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Botto M, Murthy S, Lamers MH. High-Throughput Exonuclease Assay Based on the Fluorescent Base Analogue 2-Aminopurine. ACS OMEGA 2023; 8:8285-8292. [PMID: 36910963 PMCID: PMC9996622 DOI: 10.1021/acsomega.2c06577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair, and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far been little exploited. Here, we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3' and 5' DNA ends over a wide range of protein activities and suitable for a high-throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high-throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance.
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Brovarets’ OO, Hovorun DM. Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research. J Biomol Struct Dyn 2019; 37:2716-2732. [DOI: 10.1080/07391102.2018.1495577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave, Kyiv, Ukraine
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Brovarets' OO, Voiteshenko IS, Pérez-Sánchez H, Hovorun DM. A QM/QTAIM detailed look at the Watson-Crick↔wobble tautomeric transformations of the 2-aminopurine·pyrimidine mispairs. J Biomol Struct Dyn 2017; 36:1649-1665. [PMID: 28514900 DOI: 10.1080/07391102.2017.1331864] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This work is devoted to the careful QM/QTAIM analysis of the evolution of the basic physico-chemical parameters along the intrinsic reaction coordinate (IRC) of the biologically important 2AP·T(WC)↔2AP·T*(w) and 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) tautomeric transformations obtained at each point of the IRC using original authors' methodology. Established profiles reflect the high similarity between the courses of these processes. Basing on the scrupulous analysis of the profiles of their geometric and electron-topological parameters, it was established that the dipole-active WC↔w tautomerizations of the Watson-Crick-like 2AP·T(WC)/2AP·C*(WC) mispairs, stabilized by the two classical N3H⋯N1, N2H⋯O2 and one weak C6H⋯O4/N4 H-bonds, into the wobble 2AP·T*(w)/2AP·C(w) base pairs, respectively, joined by the two classical N2H⋯N3 and O4/N4H⋯N1 H-bonds, proceed via the concerted stepwise mechanism through the sequential intrapair proton transfer and subsequent large-scale shifting of the bases relative each other, through the planar, highly stable, zwitterionic transition states stabilized by the participation of the four H-bonds - N1+H⋯O4-/N4-, N1+H⋯N3-, N2+H⋯N3-, and N2+H⋯O2-. Moreover, it was found out that the 2AP·T(WC)↔2AP·T*(w)/2AP·C*(WC)↔2AP·C(w) tautomerization reactions occur non-dissociatively and are accompanied by the consequent replacement of the 10 unique patterns of the specific intermolecular interactions along the IRC. Obtained data are of paramount importance in view of their possible application for the control and management of the proton transfer, e.g. by external electric or laser fields.
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Affiliation(s)
- Ol'ha O Brovarets'
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., Kyiv 03680 , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., Kyiv 03022 , Ukraine
| | - Ivan S Voiteshenko
- b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., Kyiv 03022 , Ukraine
| | - Horacio Pérez-Sánchez
- c Computer Science Department , Bioinformatics and High Performance Computing (BIO-HPC) Research Group, Universidad Católica San Antonio de Murcia (UCAM) , Guadalupe, Murcia 30107 , Spain
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., Kyiv 03680 , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., Kyiv 03022 , Ukraine
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Brovarets' OO, Pérez-Sánchez H. Whether 2-aminopurine induces incorporation errors at the DNA replication? A quantum-mechanical answer on the actual biological issue. J Biomol Struct Dyn 2016; 35:3398-3411. [PMID: 27794627 DOI: 10.1080/07391102.2016.1253504] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this paper, we consider the mutagenic properties of the 2-aminopurine (2AP), which has intrigued molecular biologists, biophysicists and physical chemists for a long time and been widely studied by both experimentalists and theorists. We have shown for the first time using QM calculations, that 2AP very effectively produces incorporation errors binding with cytosine (C) into the wobble (w) C·2AP(w) mispair, which is supported by the N4H⋯N1 and N2H⋯N3 H-bonds and is tautomerized into the Watson-Crick (WC)-like base mispair C*·2AP(WC) (asterisk denotes the mutagenic tautomer of the base), that quite easily in the process of the thermal fluctuations acquires enzymatically competent conformation. 2AP less effectively produces transversions forming the wobble mispair with A base - A·2AP(w), stabilized by the participation of the N6H⋯N1 and N2H⋯N1 H-bonds, followed by further tautomerization A·2AP(w) → A*·2AP(WC) and subsequent conformational transition A*·2AP(WC) → A*·2APsyn thus acquiring enzymatically competent structure. In this case, incorporation errors occur only in those case, when 2AP belongs to the incoming nucleotide. Thus, answering the question posed in the title of the article, we affirm for certain that 2AP induces incorporation errors at the DNA replication. Obtained results are consistent well with numerous experimental data.
