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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] [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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Kostov O, Liboska R, Páv O, Novák P, Rosenberg I. Solid-Phase Synthesis of Phosphorothioate/Phosphonothioate and Phosphoramidate/Phosphonamidate Oligonucleotides. Molecules 2019; 24:molecules24101872. [PMID: 31096640 PMCID: PMC6571627 DOI: 10.3390/molecules24101872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 11/30/2022] Open
Abstract
We have developed a robust solid-phase protocol which allowed the synthesis of chimeric oligonucleotides modified with phosphodiester and O-methylphosphonate linkages as well as their P-S and P-N variants. The novel O-methylphosphonate-derived modifications were obtained by oxidation, sulfurization, and amidation of the O-methyl-(H)-phosphinate internucleotide linkage introduced into the oligonucleotide chain by H-phosphonate chemistry using nucleoside-O-methyl-(H)-phosphinates as monomers. The H-phosphonate coupling followed by oxidation after each cycle enabled us to successfully combine H-phosphonate and phosphoramidite chemistries to synthesize diversely modified oligonucleotide strands.
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Affiliation(s)
- Ondřej Kostov
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Pavel Novák
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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Liu C, Cozens C, Jaziri F, Rozenski J, Maréchal A, Dumbre S, Pezo V, Marlière P, Pinheiro VB, Groaz E, Herdewijn P. Phosphonomethyl Oligonucleotides as Backbone-Modified Artificial Genetic Polymers. J Am Chem Soc 2018; 140:6690-6699. [DOI: 10.1021/jacs.8b03447] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chao Liu
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Faten Jaziri
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Shrinivas Dumbre
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Valérie Pezo
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Philippe Marlière
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Vitor B. Pinheiro
- University College London, Gower Street, London WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, U.K
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- iSSB, Genopole, CNRS, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, 91030 Evry Cedex, France
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Kostov O, Páv O, Rosenberg I. Nucleoside-O-Methyl-(H)-Phosphinates: Novel Monomers for the Synthesis of Methylphosphonate Oligonucleotides Using H-Phosphonate Chemistry. ACTA ACUST UNITED AC 2017; 70:4.76.1-4.76.22. [PMID: 28921496 DOI: 10.1002/cpnc.35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit comprises the straightforward synthesis of protected 2'-deoxyribonucleoside-O-methyl-(H)-phosphinates in both 3'- and 5'-series. These compounds represent a new class of monomers compatible with the solid-phase synthesis of oligonucleotides using H-phosphonate chemistry and are suitable for the preparation of both 3'- and 5'-O-methylphosphonate oligonucleotides. The synthesis of 4-toluenesulfonyloxymethyl-(H)-phosphinic acid as a new reagent for the preparation of O-methyl-(H)-phosphinic acid derivatives is described. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ondřej Kostov
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - Ondřej Páv
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - Ivan Rosenberg
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
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