1
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Lukina MV, Zhdanova PV, Koval VV. Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase. Curr Issues Mol Biol 2024; 46:4119-4132. [PMID: 38785521 PMCID: PMC11120029 DOI: 10.3390/cimb46050253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in human cells. OGG1 is a bifunctional DNA glycosylase with N-glycosylase and AP lyase activities. Aspects of the detailed mechanism underlying the recognition of 8-oxoguanine among numerous intact bases and its subsequent interaction with the enzyme's active site amino acid residues are still debated. The main objective of our work was to determine the effect (structural and thermodynamic) of introducing an oxoG-clamp in model DNA substrates on the process of 8-oxoG excision by OGG1. Towards that end, we used DNA duplexes modeling OGG1-specific lesions: 8-oxoguanine or an apurinic/apyrimidinic site with either cytidine or the oxoG-clamp in the complementary strand opposite to the lesion. It was revealed that there was neither hydrolysis of the N-glycosidic bond at oxoG nor cleavage of the sugar-phosphate backbone during the reaction between OGG1 and oxoG-clamp-containing duplexes. Possible structural reasons for the absence of OGG1 enzymatic activity were studied via the stopped-flow kinetic approach and molecular dynamics simulations. The base opposite the damage was found to have a critical effect on the formation of the enzyme-substrate complex and the initiation of DNA cleavage. The oxoG-clamp residue prevented the eversion of the oxoG base into the OGG1 active site pocket and impeded the correct convergence of the apurinic/apyrimidinic site of DNA and the attacking nucleophilic group of the enzyme. An obtained three-dimensional model of the OGG1 complex with DNA containing the oxoG-clamp, together with kinetic data, allowed us to clarify the role of the contact of amino acid residues with DNA in the formation of (and rearrangements in) the enzyme-substrate complex.
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Affiliation(s)
- Maria V. Lukina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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2
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Taniguchi Y. Development of Artificial Nucleoside Analogues for the Recognition and Detection of Damaged Nucleoside in DNA. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Karwowski BT. The Influence of Single, Tandem, and Clustered DNA Damage on the Electronic Properties of the Double Helix: A Theoretical Study. Molecules 2020; 25:molecules25143126. [PMID: 32650559 PMCID: PMC7397046 DOI: 10.3390/molecules25143126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/28/2022] Open
Abstract
Oxidatively generated damage to DNA frequently appears in the human genome as the effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents, such as ionization radiation. In this paper, the electronic properties of single, tandem, and clustered DNA damage in comparison with native ds-DNA are discussed as a comparative analysis for the first time. A single lesion—8-oxo-7,8-dihydro-2′-deoxyguanosine (Goxo), a tandem lesion—(5′S) and (5′R) 5′,8-cyclo-2′-deoxyadenosine (cdA), and the presence of both of them in one helix turn as clustered DNA damage were chosen and taken into consideration. The lowest vertical and adiabatic potential (VIP ~ 5.9 and AIP ~ 5.5 eV, respectively) were found for Goxo, independently of the discussed DNA lesion type and their distribution within the double helix. Moreover, the VIP and AIP were assigned for ds-trimers, ds- dimers and single base pairs isolated from parental ds-hexamers in their neutral and cationic forms. The above results were confirmed by the charge and spin density population, which revealed that Goxo can be considered as a cation radical point of destination independently of the DNA damage type (single, tandem, or clustered). Additionally, the different influences of cdA on the charge transfer rate were found and discussed in the context of tandem and clustered lesions. Because oligonucleotide lesions are effectively produced as a result of ionization factors, the presented data in this article might be valuable in developing a new scheme of anticancer radiotherapy efficiency.
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Affiliation(s)
- Bolesław T Karwowski
- Department of Biopharmacy, Medical University of Lodz, Muszynskiego Street 1, 90-151 Lodz, Poland
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4
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Sasaki S. Development of Novel Functional Molecules Targeting DNA and RNA. Chem Pharm Bull (Tokyo) 2019; 67:505-518. [PMID: 31155555 DOI: 10.1248/cpb.c19-00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleic acid therapeutics such as antisense and small interfering RNA (siRNA) have attracted increasing attention as innovative medicines that interfere with and/or modify gene expression systems. We have developed new functional oligonucleotides that can target DNA and RNA with high efficiency and selectivity. This review summarizes our achievements, including (1) the formation of non-natural triplex DNA for sequence-specific inhibition of transcription; (2) artificial receptor molecules for 8-oxidized-guanosine nucleosides; and (3) reactive oligonucleotides with a cross-linking agent or a functionality-transfer nucleoside for RNA pinpoint modification.
