, even in mtDNA where CpG methylation is rare. Our results suggest that hole-enhanced mutational mechanisms, such as oxidation-stabilized tautomerization and base deamination, contribute to molecular evolution.
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Affiliation(s)
- Martha Y Suárez-Villagrán
- Department of Physics, University of Houston, Houston.,Texas Center for Superconductivity, University of Houston, Houston
| | | | - John H Miller
- Department of Physics, University of Houston, Houston.,Texas Center for Superconductivity, University of Houston, Houston
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Cerón-Carrasco JP, Jacquemin D. Tuning the Optical Properties of Phenanthriplatin: Towards New Photoactivatable Analogues. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201700090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatic and High Performance Research Group (BIO-HPC); Universidad Católica San Antonio de Murcia (UCAM), Campus los Jerónimos; 30107 Murcia Spain
| | - Denis Jacquemin
- CEISAM UMR CNRS 6230; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
- Institut Universitaire de France; 1 rue Descartes 75005 Paris Cedex 5 France
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