1
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Pallan PS, Lybrand TP, Rozners E, Abramov M, Schepers G, Eremeeva E, Herdewijn P, Egli M. Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023; 62:2854-2867. [PMID: 37694722 DOI: 10.1021/acs.biochem.3c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Several efforts are currently directed at the creation and cellular implementation of alternative genetic systems composed of pairing components that are orthogonal to the natural dA/dT and dG/dC base pairs. In an alternative approach, Watson-Crick-type pairing is conserved, but one or all of the four letters of the A, C, G, and T alphabet are substituted by modified components. Thus, all four nucleobases were altered to create halogenated deazanucleic acid (DZA): dA was replaced by 7-deaza-2'-deoxyadenosine (dzA), dG by 7-deaza-2'-deoxyguanosine (dzG), dC by 5-fluoro-2'-deoxycytidine (FdC), and dT by 5-chloro-2'-deoxyuridine (CldU). This base-pairing system was previously shown to retain function in Escherichia coli. Here, we analyze the stability, hydration, structure, and dynamics of a DZA Dickerson-Drew Dodecamer (DDD) of sequence 5'-FdC-dzG-FdC-dzG-dzA-dzA-CldU-CldU-FdC-dzG-FdC-dzG-3'. Contrary to similar stabilities of DDD and DZA-DDD, osmotic stressing revealed a dramatic loss of hydration for the DZA-DDD relative to that for the DDD. The parent DDD 5'-d(CGCGAATTCGCG)-3' features an A-tract, a run of adenosines uninterrupted by a TpA step, and exhibits a hallmark narrow minor groove. Crystal structures─in the presence of RNase H─and MD simulations show increased conformational plasticity ("morphing") of DZA-DDD relative to that of the DDD. The narrow dzA-tract minor groove in one structure widens to resemble that in canonical B-DNA in a second structure. These changes reflect an indirect consequence of altered DZA major groove electrostatics (less negatively polarized compared to that in DNA) and hydration (reduced compared to that in DNA). Therefore, chemical modifications outside the minor groove that lead to collapse of major groove electrostatics and hydration can modulate A-tract geometry.
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Affiliation(s)
- Pradeep S Pallan
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Terry P Lybrand
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mikhail Abramov
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Elena Eremeeva
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Martin Egli
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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2
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Schofield P, Taylor AI, Rihon J, Peña Martinez CD, Zinn S, Mattelaer CA, Jackson J, Dhaliwal G, Schepers G, Herdewijn P, Lescrinier E, Christ D, Holliger P. Characterization of an HNA aptamer suggests a non-canonical G-quadruplex motif. Nucleic Acids Res 2023; 51:7736-7748. [PMID: 37439359 PMCID: PMC10450178 DOI: 10.1093/nar/gkad592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/09/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
Nucleic acids not only form the basis of heredity, but are increasingly a source of novel nano-structures, -devices and drugs. This has spurred the development of chemically modified alternatives (xeno nucleic acids (XNAs)) comprising chemical configurations not found in nature to extend their chemical and functional scope. XNAs can be evolved into ligands (XNA aptamers) that bind their targets with high affinity and specificity. However, detailed investigations into structural and functional aspects of XNA aptamers have been limited. Here we describe a detailed structure-function analysis of LYS-S8-19, a 1',5'-anhydrohexitol nucleic acid (HNA) aptamer to hen egg-white lysozyme (HEL). Mapping of the aptamer interaction interface with its cognate HEL target antigen revealed interaction epitopes, affinities, kinetics and hot-spots of binding energy similar to protein ligands such as anti-HEL-nanobodies. Truncation analysis and molecular dynamics (MD) simulations suggest that the HNA aptamer core motif folds into a novel and not previously observed HNA tertiary structure, comprising non-canonical hT-hA-hT/hT-hT-hT triplet and hG4-quadruplex structures, consistent with its recognition by two different G4-specific antibodies.
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Affiliation(s)
- Peter Schofield
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK
| | - Jérôme Rihon
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Cristian D Peña Martinez
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Sacha Zinn
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Charles-Alexandre Mattelaer
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Gurpreet Dhaliwal
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK
| | - Guy Schepers
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Piet Herdewijn
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Eveline Lescrinier
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
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3
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Gasse C, Srivastava P, Schepers G, Jose J, Hollenstein M, Marlière P, Herdewijn P. Controlled E. coli Aggregation Mediated by DNA and XNA Hybridization. Chembiochem 2023; 24:e202300191. [PMID: 37119472 DOI: 10.1002/cbic.202300191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/01/2023]
Abstract
Chemical cell surface modification is a fast-growing field of research, due to its enormous potential in tissue engineering, cell-based immunotherapy, and regenerative medicine. However, engineering of bacterial tissues by chemical cell surface modification has been vastly underexplored and the identification of suitable molecular handles is in dire need. We present here, an orthogonal nucleic acid-protein conjugation strategy to promote artificial bacterial aggregation. This system gathers the high selectivity and stability of linkage to a protein Tag expressed at the cell surface and the modularity and reversibility of aggregation due to oligonucleotide hybridization. For the first time, XNA (xeno nucleic acids in the form of 1,5-anhydrohexitol nucleic acids) were immobilized via covalent, SNAP-tag-mediated interactions on cell surfaces to induce bacterial aggregation.
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Affiliation(s)
- Cécile Gasse
- Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, D-48149, Münster, Germany
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Philippe Marlière
- The European Syndicate of Synthetic Scientists and Industrialists (TESSSI), 81 rue Réaumur, 75002, Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
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4
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Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M. Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Nucleic Acids Res 2022; 50:11415-11425. [PMID: 36350642 PMCID: PMC9723616 DOI: 10.1093/nar/gkac1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1',5'-anhydrohexitol (HNA), 2'-fluoro ribose (2'F-RNA) and 2'-fluoro arabinose. L-Ala-tXNA containing HNA or 2'F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.
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Affiliation(s)
| | | | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Delphine Dorchêne
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, F-75006 Paris, France
| | - Laura Iannazzo
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Mélanie Ethève-Quelquejeu
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
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5
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Li De La Sierra Gallay I, Rietmeyer L, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, Van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M. Structural exploration of FemX interaction with tXNA conjugates : identification of one potential antibiotic. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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6
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Mattelaer CA, Maiti M, Smets L, Maiti M, Schepers G, Mattelaer HP, Rosemeyer H, Herdewijn P, Lescrinier E. Stable Hairpin Structures Formed by Xylose-Based Nucleic Acids. Chembiochem 2021; 22:1638-1645. [PMID: 33427360 DOI: 10.1002/cbic.202000803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/06/2021] [Indexed: 12/21/2022]
Abstract
Xenobiology explores synthetic nucleic acid polymers as alternative carriers of genetic information to expand the central dogma. The xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA), containing 3' epimers of riboses and deoxyriboses, are considered to be potential candidates for an orthogonal system. In this study, thermal and spectroscopic analyses show that XyNA and dXyNA form stable hairpins. The dXyNA hairpin structure determined by NMR spectroscopy contains a flexible loop that locks the stem into a stable ladder-like duplex with marginal right-handed helicity. The reduced flexibility of the dXyNA duplex observed in the stem of the hairpin demonstrates that folding of dXyNA yields more stable structures described so far.
