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Urbelienė N, Kutanovas S, Meškienė R, Gasparavičiūtė R, Tauraitė D, Koplūnaitė M, Meškys R. Application of the uridine auxotrophic host and synthetic nucleosides for a rapid selection of hydrolases from metagenomic libraries. Microb Biotechnol 2019; 12:148-160. [PMID: 30302933 PMCID: PMC6302743 DOI: 10.1111/1751-7915.13316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/23/2018] [Accepted: 08/28/2018] [Indexed: 12/01/2022] Open
Abstract
A high-throughput method (≥ 106 of clones can be analysed on a single agar plate) for the selection of ester-hydrolysing enzymes was developed based on the uridine auxotrophy of Escherichia coli strain DH10B ΔpyrFEC and the acylated derivatives 2',3',5'-O-tri-acetyluridine and 2',3',5'-O-tri-hexanoyluridine as the sole source of uridine. The proposed approach permits the selection of hydrolases belonging to different families and active towards different substrates. Moreover, the ester group of the substrate used for the selection, at least partly, determined the specificity of the selected enzymes.
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Affiliation(s)
- Nina Urbelienė
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySauletekio 7VilniusLT‐10257Lithuania
| | - Simonas Kutanovas
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySauletekio 7VilniusLT‐10257Lithuania
| | - Rita Meškienė
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySauletekio 7VilniusLT‐10257Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySauletekio 7VilniusLT‐10257Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySauletekio 7VilniusLT‐10257Lithuania
| | - Martyna Koplūnaitė
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySauletekio 7VilniusLT‐10257Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySauletekio 7VilniusLT‐10257Lithuania
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Ohura A, Itoh T, Ishida H, Saito A, Yamamoto K. Three-Component Regioselective Synthesis of Tetrahydrofuro[2,3-d]oxazoles and Their Efficient Conversion to Oxazoles. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Arisa Ohura
- Laboratory of Drug Design and Medicinal Chemistry; Showa Pharmaceutical University; 3-3165 Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
| | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry; Showa Pharmaceutical University; 3-3165 Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
| | - Hiroaki Ishida
- Laboratory of Drug Design and Medicinal Chemistry; Showa Pharmaceutical University; 3-3165 Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
| | - Akio Saito
- Division of Applied Chemistry, Institute of Engineering; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry; Showa Pharmaceutical University; 3-3165 Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
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Dudek M, Trylska J. Molecular Dynamics Simulations of l-RNA Involving Homo- and Heterochiral Complexes. J Chem Theory Comput 2017; 13:1244-1253. [DOI: 10.1021/acs.jctc.6b01075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marta Dudek
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5a, 02-106 Warsaw, Poland
- Department
of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Joanna Trylska
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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Bagmare S, Puranik VG, Fernandes M, Kumar VA. 4'-Epi-DNA: A DNA Mimic Containing 4'-hydroxymethyl-α-l-Xylo-Thymidine with Compact Backbone like RNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:445-58. [PMID: 27556783 DOI: 10.1080/15257770.2016.1202963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Synthesis of C4'-epi-DNA containing 3'→ 5″ linkages is reported for the first time. Crystal structure study of the monomer indicated that though the dihedral angle O3'-C3'-C4'-C5″ in this case would be like in RNA, the sugar conformation would remain like that in DNA. The study of the effect of this backbone configuration in DNA with respect to its binding to cDNA and RNA is reported in this note.
