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Makarska-Bialokoz M. Comparative study of binding interactions between porphyrin systems and aromatic compounds of biological importance by multiple spectroscopic techniques: A review. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 200:263-274. [PMID: 29694930 DOI: 10.1016/j.saa.2018.04.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/13/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
The specific spectroscopic and redox properties of porphyrins predestine them to fulfill the role of sensors during interacting with different biologically active substances. Monitoring of binding interactions in the systems porphyrin-biologically active compound is a key question not only in the field of physiological functions of living organisms, but also in environmental protection, notably in the light of the rapidly growing drug consumption and concurrently the production of drug effluents. Not always beneficial action of drugs on natural porphyrin systems induces to further studies, with commercially available porphyrins as the model systems. Therefore the binding process between several water-soluble porphyrins and a series of biologically active compounds (e.g. caffeine, guanine, theophylline, theobromine, xanthine, uric acid) has been studied in different aqueous solutions analyzing their absorption and steady-state fluorescence spectra, the porphyrin fluorescence lifetimes and their quantum yields. The magnitude of the binding and fluorescence quenching constants values for particular quenchers decreases in a series: uric acid > guanine > caffeine > theophylline > theobromine > xanthine. In all the systems studied there are characters of static quenching, as a consequence of the π-π-stacked non-covalent and non-fluorescent complexes formation between porphyrins and interacting compounds, accompanied simultaneously by the additional specific binding interactions. The porphyrin fluorescence quenching can be explain by the photoinduced intermolecular electron transfer from aromatic compound to the center of the porphyrin molecule, playing the role of the binding site. Presented results can be valuable for designing of new fluorescent porphyrin chemosensors or monitoring of drug traces in aqueous solutions. The obtained outcomes have also the toxicological and medical importance, providing insight into the interactions of the water-soluble porphyrins with biologically active substances.
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Affiliation(s)
- Magdalena Makarska-Bialokoz
- Department of Inorganic Chemistry, Maria Curie-Sklodowska University, M. C. Sklodowska Sq. 2, 20-031 Lublin, Poland.
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Alshykhly OR, Fleming AM, Burrows CJ. Guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin induces mutations when bypassed by DNA polymerases and is a substrate for base excision repair. Chem Res Toxicol 2015; 28:1861-71. [PMID: 26313343 DOI: 10.1021/acs.chemrestox.5b00302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Guanine (G) is a target for oxidation by reactive oxygen species in DNA, RNA, and the nucleotide pool. Damage to DNA yields products with alternative properties toward DNA processing enzymes compared to those of the parent nucleotide. A new lesion, 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), bearing a stereocenter in the base was recently identified from the oxidation of G. DNA polymerase and base excision repair processing of this new lesion has now been evaluated. Single nucleotide insertion opposite (S)-2Ih and (R)-2Ih in the template strand catalyzed by the DNA polymerases Klenow fragment exo(-), DPO4, and Hemo KlenTaq demonstrates these lesions to cause point mutations. Specifically, they promote 3-fold more G·C → C·G transversion mutations than G·C → T·A, and (S)-2Ih was 2-fold more blocking for polymerase bypass than (R)-2Ih. Both diastereomer lesions were found to be substrates for the DNA glycosylases NEIL1 and Fpg, and poorly excised by endonuclease III (Nth). The activity was independent of the base pair partner. Thermal melting, CD spectroscopy, and density functional theory geometric optimization calculations were conducted to provide insight into these polymerase and DNA glycosylase studies. These results identify that formation of the 2Ih lesions in a cell would be mutagenic in the event that they were not properly repaired.