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Affiliation(s)
- Charles-Alexandre Mattelaer
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Mohitosh Maiti
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Laurent Smets
- Research Centre for Operations Management, Faculty of Economics and Business, KU Leuven, Naamsestraat 69, 3000, Leuven, Belgium
| | - Munmun Maiti
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium.,Present address: Membrane Separations, Adsorption, Catalysis, and Spectroscopy for Sustainable Solutions (cMACS), KU Leuven (Arenberg), Celestijnenlaan 200f, Box 2454, 3001, Leuven, Belgium
| | - Helmut Rosemeyer
- Organische Materialchemie (OMC), Universität Osnabrück, Institut für Chemie neuer Materialien, Barbarastraße 7, 49076, Osnabrück, Germany
| | - Piet Herdewijn
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Eveline Lescrinier
- Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Herestraat 49, Box 1041, 3000, Leuven, Belgium
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7
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Kumar P, Degaonkar R, Guenther DC, Abramov M, Schepers G, Capobianco M, Jiang Y, Harp J, Kaittanis C, Janas MM, Castoreno A, Zlatev I, Schlegel MK, Herdewijn P, Egli M, Manoharan M. Chimeric siRNAs with chemically modified pentofuranose and hexopyranose nucleotides: altritol-nucleotide (ANA) containing GalNAc-siRNA conjugates: in vitro and in vivo RNAi activity and resistance to 5'-exonuclease. Nucleic Acids Res 2020; 48:4028-4040. [PMID: 32170309 PMCID: PMC7192627 DOI: 10.1093/nar/gkaa125] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/23/2022] Open
Abstract
In this report, we investigated the hexopyranose chemical modification Altriol Nucleic Acid (ANA) within small interfering RNA (siRNA) duplexes that were otherwise fully modified with the 2′-deoxy-2′-fluoro and 2′-O-methyl pentofuranose chemical modifications. The siRNAs were designed to silence the transthyretin (Ttr) gene and were conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand for targeted delivery to hepatocytes. Sense and antisense strands of the parent duplex were synthesized with single ANA residues at each position on the strand, and the resulting siRNAs were evaluated for their ability to inhibit Ttr mRNA expression in vitro. Although ANA residues were detrimental at the 5′ end of the antisense strand, the siRNAs with ANA at position 6 or 7 in the seed region had activity comparable to the parent. The siRNA with ANA at position 7 in the seed region was active in a mouse model. An Oligonucleotide with ANA at the 5′ end was more stable in the presence of 5′-exonuclease than an oligonucleotide of the same sequence and chemical composition without the ANA modification. Modeling studies provide insight into the origins of regiospecific changes in potency of siRNAs and the increased protection against 5′-exonuclease degradation afforded by the ANA modification.
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Affiliation(s)
- Pawan Kumar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Rohan Degaonkar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Dale C Guenther
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Marie Capobianco
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Joel Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Maja M Janas
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Adam Castoreno
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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8
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Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E. Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 2019; 47:11976-11977. [PMID: 31713624 PMCID: PMC7145540 DOI: 10.1093/nar/gkz1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Jamoliddin Razzokov
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Muhammad Usman Mirza
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium.,Centre for Research in Molecular Medicine (CRiMM), University of Lahore, Pakistan
| | - Stephen D Weeks
- Biocrystallography, KU Leuven, Herestraat 49, box 822, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Vitor B Pinheiro
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium.,University College London, Department of Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
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9
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Leonczak P, Srivastava P, Bande O, Schepers G, Lescrinier E, Herdewijn P. N8-Glycosylated 8-Azapurine and Methylated Purine Nucleobases: Synthesis and Study of Base Pairing Properties. J Org Chem 2019; 84:13394-13409. [PMID: 31617362 DOI: 10.1021/acs.joc.9b01576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report, we present the synthesis of N8-glycosylated 8-aza-2-methylhypoxanthine and 8-aza-6-thiohypoxanthine 2'-deoxynucleosides as well as methylated 2'-deoxynebularine derivatives. In vitro base pairing properties between each modified and canonical nucleobase were studied. As demonstrated by Tm, incorporation of the modified bases in DNA resulted, with few exceptions, in low stability of duplexes. Modified bases studied in this report are preferentially recognized by T (for N8-glycosylated 8-aza-2-methylhypoxanthine and methylated purines) and G (N8-glycosylated 8-aza-2-methylhypoxanthine). The base pair formed between N8-glycosylated 8-aza-6-thiohypoxanthine and N9-glycosylated 2-methyl-6-thiohypoxanthine (X2:X6) showed, to some extent, an orthogonal interaction. Based on Tm studies, the only potential self-pairing system is formed by the N8-glycosylated 8-aza-6-thiohypoxanthine nucleoside (X2) but only in the absence of canonical G and T. This study indicated that the canonical thymine base is the preferential base partner of methylated purine bases.
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Affiliation(s)
- Piotr Leonczak
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Puneet Srivastava
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Omprakash Bande
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Guy Schepers
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
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10
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Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E. Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 2019; 47:7130-7142. [PMID: 31334814 PMCID: PMC6649754 DOI: 10.1093/nar/gkz551] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/24/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
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Affiliation(s)
- Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Jamoliddin Razzokov
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Muhammad Usman Mirza
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- Centre for Research in Molecular Medicine (CRiMM), University of Lahore, Pakistan
| | - Stephen D Weeks
- Biocrystallography, KU Leuven, Herestraat 49, box 822, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Vitor B Pinheiro
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- University College London, Department of Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
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11
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Luo M, Groaz E, Froeyen M, Pezo V, Jaziri F, Leonczak P, Schepers G, Rozenski J, Marlière P, Herdewijn P. Invading Escherichia coli Genetics with a Xenobiotic Nucleic Acid Carrying an Acyclic Phosphonate Backbone (ZNA). J Am Chem Soc 2019; 141:10844-10851. [PMID: 31251601 DOI: 10.1021/jacs.9b04714] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A synthetic orthogonal polymer embracing a chiral acyclic-phosphonate backbone [(S)-ZNA] is presented that uniquely adds to the emerging family of xenobiotic nucleic acids (XNAs). (S)-ZNA consists of reiterating six-atom structural units and can be accessed in few synthetic steps from readily available phophonomethylglycerol nucleoside (PMGN) precursors. Comparative thermal stability experiments conducted on homo- and heteroduplexes made of (S)-ZNA are described that evince its high self-hybridization efficiency in contrast to poor binding of natural complements. Although preliminary and not conclusive, circular dichroism data and dynamic modeling computations provide support to a left-handed geometry of double-stranded (S)-ZNA. Nonetheless, PMGN diphosphate monomers were recognized as substrates by Escherichia coli (E. coli) polymerase I as well as being imported into E. coli cells equipped with an algal nucleotide transporter. A further investigation into the in vivo propagation of (S)-ZNA culminated with the demonstration of the first synthetic nucleic acid with an acyclic backbone that can be transliterated to DNA by the E. coli cellular machinery.