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Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
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5
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Antiviral activity spectrum of phenoxazine nucleoside derivatives. Antiviral Res 2019; 163:117-124. [PMID: 30684562 DOI: 10.1016/j.antiviral.2019.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/13/2022]
Abstract
The phenoxazine scaffold is widely used to stabilize nucleic acid duplexes, as a part of fluorescent probes for the study of nucleic acid structure, recognition, and metabolism, etc. Here we present the synthesis of phenoxazine-based nucleoside derivatives and their antiviral activity against a panel of structurally diverse viruses: enveloped DNA herpesviruses varicella zoster virus (VZV) and human cytomegalovirus, enveloped RNA tick-borne encephalitis virus (TBEV), and non-enveloped RNA enteroviruses. Studied compounds were effective against DNA and RNA viruses reproduction in cell culture. 3-(2'-Deoxy-β-D-ribofuranosyl)-1,3-diaza-2-oxophenoxazine proved to be a potent inhibitor of VZV replication with superior activity against wild type than thymidine kinase deficient strains (EC50 0.06 and 10 μM, respectively). This compound did not show cytotoxicity on all the studied cell lines. Several compounds showed promising activity against TBEV (EC50 0.35-0.91 μM), but the activity was accompanied by pronounced cytotoxicity. These compounds may be considered as a good starting point for further structure optimization as antiherpesviral or antiflaviviral compounds.
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6
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Varizhuk AM, Zatsepin TS, Golovin AV, Belyaev ES, Kostyukevich YI, Dedkov VG, Shipulin GA, Shpakovski GV, Aralov AV. Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg Med Chem 2017; 25:3597-3605. [PMID: 28396019 DOI: 10.1016/j.bmc.2017.03.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/20/2023]
Abstract
Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.
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Affiliation(s)
- Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Vavilov Str. 32, Moscow 119991, Russia
| | - Timofei S Zatsepin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia; Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia.
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Evgeny S Belyaev
- Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38/2, Moscow 119334, Russia
| | - Yury I Kostyukevich
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia
| | - Vladimir G Dedkov
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia.
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7
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Duprey JLHA, Bullen GA, Zhao ZY, Bassani DM, Peacock AFA, Wilkie J, Tucker JHR. Single Site Discrimination of Cytosine, 5-Methylcytosine, and 5-Hydroxymethylcytosine in Target DNA Using Anthracene-Tagged Fluorescent Probes. ACS Chem Biol 2016; 11:717-21. [PMID: 26580817 DOI: 10.1021/acschembio.5b00796] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The ability to discriminate between epigenetic variants in DNA is a necessary tool if we are to increase our understanding of the roles that they play in various biological processes and medical conditions. Herein, it is demonstrated how a simple two-step fluorescent probe assay can be used to differentiate all three major epigenetic variants of cytosine at a single locus site in a target strand of DNA.
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Affiliation(s)
- Jean-Louis H. A. Duprey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Gemma A. Bullen
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Zheng-yun Zhao
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Dario M. Bassani
- Univ. Bordeaux, CNRS, ISM UMR 5255 351, Cours de la Libération, 33400 Talence, France
| | - Anna F. A. Peacock
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - John Wilkie
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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8
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Edwards SK, Ono T, Wang S, Jiang W, Franzini RM, Jung JW, Chan KM, Kool ET. In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage. Chembiochem 2015; 16:1637-46. [PMID: 26073452 PMCID: PMC4586133 DOI: 10.1002/cbic.201500184] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 01/09/2023]
Abstract
The repair of oxidative damage to DNA is essential to avoid mutations that lead to cancer. Oxidized DNA bases, such as 8-oxoguanine, are a main source of these mutations, and the enzyme 8-oxoguanine glycosylase 1 (OGG1) is the chief human enzyme that excises 8-oxoguanine from DNA. The activity of OGG1 has been linked to human inflammation responses and to cancer, and researchers are beginning to search for inhibitors of the enzyme. However, measuring the activity of the enzyme typically requires laborious gel-based measurements of radiolabeled DNAs. Here we report the design and properties of fluorogenic probes that directly report on the activity of OGG1 (and its bacterial homologue Fpg) in real time as the oxidized base is excised. The probes are short, modified DNA oligomers containing fluorescent DNA bases and are designed to utilize 8-oxoguanine itself as a fluorescence quencher. Screening of combinations of fluorophores and 8-oxoguanine revealed two fluorophores, pyrene and tCo, that are strongly quenched by the damaged base. We tested 42 potential probes containing these fluorophores: the optimum probe, OGR1, yields a 60-fold light-up signal in vitro with OGG1 and Fpg. It can report on oxidative repair activity in mammalian cell lysate and with bacterial cells overexpressing a repair enzyme. Such probes might prove useful in quantifying enzyme activity and performing competitive inhibition assays.