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Affiliation(s)
- Omar R Alshykhly
- Department of Chemistry, University of Utah , 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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Alshykhly OR, Fleming A, Burrows CJ. 5-Carboxamido-5-formamido-2-iminohydantoin, in Addition to 8-oxo-7,8-Dihydroguanine, Is the Major Product of the Iron-Fenton or X-ray Radiation-Induced Oxidation of Guanine under Aerobic Reducing Conditions in Nucleoside and DNA Contexts. J Org Chem 2015; 80:6996-7007. [PMID: 26092110 PMCID: PMC4509422 DOI: 10.1021/acs.joc.5b00689] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 11/29/2022]
Abstract
Exogenously and endogenously produced reactive oxygen species attack the base and sugar moieties of DNA showing a preference for reaction at 2'-deoxyguanosine (dG) sites. In the present work, dG was oxidized by HO(•) via the Fe(II)-Fenton reaction or by X-ray radiolysis of water. The oxidized lesions observed include the 2'-deoxynucleosides of 8-oxo-7,8-dihydroguanine (dOG), spiroiminodihydantoin (dSp), 5-guanidinohydantoin (dGh), oxazolone (dZ), 5-carboxamido-5-formamido-2-iminohydantoin (d2Ih), 5',8-cyclo-2'-deoxyguanosine (cyclo-dG), and the free base guanine (Gua). Reactions conducted with ascorbate or N-acetylcysteine as a reductant under aerobic conditions identified d2Ih as the major lesion formed. Studies were conducted to identify the role of O2 and the reductant in product formation. From these studies, mechanisms are proposed to support d2Ih as a major oxidation product detected under aerobic conditions in the presence of the reductant. These nucleoside observations were then validated in oxidations of oligodeoxynucleotide and λ-DNA contexts that demonstrated high yields of d2Ih in tandem with dOG, dSp, and dGh. These results identify dG oxidation to d2Ih to occur in high yields leading to a hypothesis that d2Ih could be found from in cells stressed with HO(•). Further, the distorted ring structure of d2Ih likely causes this lesion to be highly mutagenic.
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Affiliation(s)
- Omar R. Alshykhly
- Department of Chemistry, University of
Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron
M. Fleming
- Department of Chemistry, University of
Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of
Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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Fleming AM, Alshykhly O, Orendt AM, Burrows CJ. Computational studies of electronic circular dichroism spectra predict absolute configuration assignments for the guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin. Tetrahedron Lett 2015; 56:3191-3196. [PMID: 26097262 DOI: 10.1016/j.tetlet.2014.12.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Oxidation of the guanine heterocycle by two electrons can yield the chiral product 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). The 2Ih free base enantiomers were synthesized from 2'-deoxyguanosine oxidized with a Cu(II)/H2O2 oxidant system followed by hydrolysis of the N-glycosidic bond. These isomers were each studied by electronic circular dichroism spectroscopy for determination of their absolute configurations. Time-dependent density functional theory calculations of the expected spectra were completed in both the gas phase and with solvent modeling in order to interpret the experimental spectra and provide the absolute configuration assignments.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - Omar Alshykhly
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - Anita M Orendt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA ; Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112-0190, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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Brissos RF, Caubet A, Gamez P. Possible DNA-Interacting Pathways for Metal-Based Compounds Exemplified with Copper Coordination Compounds. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500175] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Fleming AM, Alshykhly O, Zhu J, Muller JG, Burrows CJ. Rates of chemical cleavage of DNA and RNA oligomers containing guanine oxidation products. Chem Res Toxicol 2015; 28:1292-300. [PMID: 25853314 PMCID: PMC4482417 DOI: 10.1021/acs.chemrestox.5b00096] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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The nucleobase guanine in DNA (dG)
and RNA (rG) has the lowest
standard reduction potential of the bases, rendering it a major site
of oxidative damage in these polymers. Mapping the sites at which
oxidation occurs in an oligomer via chemical reagents utilizes hot
piperidine for cleaving oxidized DNA and aniline (pH 4.5) for cleaving
oxidized RNA. In the present studies, a series of time-dependent cleavages
of DNA and RNA strands containing various guanine lesions were examined
to determine the strand scission rate constants. The guanine base