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Affiliation(s)
- Min Luo
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Mathy Froeyen
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Valérie Pezo
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Faten Jaziri
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Piotr Leonczak
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Guy Schepers
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Jef Rozenski
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Philippe Marlière
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Piet Herdewijn
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
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12
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Jabgunde AM, Jaziri F, Bande O, Froeyen M, Abramov M, Nguyen H, Schepers G, Lescrinier E, Pinheiro VB, Pezo V, Marlière P, Herdewijn P. Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo. Chemistry 2018; 24:12695-12707. [DOI: 10.1002/chem.201802304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/07/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Amit M. Jabgunde
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Faten Jaziri
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Omprakash Bande
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Matheus Froeyen
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Mikhail Abramov
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Hoai Nguyen
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Guy Schepers
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Eveline Lescrinier
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
| | - Vitor B. Pinheiro
- Institute of Structural and Molecular Biology; University College London; Darwin Building, Gower Street London WC1E 6BT United Kingdom
| | - Valérie Pezo
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Philippe Marlière
- Génomique Métabolique, Genoscope; Institut François Jacob; CEA; CNRS; Univ Evry, Université Paris-Saclay; 91057 Evry France
| | - Piet Herdewijn
- KU Leuven; Rega Institute; Medicinal Chemistry; Herestraat 49 box 1041 3000 Leuven Belgium
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13
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Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J, Herdewijn P. XNA ligation using T4 DNA ligase in crowding conditions. Chem Commun (Camb) 2018; 54:6408-6411. [PMID: 29872779 DOI: 10.1039/c8cc02414f] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
T4 DNA ligase is capable of ligating 2'OMe-RNA duplexes, HNA, LNA and FANA mixed sequences in the presence of 10% w/v PEG8000 and 3 M betaine. The enzymatic joining of oligonucleotides containing multiple consecutive XNA nucleotides at the ligation site has not been reported before.
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Affiliation(s)
- Donaat Kestemont
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 box 1041, 3000 Leuven, Belgium.
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14
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Paolella C, D'Alonzo D, Schepers G, Van Aerschot A, Di Fabio G, Palumbo G, Herdewijn P, Guaragna A. Oligonucleotides containing a ribo-configured cyclohexanyl nucleoside: probing the role of sugar conformation in base pairing selectivity. Org Biomol Chem 2016; 13:10041-9. [PMID: 26293202 DOI: 10.1039/c5ob01449b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis and a preliminary evaluation of the pairing properties of ribo-cyclohexanyl nucleic acids (r-CNA) is herein reported. Incorporation of a single r-CNA nucleotide into natural duplexes did not enhance their stability, while a very high pairing selectivity for RNA was found. As deduced by comparative analysis of Tm and NMR data, a relationship between pairing selectivity and conformational preferences of the "sugar" moiety of r-CNA (and more generally of six-membered nucleic acids) was suggested.
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Affiliation(s)
- Concetta Paolella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia, 80126 Napoli, Italy.
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15
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Bande O, Braddick D, Agnello S, Jang M, Pezo V, Schepers G, Rozenski J, Lescrinier E, Marlière P, Herdewijn P. Correction: Base pairing involving artificial bases in vitro and in vivo. Chem Sci 2016; 7:1611. [PMID: 30123459 PMCID: PMC6063250 DOI: 10.1039/c5sc90070k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 11/21/2022] Open
Abstract
Correction for ‘Base pairing involving artificial bases in vitro and in vivo’ by Omprakash Bande et al., Chem. Sci., 2016, DOI: 10.1039/c5sc03474d.
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Affiliation(s)
- Omprakash Bande
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium
| | - Darren Braddick
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France . ; Tel: +32 16 337387
| | - Stefano Agnello
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium
| | - Miyeon Jang
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium
| | - Valérie Pezo
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France . ; Tel: +32 16 337387
| | - Guy Schepers
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium
| | - Jef Rozenski
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium
| | - Eveline Lescrinier
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium
| | - Philippe Marlière
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France . ; Tel: +32 16 337387
| | - Piet Herdewijn
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France . ; Tel: +32 16 337387.,Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium
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16
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Bande O, Braddick D, Agnello S, Jang M, Pezo V, Schepers G, Rozenski J, Lescrinier E, Marlière P, Herdewijn P. Base pairing involving artificial bases in vitro and in vivo. Chem Sci 2015; 7:995-1010. [PMID: 29896368 PMCID: PMC5954848 DOI: 10.1039/c5sc03474d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/28/2015] [Indexed: 01/09/2023] Open
Abstract
Herein we report the synthesis, base pairing properties and in vivo transliteration of N8-glycosylated 8-aza-deoxyguanosine and 8-aza-9-deaza-deoxyguanosine nucleotides with 8-amino-deoxyinosine, 1-N-methyl-8-amino-deoxyinosine and 7,8-dihydro-8-oxo-deoxy-inosine/adenosine/guanosine as pairing partners.
Herein we report the synthesis of N8-glycosylated 8-aza-deoxyguanosine (N8-8-aza-dG) and 8-aza-9-deaza-deoxyguanosine (N8-8-aza-9-deaza-dG) nucleotides and their base pairing properties with 5-methyl-isocytosine (d-isoCMe), 8-amino-deoxyinosine (8-NH2-dI), 1-N-methyl-8-amino-deoxyinosine (1-Me-8-NH2-dI), 7,8-dihydro-8-oxo-deoxyinosine (8-Oxo-dI), 7,8-dihydro-8-oxo-deoxyadenosine (8-Oxo-dA), and 7,8-dihydro-8-oxo-deoxyguanosine (8-Oxo-dG), in comparison with the d-isoCMe:d-isoG artificial genetic system. As demonstrated by Tm measurements, the N8-8-aza-dG:d-isoCMe base pair formed less stable duplexes as the C:G and d-isoCMe:d-isoG pairs. Incorporation of 8-NH2-dI versus the N8-8-aza-dG nucleoside resulted in a greater reduction in Tm stability, compared to d-isoCMe:d-isoG. Insertion of the methyl group at the N1 position of 8-NH2-dI did not affect duplex stability with N8-8-aza-dG, thus suggesting that the base paring takes place through Hoogsteen base pairing. The cellular interpretation of the nucleosides was studied, whereby a lack of recognition or mispairing of the incorporated nucleotides with the canonical DNA bases indicated the extent of orthogonality in vivo. The most biologically orthogonal nucleosides identified included the 8-amino-deoxyinosines (1-Me-8-NH2-dI and 8-NH2-dI) and N8-8-aza-9-deaza-dG. The 8-oxo modifications mimic oxidative damage ahead of cancer development, and the impact of the MutM mediated recognition of these 8-oxo-deoxynucleosides was studied, finding no significant impact in their in vivo assay.