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Affiliation(s)
- Seema Bagmare
- a Organic Chemistry Division , CSIR-National Chemical Laboratory , Pune , India
| | - Vedavati G Puranik
- b Center for Material Characterization , CSIR-National Chemical Laboratory , Pune , India
| | - Moneesha Fernandes
- a Organic Chemistry Division , CSIR-National Chemical Laboratory , Pune , India
| | - Vaijayanti A Kumar
- a Organic Chemistry Division , CSIR-National Chemical Laboratory , Pune , India
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Mezeiová E, Martinková M, Stanková K, Fabišíková M, Gonda J, Pilátová M, Gönciová G. Total synthesis and antiproliferative/cytotoxic profiling of 2-epi-jaspine B. Carbohydr Res 2016; 423:70-81. [DOI: 10.1016/j.carres.2016.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/15/2016] [Accepted: 01/21/2016] [Indexed: 11/16/2022]
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Gangadhara KL, Srivastava P, Rozenski J, Mattelaer HP, Leen V, Dehaen W, Hofkens J, Lescrinier E, Herdewijn P. Design and synthesis of nucleolipids as possible activated precursors for oligomer formation via intramolecular catalysis: stability study and supramolecular organization. ACTA ACUST UNITED AC 2014; 5:5. [PMID: 25558290 PMCID: PMC4279058 DOI: 10.1186/s13322-014-0005-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 10/06/2014] [Indexed: 01/15/2023]
Abstract
BACKGROUND Fatty acid vesicles are an important part of protocell models currently studied. As protocells can be considered as pre-biological precursors of cells, the models try to contribute to a better understanding of the (cellular) origin of life and emphasize on 2 major aspects: compartmentalization and replication. It has been demonstrated that lipid-based membranes are amenable to growth and division (shell replication). Furthermore compartmentalization creates a unique micro-environment in which biomolecules can accumulate and reactions can occur. Pioneering research by Sugawara, Deamer, Luisi, Szostak and Rasmussen gave more insight in obtaining autocatalytic, self-replicating vesicles capable of containing and reproducing nucleic acid sequences (core replication). Linking both core and shell replication is a challenging feat requiring thorough understanding of membrane dynamics and (auto)catalytic systems. A possible solution may lie in a class of compounds called nucleolipids, who combine a nucleoside, nucleotide or nucleobase with a lipophilic moiety. Early contributions by the group of Yanagawa mentions the prebiotic significance (as a primitive helical template) arising from the supramolecular organization of these compounds. Further contributions, exploring the supramolecular scope regarding phospoliponucleosides (e.g. 5'-dioleylphosphatidyl derivatives of adenosine, uridine and cytidine) can be accounted to Baglioni, Luisi and Berti. This emerging field of amphiphiles is being investigated for surface behavior, supramolecular assembly and even drug ability. RESULTS A series of α/β-hydroxy fatty acids and α-amino fatty acids, covalently bound to nucleoside-5'-monophosphates via a hydroxyl or amino group on the fatty acid was examined for spontaneous self-assembly in spherical aggregates and their stability towards intramolecular cleavage. Staining the resulting hydrophobic aggregates with BODIPY-dyes followed by fluorescent microscopy gave several distinct images of vesicles varying from small, isolated spheres to higher order aggregates and large, multimicrometer sized particles. Other observations include rod-like vesicle precursors. NMR was used to assess the stability of a representative sample of nucleolipids. 1D 31P NMR revealed that β-hydroxy fatty acids containing nucleotides were pH-stable while the α-analogs are acid labile. Degradation products identified by [1H-31P] heteroTOCSY revealed that phosphoesters are cleaved between sugar and phosphate, while phosphoramidates are also cleaved at the lipid-phosphate bond. For the latter compounds, the ratio between both degradation pathways is influenced by the nucleobase moiety. However no oligomerization of nucleotides was observed; nor the formation of 3'-5'-cyclic nucleotides, possible intermediates for oligonucleotide synthesis. CONCLUSIONS The nucleolipids with a deoxyribose sugar moiety form small or large vesicles, rod-like structures, vesicle aggregates or large vesicles. Some of these aggregates can be considered as intermediate forms in vesicle formation or division. However, we could not observe nucleotide polymerization or cyclic nucleotide function of these nucleolipids, regardless of the sugar moiety that is investigated (deoxyribose, ribose, xylose). To unravel this observation, the chemical stability of the constructs was studied. While the nucleolipids containing β-hydroxy fatty acids are stable as well in base as in acid circumstances, others degraded in acidic conditions. Phosphoramidate nucleolipids hydrolyzed by P-N as well as P-O bond cleavage where the ratio between both pathways depends on the nucleobase. Diester constructs with an α-hydroxy stearic acid degraded exclusively by hydrolysis of the 5'-O-nucleoside ester bond. As the compounds are too stable and harsh conditions would destruct the material itself, more reactive species such as lipid imidazolates of nucleotides need to be synthesized to further analyze the potential polymerization process. Graphical AbstractVesicle information of a nucleolipid consisting of a nucleoside 5'-monophosphate and a α-hydroxy fatty acid.
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Affiliation(s)
- Kishore Lingam Gangadhara
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Minderbroederstraat-10, 3000 Leuven, Belgium
| | - Puneet Srivastava
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Minderbroederstraat-10, 3000 Leuven, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Minderbroederstraat-10, 3000 Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Minderbroederstraat-10, 3000 Leuven, Belgium ; Department of Chemistry, Molecular Design and Synthesis, KU Leuven, Leuven, Belgium
| | - Volker Leen
- Department of Chemistry, Molecular Design and Synthesis, KU Leuven, Leuven, Belgium
| | - Wim Dehaen
- Department of Chemistry, Molecular Design and Synthesis, KU Leuven, Leuven, Belgium
| | - Johan Hofkens
- Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Leuven, Belgium
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Minderbroederstraat-10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Minderbroederstraat-10, 3000 Leuven, Belgium
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D'Alonzo D, Guaragna A, Palumbo G. Exploring the role of chirality in nucleic acid recognition. Chem Biodivers 2012; 8:373-413. [PMID: 21404424 DOI: 10.1002/cbdv.201000303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, via Cinthia, 4, I-80126 Napoli.