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Affiliation(s)
- Sarah K Edwards
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Toshikazu Ono
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
- Present Address: Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 (Japan)
| | - Shenliang Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Wei Jiang
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | | | - Jong Wha Jung
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
- Present Address: College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 702-701 (Republic of Korea)
| | - Ke Min Chan
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA).
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9
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Fuchi Y, Sasaki S. New NitroG-Grasp Molecules with Enhanced Capture Reactivity for 8-Nitroguanosine in the Aqueous Media. Chem Pharm Bull (Tokyo) 2015; 63:913-9. [DOI: 10.1248/cpb.c15-00550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yasufumi Fuchi
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
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10
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Nakagawa O. [Development of artificial nucleic acids functionalized for damaged gene diagnosis, gene inhibition and delivery system]. YAKUGAKU ZASSHI 2014; 134:1319-29. [PMID: 25452241 DOI: 10.1248/yakushi.14-00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial nucleic acids have recently been widely used with their properties optimized for various technologies such as the inhibition of gene expression (antisense/antigene strategies, RNA interference) and genetic diagnosis (single nucleotide polymorphism (SNP), damaged nucleobase). For practical application of nucleic acid therapeutics, establishment of an effective delivery system for oligonucleotides is also required because of their poor permeability into cells. Various useful delivery technologies including lipoplexes formed using cationic lipids and polyplexes made with cationic polymers have been developed; however, there is no crucial tool for oligonucleotide therapeutics at present. If technologies of functional nucleic acids and adequate delivery systems are cooperatively developed, the realization of nucleic acid therapeutics might be effectively accelerated. Based on this concept, we have been cooperatively developing these technologies based on organic synthetic chemistry during the past decade. This paper summarizes our recent results: 1) development of a specific fluorescent probe for 8-oxoguanine; 2) synthesis and evaluation of a prodrug-type small interfering RNA (siRNA) molecule; and 3) targeted intracellular delivery of oligonucleotides via conjugation with receptor-targeted ligands.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University
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11
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Fuchi Y, Sasaki S. Efficient Covalent Capture of 8-Nitroguanosine via a Multiple Hydrogen-Bonded Complex. Org Lett 2014; 16:1760-3. [DOI: 10.1021/ol500452r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yasufumi Fuchi
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical
Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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12
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Taniguchi Y, Fukabori K, Kikukawa Y, Koga Y, Sasaki S. 2,6-Diaminopurine nucleoside derivative of 9-ethyloxy-2-oxo-1,3-diazaphenoxazine (2-amino-Adap) for recognition of 8-oxo-dG in DNA. Bioorg Med Chem 2014; 22:1634-41. [DOI: 10.1016/j.bmc.2014.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 01/14/2014] [Accepted: 01/18/2014] [Indexed: 10/25/2022]
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13
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Lou C, Dallmann A, Marafini P, Gao R, Brown T. Enhanced H-bonding and π-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue. Chem Sci 2014. [DOI: 10.1039/c4sc00948g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Combining enhanced π-stacking, H-bonding and electrostatic attraction in a single C-monomer greatly increases DNA duplex stability and massively destabilises mismatches.
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Affiliation(s)
- Chenguang Lou
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
| | - Andre Dallmann
- Institute of Structural Biology
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich and Chair of Biomolecular NMR
- TU München
- 85747 Garching, Germany
| | - Pietro Marafini
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
- Department of Chemistry
| | - Rachel Gao
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
- Department of Chemistry
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14
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Nucleosides 8 [18]: Ribosylation of Fused Quinazolines—Synthesis of New [1,2,4]Triazolo[5,1-b]- and [1,2,4]Triazino[3,2-b]quinazoline Nucleosides of Fluorescence Interest. J CHEM-NY 2013. [DOI: 10.1155/2013/612756] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
[1,2,4]Triazolo[5,1-b]- and [1,2,4]triazino[3,2-b] quinazolines have been ribosylated by coupling with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose and by using the silylation method, followed by debenzoylation by methanolic sodium methoxide to afford the corresponding free N-nucleosides. Nucleosides obtained have been identified by their spectral analysis. From the UV-visible and fluorescence studies of some nucleosides synthesized, it is found that they have fluorescence properties.