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Affiliation(s)
- Omprakash Bande
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Darren Braddick
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Stefano Agnello
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Miyeon Jang
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Valérie Pezo
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Guy Schepers
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Jef Rozenski
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Eveline Lescrinier
- Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
| | - Philippe Marlière
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France
| | - Piet Herdewijn
- iSSB - CNRS FRE3561 , University of Evry-Val-d'Essonne , 5 rue Henri Desbruères, Genopole Campus 1, Bât. 6 , F-91030 Évry Cedex , France.,Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , 3000 Leuven , Belgium . ; Tel: +32 16 337387
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Hansen KS, Réthoré PE, Palma J, Hevia BG, Prospathopoulos J, Peña A, Ott S, Schepers G, Palomares A, van der Laan MP, Volker P. Simulation of wake effects between two wind farms. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/1742-6596/625/1/012008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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D'Alonzo D, Froeyen M, Schepers G, Di Fabio G, Van Aerschot A, Herdewijn P, Palumbo G, Guaragna A. 1',5'-Anhydro-L-ribo-hexitol Adenine Nucleic Acids (α-L-HNA-A): Synthesis and Chiral Selection Properties in the Mirror Image World. J Org Chem 2015; 80:5014-22. [PMID: 25853790 DOI: 10.1021/acs.joc.5b00406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and a preliminary investigation of the base pairing properties of (6' → 4')-linked 1',5'-anhydro-L-ribo-hexitol nucleic acids (α-L-HNA) have herein been reported through the study of a model oligoadenylate system in the mirror image world. Despite its considerable preorganization due to the rigidity of the "all equatorial" pyranyl sugar backbone, α-L-HNA represents a versatile informational biopolymer, in view of its capability to cross-communicate with natural and unnatural complements in both enantiomeric forms. This seems the result of an inherent flexibility of the oligonucleotide system, as witnessed by the singular formation of iso- and heterochiral associations composed of regular, enantiomorphic helical structures. The peculiar properties of α-L-HNA (and most generally of the α-HNA system) provide new elements in our understanding of the structural prerequisites ruling the stereoselectivity of the hybridization processes of nucleic acids.
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Affiliation(s)
- Daniele D'Alonzo
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Mathy Froeyen
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Guy Schepers
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Giovanni Di Fabio
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Arthur Van Aerschot
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Giovanni Palumbo
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Annalisa Guaragna
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
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Venkatesham A, Kachare D, Schepers G, Rozenski J, Froeyen M, Van Aerschot A. Hybridisation potential of 1',3'-Di-O-methylaltropyranoside nucleic acids. Molecules 2015; 20:4020-41. [PMID: 25741897 PMCID: PMC6272658 DOI: 10.3390/molecules20034020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/16/2015] [Accepted: 02/24/2015] [Indexed: 01/16/2023] Open
Abstract
In further study of our series of six-membered ring-containing nucleic acids, different 1',3'-di-O-methyl altropyranoside nucleoside analogs (DMANA) were synthesized comprising all four base moieties, adenine, cytosine, uracil and guanine. Following assembly into oligonucleotides (ONs), their affinity for natural oligonucleotides was evaluated by thermal denaturation of the respective duplexes. Data were compared with results obtained previously for both anhydrohexitol (HNAs) and 3'-O-methylated altrohexitol modified ONs (MANAs). We hereby demonstrate that ONs modified with DMANA monomers, unlike some of our previously described analogues with constrained 6-membered hexitol rings, did not improve thermodynamic stability of dsRNA complexes, most probably in view of an energetic penalty when forced in the required 1C4 pairing conformation. Overall, a single incorporation was more or less tolerated or even positive for the adenine congener, but incorporation of a second modification afforded a slight destabilization (except for A), while a fully modified sequence displayed a thermal stability of -0.3 °C per modification. The selectivity of pairing remained very high, and the new modification upon incorporation into a DNA strand, strongly destabilized the corresponding DNA duplexes. Unfortunately, this new modification does not bring any advantage to be further evaluated for antisense or siRNA applications.
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Affiliation(s)
- Akkaladevi Venkatesham
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Dhuldeo Kachare
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
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20
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Bande O, Abu El Asrar R, Braddick D, Dumbre S, Pezo V, Schepers G, Pinheiro VB, Lescrinier E, Holliger P, Marlière P, Herdewijn P. Isoguanine and 5-methyl-isocytosine bases, in vitro and in vivo. Chemistry 2015; 21:5009-22. [PMID: 25684598 PMCID: PMC4531829 DOI: 10.1002/chem.201406392] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 11/10/2022]
Abstract
The synthesis, base-pairing properties and in vitro and in vivo characteristics of 5-methyl-isocytosine (isoCMe) and isoguanine (isoG) nucleosides, incorporated in an HNA(h) (hexitol nucleic acid)–DNA(d) mosaic backbone, are described. The required h-isoG phosphoramidite was prepared by a selective deamination as a key step. As demonstrated by Tm measurements the hexitol sugar showed slightly better mismatch discrimination against dT. The d-isoG base mispairing follows the order T>G>C while the h-isoG base mispairing follows the order G>C>T. The h- and d-isoCMe bases mainly mispair with G. Enzymatic incorporation experiments show that the hexitol backbone has a variable effect on selectivity. In the enzymatic assays, isoG misincorporates mainly with T, and isoCMe misincorporates mainly with A. Further analysis in vivo confirmed the patterns of base-pair interpretation for the deoxyribose and hexitol isoCMe/isoG bases in a cellular context, through incorporation of the bases into plasmidic DNA. Results in vivo demonstrated that mispairing and misincorporation was dependent on the backbone scaffold of the base, which indicates rational advances towards orthogonality.
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Affiliation(s)
- Omprakash Bande
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven (Belgium)
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21
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Pezo V, Schepers G, Lambertucci C, Marlière P, Herdewijn P. Probing ambiguous base-pairs by genetic transformation with XNA templates. Chembiochem 2014; 15:2255-8. [PMID: 25158283 DOI: 10.1002/cbic.201402226] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Indexed: 11/11/2022]
Abstract
The templating potential of anhydrohexitol oligonucleotides bearing ambiguous bases was studied in vivo, by using a selection screen for mosaic heteroduplex plasmids in Escherichia coli. 1,5-Anhydro-2,3-dideoxy-2-(5-nitroindazol-1-yl)-D-arabino-hexitol showed the greatest ambiguity among the three nucleosides tested. At most two successive ambiguous bases could be tolerated on hexitol templates read in bacterial cells. Hexitol nucleosides bearing simplified heterocycles thus stand as promising monomers for generating random DNA sequences in vivo from defined synthetic oligonucleotides.