lesions 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin
(Sp), 5-guanidinohydantoin (Gh), 2,2,4-triamino-2H-oxazol-5-one (Z), and 5-carboxamido-5-formamido-2-iminohydantoin
(2Ih) were evaluated in piperidine-treated DNA and aniline-treated
RNA. These data identified wide variability in the chemical lability
of the lesions studied in both DNA and RNA. Further, the rate constants
for cleaving lesions in RNA were generally found to be significantly
smaller than for lesions in DNA. The OG nucleotides were poorly cleaved
in DNA and RNA; Sp nucleotides were slowly cleaved in DNA and did
not cleave significantly in RNA; Gh and Z nucleotides cleaved in both
DNA and RNA at intermediate rates; and 2Ih oligonucleotides cleaved
relatively quickly in both DNA and RNA. The data are compared and
contrasted with respect to future experimental design.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Omar Alshykhly
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Judy Zhu
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - James G Muller
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Tomaszewska-Antczak A, Guga P, Nawrot B, Pratviel G. Guanosine in a single stranded region of anticodon stem-loop tRNA models is prone to oxidatively generated damage resulting in dehydroguanidinohydantoin and spiroiminodihydantoin lesions. Chemistry 2015; 21:6381-5. [PMID: 25771988 DOI: 10.1002/chem.201406409] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/24/2015] [Indexed: 01/18/2023]
Abstract
Oxidation of RNA hairpin models corresponding to anticodon stem-loop (ASL) of transfer RNA led to RNA damage consisting solely of a unique loop guanine oxidation. Manganese porphyrin/oxone treatment of RNA resulted in dehydroguanidinohydantoin (DGh; major) and/or spiroiminodihydantoin (Sp) lesions. Ribose damage was not observed. This two-electron transfer oxidation reaction allowed the identification of guanine oxidation products for further study of RNA species carrying a unique lesion at a single G to investigate their biological impact.
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Affiliation(s)
- Agnieszka Tomaszewska-Antczak
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz (Poland)
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Chen X, Fleming AM, Muller JG, Burrows CJ. Endonuclease and Exonuclease Activities on Oligodeoxynucleotides Containing Spiroiminodihydantoin Depend on the Sequence Context and the Lesion Stereochemistry. NEW J CHEM 2013; 37:3440-3449. [PMID: 24563606 PMCID: PMC3929292 DOI: 10.1039/c3nj00418j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
8-Oxo-7,8-dihydro-2'-deoxyguanosine (dOG), a well-studied oxidation product of 2'-deoxyguanosine (dG), is prone to facile further oxidation forming spiroiminodihydantoin 2'-deoxyribonucleoside (dSp) in the nucleotide pool and in single-stranded oligodeoxynucleotides (ODNs). Many methods for quantification of damaged lesions in the genome rely on digestion of DNA with exonucleases or endonucleases and dephosphorylation followed by LC-MS analysis of the resulting nucleosides. In this study, enzymatic hydrolysis of dSp-containing ODNs was investigated with snake venom phosphodiesterase (SVPD), spleen phosphodiesterase (SPD) and nuclease P1. SVPD led to formation of a dinucleotide, 5'-d(Np[Sp])-3' (N = any nucleotide) that included the undamaged nucleotide on the 5' side of dSp as the final product. This dinucleotide was a substrate for both SPD and nuclease P1. A kinetic study of the activity of SPD and nuclease P1 showed a sequence dependence on the nucleotide 5' to the lesion with rates in the order dG>dA>dT>dC. In addition, the two diastereomers of dSp underwent digestion at significantly different rates with dSp1>dSp2; nuclease P1 hydrolyzed the 5'-d(Np[Sp1])-3' dinucleotide two- to six-fold faster than the corresponding 5'-d(Np[Sp2])-3', while for SPD the difference was two-fold. These rates are chemically reasoned based on dSp diastereomer differences in the syn vs. anti glycosidic bond orientation. A method for the complete digestion of dSp-containing ODNs is also outlined based on treatment with nuclease P1 and SVPD. These findings have significant impact on the development of methods to detect dSp levels in cellular DNA.
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Affiliation(s)
- Xin Chen
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, U.S.A
| | - Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, U.S.A
| | - James G. Muller
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, U.S.A
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, U.S.A
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Trzcionka J, Irvoas J, Pratviel G. The protonation state of trans axial water molecule switches: the reactivity of high-valent manganese-oxo porphyrin. NEW J CHEM 2013. [DOI: 10.1039/c3nj01004j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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