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15
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Zhang Q, Wang Y, Meng X, Dhar R, Huang H. Triple-stranded DNA containing 8-oxo-7,8-dihydro-2'-deoxyguanosine: implication in the design of selective aptamer sensors for 8-oxo-7,8-dihydroguanine. Anal Chem 2012; 85:201-7. [PMID: 23237478 DOI: 10.1021/ac3033323] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
8-Oxo-7,8-dihydroguanine (8-oxoG, or OG) as a free base has been widely considered as a biomarker for DNA oxidative damage. Currently no fluorescence sensor has been developed to directly detect 8-oxoG less than 100 nM. In this study, two triple-stranded DNAs were selected as the scaffolds to rationally design DNA aptamer sensors for 8-oxoG. The cavity was created by deleting the 8-oxodG nucleoside in a triplex containing an A·OG-C triad or a C·OG-A triad. The results showed that the fluorescence of both sensors were completely quenched by 8-oxoG. The detection ranges of the two sensors were different, while the combined range was comparable to the detection range of an antibody-based method. This result is expected to enable a fast, low-cost, and reusable method to measure 8-oxoG concentration.
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Affiliation(s)
- Qian Zhang
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, 07102, United States
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16
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Zhang B, Guo LH, Greenberg MM. Quantification of 8-oxodGuo lesions in double-stranded DNA using a photoelectrochemical DNA sensor. Anal Chem 2012; 84:6048-53. [PMID: 22746252 PMCID: PMC3872968 DOI: 10.1021/ac300866u] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exposure of DNA to oxidative stress conditions results in the generation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo). 8-OxodGuo is genotoxic if left unrepaired. We quantified 8-oxodGuo lesions in double-stranded DNA films by using a photoelectrochemical DNA sensor in conjunction with a specific covalent labeling method. A lesion-containing DNA film was assembled on a SnO(2) nanoparticle modified indium tin oxide electrode through layer-by-layer electrostatic adsorption. The lesions were covalently labeled with a biotin conjugated spermine derivative, and ruthenium tris(bipyridine) labeled streptavidin was introduced as the signal reporter molecule. Photocurrent increased with the number of lesions in the strand and decreased as the film was diluted with intact DNA. Quantification of 8-oxodGuo was achieved with an estimated detection limit of ∼1 lesion in 650 bases or 1.6 fmol of 8-oxodGuo on the electrode. Incubation of the film with a DNA base excision repair enzyme, E. coli formamidopyrimidine-DNA glycosylase (Fpg), resulted in complete loss of the signal, indicating efficient excision of the isolated lesions in the nucleotide. Oxidatively generated DNA damage to a double-stranded calf thymus DNA film by the Fenton reaction was then assessed. One 8-oxodGuo lesion in 520 bases was detected in DNA exposed to 50 μM Fe(2+)/200 μM H(2)O(2). Treatment with Fpg reduced the photocurrent by 50%, indicating only partial excision of 8-oxodGuo. This suggests that tandem lesions, which are resistant to Fpg excision, are generated by the Fenton reaction. Unlike repair enzyme dependent methods, the sensor recognizes 8-oxodGuo in tandem lesions and can avoid underestimating DNA damage.
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Affiliation(s)
- Bintian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liang-Hong Guo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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17
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Roy J, Chirania P, Ganguly S, Huang H. A DNA aptamer sensor for 8-oxo-7,8-dihydroguanine. Bioorg Med Chem Lett 2011; 22:863-7. [PMID: 22209455 DOI: 10.1016/j.bmcl.2011.12.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/06/2011] [Accepted: 12/08/2011] [Indexed: 10/14/2022]
Abstract
Abasic site-containing DNA duplex is a versatile structural motif that can be used for the design of purine aptamers and sensors. In this study, several modifications were introduced to the abasic site to explore possible specific binding of free 8-oxoG, a product of DNA base excision repair. The nucleoside opposite the abasic site was replaced by pyrrolo-dC as a reporter group. Binding of 8-oxoG quenched pyrrolo-dC fluorescence by as much as 70%. In contrast, adenine, guanine, thymine, and cytosine showed only minimal fluorescence quenching effect. The best aptamer binds 8-oxoG with a dissociation constant of 5.5±0.8μM. This sensor can be used to accurately measure 8-oxoG concentrations in the presence of guanine.