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Affiliation(s)
- Valérie Pezo
- CEA, DSV, IG, Genoscope, 2 rue Gaston Crémieux 91057 Evry Cedex (France); ISSB, Génopole genavenir6, Equipe Xénome, 5 rue Henri Desbruères 91030 Evry Cedex (France)
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D'Alonzo D, Amato J, Schepers G, Froeyen M, Van Aerschot A, Herdewijn P, Guaragna A. Enantiomeric Selection Properties of β-homoDNA: Enhanced Pairing for Heterochiral Complexes. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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D'Alonzo D, Amato J, Schepers G, Froeyen M, Van Aerschot A, Herdewijn P, Guaragna A. Enantiomeric selection properties of β-homoDNA: enhanced pairing for heterochiral complexes. Angew Chem Int Ed Engl 2013; 52:6662-5. [PMID: 23670912 DOI: 10.1002/anie.201301659] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia 21, 80126 Napoli, Italy.
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Chatelain G, Schepers G, Rozenski J, Van Aerschot A. Hybridization potential of oligonucleotides comprising 3'-O-methylated altritol nucleosides. Mol Divers 2012; 16:825-37. [PMID: 23054535 DOI: 10.1007/s11030-012-9402-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/25/2012] [Indexed: 10/27/2022]
Abstract
A series of 3'-O-methylated-d-altrohexitol nucleoside analogs (MANA) was synthesized comprising all four base moieties, adenine, cytosine, uracil, and guanine. These monomers were incorporated into oligonucleotides (ONs) by automated solid phase synthesis and the thermal and thermodynamic stability of all new modified constructs were evaluated. Data were compared with results obtained for both anhydrohexitol (HNAs) and 3'-O-altrohexitol-modified ONs (ANAs). We hereby demonstrate that ONs modified with MANA monomers have an improved thermal and thermodynamic stability compared to RNA, ANA, or HNA containing ONs of which the extent depends on the number of incorporated moieties and their position in the sequence. Thermodynamic analysis afforded comparable or even improved results in comparison with the incorporation of locked nucleic acids. While the specificity of these new synthons is slightly lower compared to mismatches within RNA double strands, it is similar to the discrimination potential of other hexitol modifications (HNA and ANA) which already proved their biologic interest, highlighting the potential of MANA constructs in antisense and in siRNA applications.
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Affiliation(s)
- G Chatelain
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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van Aerschot A, Saison-Behmoaras T, Rozenski J, Hendrix C, Schepers G, Verhoeven G, Herdewijn P. Conjugation of Oligonucleotides to 3′-Polar Moieties. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bscb.19951041208] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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D'Alonzo D, Van Aerschot A, Guaragna A, Palumbo G, Schepers G, Capone S, Rozenski J, Herdewijn P. Synthesis and base pairing properties of 1',5'-anhydro-L-hexitol nucleic acids (L-HNA). Chemistry 2010; 15:10121-31. [PMID: 19739223 DOI: 10.1002/chem.200901847] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Oligonucleotides composed of 1',5'-anhydro-arabino-hexitol nucleosides belonging to the L series (L-HNA) were prepared and preliminarily studied as a novel potential base-pairing system. Synthesis of enantiopure L-hexitol nucleotide monomers equipped with a 2'-(N(6)-benzoyladenin-9-yl) or a 2'-(thymin-1-yl) moiety was carried out by a de novo approach based on a domino reaction as key step. The L oligonucleotide analogues were evaluated in duplex formation with natural complements as well as with unnatural sugar-modified oligonucleotides. In many cases stable homo- and heterochiral associations were found. Besides T(m) measurements, detection of heterochiral complexes was unambiguously confirmed by LC-MS studies. Interestingly, circular dichroism measurements of the most stable duplexes suggested that L-HNA form left-handed helices with both D and L oligonucleotides.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università Federico II, Napoli, via Cinthia 4, 80126 Napoli, Italy
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Wang G, Bobkov GV, Mikhailov SN, Schepers G, Van Aerschot A, Rozenski J, Van der Auweraer M, Herdewijn P, De Feyter S. Detection of RNA hybridization by pyrene-labeled probes. Chembiochem 2009; 10:1175-85. [PMID: 19373795 DOI: 10.1002/cbic.200900031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Powerful pyrene probes: Two kinds of pyrene-labeled oligonucleotides (HNA- and RNA-skeleton probes) were explored. The enhanced fluorescence intensity in the monomer region and the disappearance of aggregate/excimer emission in duplexes has been successfully used to detect the hybridization of oligonucleotides. By covalently attaching pyrene chromophores with different linkers onto altritol nucleotides or ribonucleotides, and by varying the number of these pyrene modified altritol nucleotides and ribonucleotides in HNA (hexitol nucleic acid) and RNA, respectively, we have explored the general applicability of pyrene absorbance and especially fluorescence as a probe to monitor RNA hybridization. The results reveal that the backbone of the probes, the number of pyrene units attached and the nature of the tether can all substantially affect the absorbance and fluorescence properties of the probes both in single strand and double strand form. Moreover, the strength of hybridization is also affected. The disappearance of pyrene aggregate/excimer emission and simultaneous increase in monomer emission intensity of the multipyrene-labeled probes has been successfully used to monitor the hybridization of oligonucleotides, including a hairpin structure. Differences in optical response between the HNA- and RNA-skeleton probes upon hybridization indicate that the interaction of pyrene with the nucleobases in both types of duplexes is different.
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Affiliation(s)
- Guojie Wang
- Department of Chemistry, Division of Molecular and Nanomaterials, Laboratory of Photochemistry and Spectroscopy, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, 3001 Leuven, Belgium
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Zhou D, Schepers G, Van Aerschot A. A simple nucleic acid alternative: aminopropyl nucleic acids (APNAs). Nucleosides Nucleotides Nucleic Acids 2008; 26:1665-8. [PMID: 18066848 DOI: 10.1080/15257770701493625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aminopropyl nucleic acids are constitutionally simple nucleic acids alternatives with one chiral center per nucleotide and with the constitutional potential to hybridize with RNA. Both R and S isomers of the 3'-or 2'-aminopropyl nucleosides were incorporated either into DNA or likewise were used for fully modified sequences. The (R)-adenine analogue, yielding (S)-APNA, can be considered as a candidate for universal base pairing.