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Bundgaard Jensen T, Pasternak A, Stahl Madsen A, Petersen M, Wengel J. Synthesis and structural characterization of 2'-fluoro-α-L-RNA-modified oligonucleotides. Chembiochem 2011; 12:1904-11. [PMID: 21728225 DOI: 10.1002/cbic.201100161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Indexed: 11/07/2022]
Abstract
We describe the synthesis and binding properties of oligonucleotides that contain one or more 2'-fluoro-α-L-RNA thymine monomer(s). Incorporation of 2'-fluoro-α-L-RNA thymine into oligodeoxynucleotides decreased thermal binding stability slightly upon hybridization with complementary DNA and RNA with the smallest destabilization towards RNA. Thermodynamic data show that the duplex formation with 2'-fluoro-α-L-RNA nucleotides is enthalpically disfavored but entropically favored. 2'-Fluoro-α-L-RNA nucleotides exhibit very good base pairing specificity following Watson--Crick rules. The 2'-fluoro-α-L-RNA monomer was designed as a monocyclic mimic of the bicyclic α-L-LNA, and molecular modeling showed that this indeed is the case as the 2'-fluoro monomer adopts a C3'-endo/C2'-exo sugar pucker. Molecular modeling of modified duplexes show that the 2'-fluoro-α-L-RNA nucleotides partake in Watson--Crick base pairing and nucleobase stacking when incorporated in duplexes while the unnatural α-L-ribo configured geometry of the sugar is absorbed by changes in the sugar-phosphate backbone torsion angles. The duplex behavior of our new nucleotide follows that of α-L-LNA, by and large.
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Affiliation(s)
- Troels Bundgaard Jensen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Mehellou Y, Valente R, Mottram H, Walsby E, Mills KI, Balzarini J, McGuigan C. Phosphoramidates of 2'-beta-D-arabinouridine (AraU) as phosphate prodrugs; design, synthesis, in vitro activity and metabolism. Bioorg Med Chem 2010; 18:2439-46. [PMID: 20299228 PMCID: PMC7125968 DOI: 10.1016/j.bmc.2010.02.059] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 02/23/2010] [Accepted: 02/25/2010] [Indexed: 11/06/2022]
Abstract
2′-β-d-Arabinouridine (AraU), the uridine analogue of the anticancer agent AraC, was synthesized and evaluated for antiviral activity and cytotoxicity. In addition, a series of AraU monophosphate prodrugs in the form of triester phosphoramidates (ProTides) were also synthesized and tested against a range of viruses, leukaemia and solid tumour cell lines. Unfortunately, neither the parent compound (AraU) nor any of its ProTides showed antiviral activity, nor potent inhibitory activity against any of the cancer cell lines. Therefore, the metabolism of AraU phosphoramidates to release AraU monophosphate was investigated. The results showed carboxypeptidase Y, hog liver esterase and crude CEM tumor cell extracts to hydrolyse the ester motif of phosphoramidates with subsequent loss of the aryl group, while molecular modelling studies suggested that the AraU l-alanine aminoacyl phosphate derivative might not be a good substrate for the phosphoramidase enzyme Hint-1. These findings are in agreement with the observed disappearance of intact prodrug and concomitant appearance of the corresponding phosphoramidate intermediate derivative in CEM cell extracts without measurable formation of araU monophosphate. These findings may explain the poor antiviral/cytostatic potential of the prodrugs.
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Affiliation(s)
- Youcef Mehellou
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
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Gupta P, Maity J, Shakya G, Prasad AK, Parmar VS, Wengel J. Synthesis and hybridization studies of α-configured arabino nucleic acids. Org Biomol Chem 2009; 7:2389-401. [DOI: 10.1039/b905019c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.
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Affiliation(s)
- Alexander J A Cobb
- School of Pharmacy, University of Reading, Whiteknights, Reading, Berks RG6 6AD, UK.
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Bercier A, Plantier-Royon R, Portella C. Convenient conversion of wheat hemicelluloses pentoses (D-xylose and L-arabinose) into a common intermediate. Carbohydr Res 2007; 342:2450-5. [PMID: 17692299 DOI: 10.1016/j.carres.2007.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 07/06/2007] [Accepted: 07/12/2007] [Indexed: 11/28/2022]
Abstract
The transformation of D-xylose and L-arabinose, the two major components of wheat straw and bran, into a unique multifunctional, optically pure, five-carbon synthon has been achieved. The synthetic sequence requires three steps: suitable protection of the hydroxyl groups of the pentoses, introduction of an iodide at the C-5 position and zinc-mediated opening of the furanose ring leading to the formation of a common substituted pent-4-enal.
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Affiliation(s)
- Ariane Bercier
- Laboratoire Réactions Sélectives et Applications, Associé au CNRS (UMR 6519), Université de Reims, Faculté des Sciences, BP 1039, F-51687 Reims France
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