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Affiliation(s)
- Jyoti Roy
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
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18
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Taniguchi Y, Koga Y, Fukabori K, Kawaguchi R, Sasaki S. OFF-to-ON type fluorescent probe for the detection of 8-oxo-dG in DNA by the Adap-masked ODN probe. Bioorg Med Chem Lett 2011; 22:543-6. [PMID: 22119473 DOI: 10.1016/j.bmcl.2011.10.093] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 10/11/2011] [Accepted: 10/26/2011] [Indexed: 10/15/2022]
Abstract
We have recently reported that Adap (adenosine-1,3-diazaphenoxazine) is an artificial nucleoside analogue for the specific recognition by multiple hydrogen bonding and that its fluorescence is selectively quenched with 8-oxo-2'-deoxyguanosine (8-oxo-dG) in DNA. We now report the development of a new OFF-to-ON type FRET probe, in which one strand contains Adap and another contains natural nucleotides for the formation of a less stable double strand. Each strand was labeled with Cy3 or BHQ2 at the 5'-end or 3'-end, respectively. It was expected in this system that fluorescence of the duplex probe is first quenched by FRET, but the target DNA strand containing 8-oxo-dG at the complementary site of Adap would enhance the displacement reaction of the less stable duplex probe that results in the fluorescence recovery. The results showed that the duplex probe containing the Adap-T base pair exhibited a complete discrimination between 8-oxo-dG and dG in DNA by fluorescence enhancement.
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Affiliation(s)
- Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Koga Y, Fuchi Y, Nakagawa O, Sasaki S. Optimization of fluorescence property of the 8-oxodGclamp derivative for better selectivity for 8-oxo-2′-deoxyguanosine. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.03.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hirose W, Sato K, Matsuda A. Fluorescence Properties of 5-(5,6-Dimethoxybenzothiazol-2-yl)-2′-deoxyuridine (dbtU) and Oligodeoxyribonucleotides Containing dbtU. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100818] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Taniguchi Y, Kawaguchi R, Sasaki S. Adenosine-1,3-diazaphenoxazine derivative for selective base pair formation with 8-oxo-2'-deoxyguanosine in DNA. J Am Chem Soc 2011; 133:7272-5. [PMID: 21524070 DOI: 10.1021/ja200327u] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The selective detection of 8-oxo-2'-deoxyguanosine (8-oxo-dG) in DNA without chemical or enzymatic treatment is an attractive tool for genomic research. We designed and synthesized the non-natural nucleoside analogue, the adenosine-1,3-diazaphenoxazine (Adap) derivative, for selective recognition of 8-oxo-dG in DNA. This study clearly showed that Adap has a highly selective stabilizing effect on the duplex containing the Adap-8-oxo-dG base pair. Furthermore, the fluorescent property of Adap was shown to be useful for the selective detection of 8-oxo-dG in the duplex DNA. To the best of our knowledge, this is the first successful demonstration of a non-natural nucleoside with a high selectivity for 8-oxo-dG in DNA.
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Affiliation(s)
- Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582 Japan
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 665] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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Dahlmann HA, Vaidyanathan VG, Sturla SJ. Investigating the biochemical impact of DNA damage with structure-based probes: abasic sites, photodimers, alkylation adducts, and oxidative lesions. Biochemistry 2009; 48:9347-59. [PMID: 19757831 PMCID: PMC2789562 DOI: 10.1021/bi901059k] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA sustains a wide variety of damage, such as the formation of abasic sites, pyrimidine dimers, alkylation adducts, or oxidative lesions, upon exposure to UV radiation, alkylating agents, or oxidative conditions. Since these forms of damage may be acutely toxic or mutagenic and potentially carcinogenic, it is of interest to gain insight into how their structures impact biochemical processing of DNA, such as synthesis, transcription, and repair. Lesion-specific molecular probes have been used to study polymerase-mediated translesion DNA synthesis of abasic sites and TT dimers, while other probes have been developed for specifically investigating the alkylation adduct O(6)-Bn-G and the oxidative lesion 8-oxo-G. In this review, recent examples of lesion-specific molecular probes are surveyed; their specificities of incorporation opposite target lesions compared to unmodified nucleotides are discussed, and limitations of their applications under physiologically relevant conditions are assessed.
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Affiliation(s)
| | | | - Shana J. Sturla
- To whom correspondence should be addressed: ; Phone: 612-626-0496; Fax: 612-624-0139
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