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Affiliation(s)
- Ding Zhou
- Laboratory of Medicinal Chemistry, Rega Institute, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Abramov M, Schepers G, Van Aerschot A, Herdewijn P. Fmoc-Protected Altritol Phosphoramidite Building Blocks and Their Application in the Synthesis of Altritol Nucleic Acids (ANAs). European J Org Chem 2007. [DOI: 10.1002/ejoc.200600868] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Lambertucci C, Schepers G, Cristalli G, Herdewijn P, Aerschot AV. Synthesis and evaluation of hexitol nucleoside congeners as ambiguous nucleosides. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.01.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Mikhailov SN, Efimtseva EV, Rodionov AA, Shelkunova AA, Rozenski J, Emmerechts G, Schepers G, Van Aerschot A, Herdewijn P. Synthesis of RNA containing O-beta-D-ribofuranosyl-(1''-2')-adenosine-5''-phosphate and 1-methyladenosine, minor components of tRNA. Chem Biodivers 2007; 2:1153-63. [PMID: 17193197 DOI: 10.1002/cbdv.200590085] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
tRNA is best known for its function as amino acid carrier in the translation process, using the anticodon loop in the recognition process with mRNA. However, the impact of tRNA on cell function is much wider, and mutations in tRNA can lead to a broad range of diseases. Although the cloverleaf structure of tRNA is well-known based on X-ray-diffraction studies, little is known about the dynamics of this fold, the way structural dynamics of tRNA is influenced by the modified nucleotides present in tRNA, and their influence on the recognition of tRNA by synthetases, ribosomes, and other biomolecules. One of the reasons for this is the lack of good synthetic methods to incorporate modified nucleotides in tRNA so that larger amounts become available for NMR studies. Except of 2'-O-methylated nucleosides, only one other sugar-modified nucleoside is present in tRNA, i.e., 2'-O-beta-D-ribofuranosyl nucleosides. The T loop of tRNA often contains charged modified nucleosides, of which 1-methyladenosine and phosphorylated disaccharide nucleosides are striking examples. A protecting-group strategy was developed to introduce 1-methyladenosine and 5''-O-phosphorylated 2'-O-(beta-D-ribofuranosyl)-beta-D-ribofuranosyladenine in the same RNA fragment. The phosphorylation of the disaccharide nucleoside was performed after the assembly of the RNA on solid support. The modified RNA was characterized by mass-spectrometry analysis from the RNase T1 digestion fragments. The successful synthesis of this T loop of the tRNA of Schizosaccharomyces pombe initiator tRNA(Met) will be followed by its structural analysis by NMR and by studies on the influence of these modified nucleotides on dynamic interactions within the complete tRNA.
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Affiliation(s)
- Sergey N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991, Russia.
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Zedler BK, Kinser R, Oey J, Nelson B, Roethig HJ, Walk RA, Kuhl P, Rustemeier K, Schepers G, Von Holt K, Tricker AR. Biomarkers of exposure and potential harm in adult smokers of 3-7 mg tar yield (Federal Trade Commission) cigarettes and in adult non-smokers. Biomarkers 2006; 11:201-20. [PMID: 16760130 DOI: 10.1080/13547500600576260] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The paper reports levels of 24-h urine nicotine and five of its major metabolites (expressed as nicotine-equivalents) and blood carboxyhaemoglobin as biomarkers of exposure to particulate- and gas-phase cigarette smoke, respectively, from an exploratory pilot study of adult smokers of 3.0-6.9 mg tar delivery (Federal Trade Commission (FTC) method) cigarettes. On multiple occasions over 6 weeks, blood high-sensitivity C-reactive protein (hs-CRP), fibrinogen, HDL- and LDL-cholesterol, and 24-h urine 8-epi-prostaglandin F2alpha (8-epi-PGF2alpha) and 11-dehydro-thromboxane B2 (11-dehydro-TxB2) were also evaluated as biomarkers of potential harm. All the biomarkers examined, except for LDL-cholesterol, discriminated with high sensitivity and specificity between adult smokers and non-smokers overall. Except for HDL-cholesterol, all biomarker medians were greater in adult smokers than in non-smokers: urine nicotine-equivalents 64.514 versus < 0.034 nmol mg-1 creatinine (p<0.001), carboxyhaemoglobin 4.0 versus 0.4% saturation (p<0.001), hs-CRP 0.27 versus 0.12 mg dl-1 (p=0.05), fibrinogen 292 versus 248 mg dl-1 (p<0.001), HDL-cholesterol 46 versus 53 mg dl-1 (p=0.003), LDL-cholesterol 119 versus 109 mg dl-1 (p=0.18), urine 8-epi-PGF2alpha 1935 versus 1034 pg mg-1 creatinine (p<0.001) and urine 11-dehydro-TxB2 973 versus 710 pg mg-1 creatinine (p<0.001). All the biomarkers of exposure and most of the biomarkers of potential harm showed no time of sampling (by visit week) effect.
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Affiliation(s)
- B K Zedler
- Philip Morris USA, Richmond, VA 23261, USA.
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Gu P, Schepers G, Griebel C, Rozenski J, Gais HJ, Herdewijn P, Van Aerschot A. Enzymatic resolution and base pairing properties of D- and L-cyclohexenyl nucleic acids (CeNA). Nucleosides Nucleotides Nucleic Acids 2005; 24:993-8. [PMID: 16248079 DOI: 10.1081/ncn-200060326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An enzymatic transesterification reaction afforded large scale resolution of the cyclohexenol precursor needed for preparation of both series of CeNA building blocks. CeNA oligos of "D-like" chirality display a strong and selective interaction with RNA, while preserving RNase H activity, and therefore have potential as antisense constructs. CeNAs of opposite chirality form a self-pairing system on their own.
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Affiliation(s)
- Ping Gu
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
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Storry CH, Speck A, Le Sage D, Guise N, Gabrielse G, Grzonka D, Oelert W, Schepers G, Sefzick T, Pittner H, Herrmann M, Walz J, Hänsch TW, Comeau D, Hessels EA. First laser-controlled antihydrogen production. Phys Rev Lett 2004; 93:263401. [PMID: 15697977 DOI: 10.1103/physrevlett.93.263401] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Indexed: 05/24/2023]
Abstract
Lasers are used for the first time to control the production of antihydrogen (H ). Sequential, resonant charge exchange collisions are involved in a method that is very different than the only other method used so far-producing slow H during positron cooling of antiprotons in a nested Penning trap. Two attractive features are that the laser frequencies determine the H binding energy, and that the production of extremely cold H should be possible in principle-likely close to what is needed for confinement in a trap, as needed for precise laser spectroscopy.
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Affiliation(s)
- C H Storry
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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Abstract
Cyclohexene nucleic acids (CeNA) with a D-like configuration form very stable self-complementary duplexes and stable duplexes with RNA. An increased duplex stability with Delta T(m)/mod of +1.2 degrees C is observed. The duplex with DNA is less stable. Excellent mismatch discrimination has been observed as well for the duplex with DNA as for the duplex with RNA. The results obtained with mixed CeNA sequences warrant antisense studies with CeNA. The CeNAs of opposite chirality constitute a self-pairing system on their own, resembling L-RNA sequences.