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Affiliation(s)
- Ol'ha O Brovarets'
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., Kyiv 03680 , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., Kyiv 03022 , Ukraine
| | - Horacio Pérez-Sánchez
- c Computer Science Department, Bioinformatics and High Performance Computing (BIO-HPC) Research Group , Universidad Católica San Antonio de Murcia (UCAM) , Murcia 30107 , Spain
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Greiner VJ, Kovalenko L, Humbert N, Richert L, Birck C, Ruff M, Zaporozhets OA, Dhe-Paganon S, Bronner C, Mély Y. Site-Selective Monitoring of the Interaction of the SRA Domain of UHRF1 with Target DNA Sequences Labeled with 2-Aminopurine. Biochemistry 2015; 54:6012-20. [PMID: 26368281 DOI: 10.1021/acs.biochem.5b00419] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
UHRF1 plays a central role in the maintenance and transmission of epigenetic modifications by recruiting DNMT1 to hemimethylated CpG sites via its SET and RING-associated (SRA) domain, ensuring error-free duplication of methylation profiles. To characterize SRA-induced changes in the conformation and dynamics of a target 12 bp DNA duplex as a function of the methylation status, we labeled duplexes by the environment-sensitive probe 2-aminopurine (2-Ap) at various positions near or far from the central CpG recognition site containing either a nonmodified cytosine (NM duplex), a methylated cytosine (HM duplex), or methylated cytosines on both strands (BM duplex). Steady-state and time-resolved fluorescence indicated that binding of SRA induced modest conformational and dynamical changes in NM, HM, and BM duplexes, with only slight destabilization of base pairs, restriction of global duplex flexibility, and diminution of local nucleobase mobility. Moreover, significant restriction of the local motion of residues flanking the methylcytosine in the HM duplex suggested that these residues are more rigidly bound to SRA, in line with a slightly higher affinity of the HM duplex as compared to that of the NM or BM duplex. Our results are consistent with a "reader" role, in which the SRA domain scans DNA sequences for hemimethylated CpG sites without perturbation of the structure of contacted nucleotides.
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Affiliation(s)
- Vanille J Greiner
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie , 74 route du Rhin, 67401 Illkirch, France
| | - Lesia Kovalenko
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie , 74 route du Rhin, 67401 Illkirch, France.,Analytical Chemistry Department, Taras Shevchenko National University of Kyiv , 64 Volodymyrska Street, 01033 Kyiv, Ukraine
| | - Nicolas Humbert
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie , 74 route du Rhin, 67401 Illkirch, France
| | - Ludovic Richert
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie , 74 route du Rhin, 67401 Illkirch, France
| | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg , 1 rue Laurent Fries, Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg , 1 rue Laurent Fries, Illkirch, France
| | - Olga A Zaporozhets
- Analytical Chemistry Department, Taras Shevchenko National University of Kyiv , 64 Volodymyrska Street, 01033 Kyiv, Ukraine
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School , 360 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Christian Bronner
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie , 74 route du Rhin, 67401 Illkirch, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg , 1 rue Laurent Fries, Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie , 74 route du Rhin, 67401 Illkirch, France
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2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
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Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction–modification enzyme. Biochem Biophys Res Commun 2014; 449:120-5. [DOI: 10.1016/j.bbrc.2014.04.162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 11/23/2022]
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Ma L, Wu X. WITHDRAWN: Type III restriction-modification enzyme EcoP15I's base flipping mechanism and its mismatch cleavage on two head-to-head oriented recognition sites. Biochem Biophys Res Commun 2014:S0006-291X(14)00373-8. [PMID: 24589737 DOI: 10.1016/j.bbrc.2014.02.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Long Ma
- Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Xiaohua Wu
- EaStChem School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JJ, UK
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9
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Bianchi C, Zangi R. Dual base-flipping of cytosines in a CpG dinucleotide sequence. Biophys Chem 2013; 187-188:14-22. [PMID: 24469333 DOI: 10.1016/j.bpc.2013.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 12/30/2022]
Abstract
Simultaneous flipped-out conformation of two neighboring bases on opposite strands of DNAs has been observed in several X-ray structures. It has also been detected for two cytosines on opposite strands in different contexts of CpG sites. In this paper, we study by MD simulations the dual base flipping of the two cytosines in hemi-methylated CpG site. We calculate the potential of mean force of flipping-out the unmethylated cytosine in three model systems. The first is for DNA bound to the regulatory protein UHRF1. In this case, the methyl-cytosine on the complementary strand is flipped-out into the binding pocket of the SRA domain of the protein. The other two systems are for unbound DNAs in which the methyl-cytosine is either intra-helical or extra-helical. We find that when the methyl-cytosine is flipped-out it is easier to flip-out the other (unmethylated) cytosine on the opposite strand by about 14-16kJ/mol. This lower penalty for dual-base flipping is observed for both the bound and unbound states of the DNA. Analyses of the hydrogen bond network and stacking interactions within the CpG site indicate that the lower penalty is due to stabilization of the dual-base flipped-out conformation via interactions involving the orphan guanines. The results presented in this paper suggest that the extra-helical conformation of the methyl-cytosine recognized by UHRF1 can facilitate the base-flipping process of the target cytosine to be methylated by Dnmt1.
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Affiliation(s)
- Caterina Bianchi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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10
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Li B, Ju H. Label-free optical biosensors based on a planar optical waveguide. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7401-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Bianchi C, Zangi R. Base-Flipping Propensities of Unmethylated, Hemimethylated, and Fully Methylated CpG Sites. J Phys Chem B 2013; 117:2348-58. [DOI: 10.1021/jp312145b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Caterina Bianchi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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