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Affiliation(s)
- Ping Gu
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, B-3000 Leuven, Belgium
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Wu T, Froeyen M, Schepers G, Mullens K, Rozenski J, Busson R, Van Aerschot A, Herdewijn P. Synthesis and stability of oligonucleotides containing acyclic achiral nucleoside analogues with two base moieties. Org Lett 2004; 6:51-4. [PMID: 14703348 DOI: 10.1021/ol0360647] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] Nucleotide building blocks with two base moieties were synthesized and incorporated into oligonucleotides. One of the two bases is involved in base pairing within the double helix, while the other base is sticking out of the minor groove. This system may be used for presenting sequence information at the outside of the helix.
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Affiliation(s)
- Tongfei Wu
- Laboratory of Medicinal Chemistry, Rega Institute for Medicinal Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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37
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Gabrielse G, Speck A, Storry CH, LeSage D, Guise N, Grzonka D, Oelert W, Schepers G, Sefzick T, Pittner H, Walz J, Hänsch TW, Comeau D, Hessels EA. First measurement of the velocity of slow antihydrogen atoms. Phys Rev Lett 2004; 93:073401. [PMID: 15324235 DOI: 10.1103/physrevlett.93.073401] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Indexed: 05/24/2023]
Abstract
The speed of antihydrogen atoms is deduced from the fraction that passes through an oscillating electric field without ionizing. The weakly bound atoms used for this first demonstration travel about 20 times more rapidly than the average thermal speed of the antiprotons from which they form, if these are in thermal equilibrium with their 4.2 K container. The method should be applicable to much more deeply bound states, which may well be moving more slowly, and should aid the quest to lower the speed of the atoms as required if they are to be trapped for precise spectroscopy.
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Affiliation(s)
- G Gabrielse
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
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Van Aerschot A, Schepers G, Busson R, Neyts J, De Clercq E, Herdewijn P. Synthesis and antiviral evaluation of ribavirin congeners containing a hexitol moiety. Nucleosides Nucleotides Nucleic Acids 2003; 22:849-51. [PMID: 14565294 DOI: 10.1081/ncn-120022669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Several ribavirin congeners containing a hexitol moiety were prepared via ring opening of two different epoxides with the methylcarboxylate ester of triazole and further elaboration. Unfortunately, none of the newly synthesized compounds displayed appreciable antiviral activity.
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Affiliation(s)
- A Van Aerschot
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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Mikhailov SN, Efimtseva EV, Ermolinsky BS, Bobkov GV, Andreeva OI, Golubeva AS, Kochetkov SN, Van Aerschot A, Schepers G, Herdewijn P. Oligonucleotides containing disaccharide nucleosides: synthesis, physicochemical, and substrate properties. Nucleosides Nucleotides Nucleic Acids 2003; 22:1117-8. [PMID: 14565358 DOI: 10.1081/ncn-120022750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The efficient synthesis of oligonucleotides containing 2'-O-beta-D-ribofuranosyl (and beta-D-ribopyranosyl)nucleosides, 2'-O-alpha-D-arabinofuranosyl (and alpha-L-arabinofuranosyl)nucleosides. 2'-O-beta-D-erythrofuranosylnucleosides, and 2'-O-(5'-amino-5-deoxy-beta-D-ribofuranosyl)nucleosides have been developed.
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Affiliation(s)
- S N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Van Aerschot A, Marchand A, Schepers G, Van den Eynde W, Rozenski J, Busson R, Herdewijn P. Methylated hexitol nucleic acids, towards congeners with improved antisense potential. Nucleosides Nucleotides Nucleic Acids 2003; 22:1227-9. [PMID: 14565386 DOI: 10.1081/ncn-120022842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In an effort to further improve the hybridisation potential of anhydro-hexitol nucleoside analogues, the 1'-methoxyl and 3'-methoxyl substituents were introduced and evaluated for their antisense potential. In view of the selectivity of pairing with RNA, especially the introduction of a 3'-O-alkyl moiety deserves further study.
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Affiliation(s)
- A Van Aerschot
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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Van Miert E, Teredesai A, Schepers G, Friedrichs B, Vanscheeuwijck P. 380 Comparative inhalation study of the standard reference cigarettes 1R4F and 2R4F. Toxicol Lett 2003. [DOI: 10.1016/s0378-4274(03)90379-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Terpstra PM, Teredesai A, Vanscheeuwijck PM, Verbeeck J, Schepers G, Radtke F, Kuhl P, Gomm W, Anskeit E, Patskan G. Toxicological evaluation of an electrically heated cigarette. Part 4: Subchronic inhalation toxicology. J Appl Toxicol 2003; 23:349-62. [PMID: 12975774 DOI: 10.1002/jat.926] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The biological activity of mainstream smoke from an electrically heated cigarette (EHC) with controlled combustion and from the University of Kentucky Reference Cigarette 1R4F was determined in Sprague Dawley rats exposed nose-only for 90 days, 6 h a day, 7 days per week. For an equivalent response comparison between the two cigarette types, two doses were chosen for the EHC where the anticipated results were in the dynamic range of the 1R4F dose-response curve (four concentrations) for most end points. The number of cigarettes smoked per m(3) of diluted smoke resulted in total particulate matter concentrations of 40 and 90 microg l (-1) for the EHC and 40-170 microg l (-1) for the 1R4F. Biomonitoring indicated achievement of target doses. Mainstream smoke yields were lower for the EHC, with the exception of formaldehyde. No smoke-related mortality, remarkable in-life observations or abnormal gross pathological findings were observed. Smoke- and dose-related clinical pathology and organ weight changes included: increases in segmented neutrophils, some liver parameters and lung and adrenal weight relative to body weight; and decreases in lymphocytes, glucose concentration and spleen weight. Smoke-related histopathological findings in the respiratory tract included epithelial cell hyperplasia, squamous metaplasia, atrophy and accumulation of pigmented alveolar macrophages; they were mostly dose-dependent, more pronounced in the upper than lower respiratory tract and completely or partially reversed by 6 weeks post-inhalation. Qualitatively, the biological effects seen for the EHC and the 1R4F were comparable and similar to those observed in other mainstream smoke inhalation studies. Quantitatively, the biological activity of the EHC mainstream smoke was, on average, 65% lower than that of the 1R4F mainstream smoke on an equal cigarette basis and equivalent activity on an equal TPM basis.
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Affiliation(s)
- P M Terpstra
- Philip Morris Research Laboratories bvba, Grauwmeer 14, B-3001 Leuven, Belgium.
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Van Aerschot A, Schepers G, Busson R, Rozenski J, Neyts J, De Clercq E, Herdewijn P. Ribavirin derivatives with a hexitol moiety: synthesis and antiviral evaluation. Antivir Chem Chemother 2003; 14:23-30. [PMID: 12790513 DOI: 10.1177/095632020301400102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Current standard therapy for the treatment of chronic infections with hepatitis C virus consists of combination therapy with (pegylated) interferon-alpha and ribavirin. 1,5-Anhydrohexitol nucleoside analogues are constrained congeners known to mimic the ribonucleoside conformation. Within this series some analogues are endowed with strong antiviral properties, particularly against herpesviruses. The six-membered anhydrohexitol ring was, therefore, combined with the triazolyl carboxamide moiety of ribavirin, thus providing a new series of ribavirin analogues. None of the newly synthesized compounds elicited any substantial antiviral activity, neither against herpes simplex virus type 1 and 2, nor against bovine viral diarrhoea virus (a surrogate for hepatitis C virus) or the yellow fever virus.
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Affiliation(s)
- Arthur Van Aerschot
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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44
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Gabrielse G, Bowden NS, Oxley P, Speck A, Storry CH, Tan JN, Wessels M, Grzonka D, Oelert W, Schepers G, Sefzick T, Walz J, Pittner H, Hänsch TW, Hessels EA. Driven production of cold antihydrogen and the first measured distribution of antihydrogen states. Phys Rev Lett 2002; 89:233401. [PMID: 12485006 DOI: 10.1103/physrevlett.89.233401] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Indexed: 05/24/2023]
Abstract
Cold antihydrogen is produced when antiprotons are repeatedly driven into collisions with cold positrons within a nested Penning trap. Efficient antihydrogen production takes place during many cycles of positron cooling of antiprotons. A first measurement of a distribution of antihydrogen states is made using a preionizing electric field between separated production and detection regions. Surviving antihydrogen is stripped in an ionization well that captures and stores the freed antiproton for background-free detection.
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Affiliation(s)
- G Gabrielse
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
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Gabrielse G, Bowden NS, Oxley P, Speck A, Storry CH, Tan JN, Wessels M, Grzonka D, Oelert W, Schepers G, Sefzick T, Walz J, Pittner H, Hänsch TW, Hessels EA. Background-free observation of cold antihydrogen with field-ionization analysis of its states. Phys Rev Lett 2002; 89:213401. [PMID: 12443407 DOI: 10.1103/physrevlett.89.213401] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2002] [Indexed: 05/24/2023]
Abstract
A background-free observation of cold antihydrogen atoms is made using field ionization followed by antiproton storage, a detection method that provides the first experimental information about antihydrogen atomic states. More antihydrogen atoms can be field ionized in an hour than all the antimatter atoms that have been previously reported, and the production rate per incident high energy antiproton is higher than ever observed. The high rate and the high Rydberg states suggest that the antihydrogen is formed via three-body recombination.
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Affiliation(s)
- G Gabrielse
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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Stabbert R, Schepers G, Stinn WS, Haussmann HJ. Hemoglobin adducts in rats chronically exposed to room-aged cigarette sidestream smoke and diesel engine exhaust. Adv Exp Med Biol 2002; 500:153-6. [PMID: 11764929 DOI: 10.1007/978-1-4615-0667-6_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Under controlled conditions with exaggerated concentrations of environmental aerosols, the biologically effective dose markers suggested in the literature as being specific for ETS (i.e., HPB Hb adducts for TSNA exposure) and DEE (i.e., l-aminopyrene Hb adducts for l-nitropyrene exposure) did not respond. A slight but dose-dependent increase in 4-ABP Hb adduct levels was seen in RASS-exposed rats.
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Affiliation(s)
- R Stabbert
- INBIFO Institut für biologische Forschung, Cologne, Germany
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Kerremans L, Schepers G, Rozenski J, Busson R, Van Aerschot A, Herdewijn P. Hybridization between "six-membered" nucleic acids: RNA as a universal information system. Org Lett 2001; 3:4129-32. [PMID: 11784159 DOI: 10.1021/ol016183r] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Within the polyA:polyT recognition system, cross-pairing between several nucleic acids with a phosphorylated six-membered carbohydrate (mimic) as repeating unit in the backbone structure has been observed. All investigated nucleic acids (except for beta-homo-DNA) hybridize with RNA, leaving RNA as a versatile biopolymer for informational transfer. [reaction: see text]
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Affiliation(s)
- L Kerremans
- Katholieke Universiteit Leuven, Rega Institute, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Van Aerschot A, Meldgaard M, Schepers G, Volders F, Rozenski J, Busson R, Herdewijn P. Improved hybridisation potential of oligonucleotides comprising O-methylated anhydrohexitol nucleoside congeners. Nucleic Acids Res 2001; 29:4187-94. [PMID: 11600707 PMCID: PMC60215 DOI: 10.1093/nar/29.20.4187] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hybridising potential of anhydrohexitol nucleoside analogues (HNAs) is well documented, but tedious synthesis of the monomers hampers their development. In a search for better analogues, the synthesis of two new methylated anhydrohexitol congeners 1 and 2 was accomplished and the physico-chemical properties of their respective oligomers were evaluated. Generally, oligonucleotides (ONs) containing the 3'-O-methyl derivative 1 showed a small increase in thermal stability towards complementary sequences as compared to HNA. Compared to the altritol modification, 3'-O-methylation seems to cause a small decrease in thermal stability of duplexes, especially when targeting RNA. These results suggest the possibility of derivatisation of the 3'-hydroxyl group of altritol-containing congeners without significantly affecting the thermal stability of the duplexes. The methyl glycosidic analogues 2 likewise increased the affinity for RNA in comparison with well-known HNA, while at the same time being economically more favorable monomers. However, homopolymers of 2 displayed self-pairing, but not so homopolymers of 1. Upon incorporation of the hexitols within RNA sequences in an effort to induce a beneficial pre-organised structure, the positive effect of the 3'-O-methyl derivative 1 proved larger than that of 2.
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Affiliation(s)
- A Van Aerschot
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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Abstract
The SOX family of developmental transcription factors is known to play critical roles in cell lineage specification, fate determination and differentiation during development in diverse phyla. Their importance is underscored by their involvement in a number of human diseases and mouse mutants, and by targeted mutation in mice. SOX8 is broadly expressed during development and is located on human chromosome 16p and within the t-complex on mouse chromosome 17, in the vicinity of two mutations t(w18) and t(h20). Here we analyse mutant genomic DNA to show that the Sox8 gene locus lies outside the deletion regions of both t(w18) and t(h20) and between these deletions. These data exclude Sox8 from contributing to the t(w18) and t(h20) phenotypes, and provide an additional marker for structural characterization of this complex genomic region.
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Affiliation(s)
- G Schepers
- Centre for Molecular and Cellular Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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