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Qian K, Shepard SM, Xin T, Park G, Cummins CC. Stabilized Molecular Diphosphorus Pentoxide, P 2O 5L 2 (L = N-Donor Base), in the Synthesis of Condensed Phosphate-Organic Molecule Conjugates. J Am Chem Soc 2023; 145:6045-6050. [PMID: 36913316 PMCID: PMC10038927 DOI: 10.1021/jacs.3c00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Commercial phosphorus pentoxide reacts with some N-donor bases to give the adducts P2O5L2 and P4O10L3 (L = DABCO, pyridine, 4-tert-butylpyridine). The DABCO adducts were structurally characterized by single-crystal X-ray diffraction. It is proposed that P2O5L2 and P4O10L3 undergo interconversion through a "phosphate-walk" mechanism, which was evaluated using DFT calculations. P2O5(pyridine)2 (1) efficiently transfers monomeric diphosphorus pentoxide to phosphorus oxyanion nucleophiles, yielding substituted trimetaphosphates and cyclo-phosphonate-diphosphates (P3O8R)2- (R1 = nucleosidyl, phosphoryl, alkyl, aryl, vinyl, alkynyl, H, F). Hydrolytic ring-opening of these compounds forms linear derivatives [R1(PO3)2PO3H]3-, and nucleophilic ring-opening gives linear disubstituted [R1(PO3)2PO2R2]3- compounds.
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Affiliation(s)
- Kevin Qian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Tiansi Xin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Gyeongjin Park
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, 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; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, 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
| | - Ivo Sarac
- Institut Pasteur, 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
| | - Marcel Hollenstein
- Institut Pasteur, 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.
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Hodgson DR. Physicochemical Aspects of Aqueous and Nonaqueous Approaches to the Preparation of Nucleosides, Nucleotides and Phosphate Ester Mimics. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Depaix A, Peyrottes S, Roy B. One-Pot Synthesis of Nucleotides and Conjugates in Aqueous Medium. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
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Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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Chakarawet K, Knopf I, Nava M, Jiang Y, Stauber JM, Cummins CC. Crystalline Metaphosphate Acid Salts: Synthesis in Organic Media, Structures, Hydrogen-Bonding Capability, and Implication of Superacidity. Inorg Chem 2016; 55:6178-85. [DOI: 10.1021/acs.inorgchem.6b00749] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Khetpakorn Chakarawet
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ioana Knopf
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Matthew Nava
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yanfeng Jiang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia M. Stauber
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christopher C. Cummins
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Dellafiore MA, Montserrat JM, Iribarren AM. Modified Nucleoside Triphosphates for In-vitro Selection Techniques. Front Chem 2016; 4:18. [PMID: 27200340 PMCID: PMC4854868 DOI: 10.3389/fchem.2016.00018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022] Open
Abstract
The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed.
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Affiliation(s)
- María A Dellafiore
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET) Ciudad Autónoma de Buenos Aires, Argentina
| | - Javier M Montserrat
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET)Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Ciencias, Universidad Nacional de General SarmientoLos Polvorines, Argentina
| | - Adolfo M Iribarren
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET)Ciudad Autónoma de Buenos Aires, Argentina; Laboratorio de Biotransformaciones, Universidad Nacional de QuilmesBernal, Argentina
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Korhonen HJ, Bolt HL, Hodgson DRW. A procedure for the preparation and isolation of nucleoside-5'-diphosphates. Beilstein J Org Chem 2015; 11:469-72. [PMID: 25977720 PMCID: PMC4419508 DOI: 10.3762/bjoc.11.52] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/25/2015] [Indexed: 11/30/2022] Open
Abstract
Tris[bis(triphenylphosphoranylidene)ammonium] pyrophosphate (PPN pyrophosphate) was used in the SN2 displacements of the tosylate ion from 5’-tosylnucleosides to afford nucleoside-5’-diphosphates. Selective precipitation permitted the direct isolation of nucleoside-5’-diphosphates from crude reaction mixtures.
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Affiliation(s)
- Heidi J Korhonen
- Department of Chemistry, Science Laboratories, Durham University, South Road, Durham, DH1 3LE, United Kingdom, ; Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland
| | - Hannah L Bolt
- Department of Chemistry, Science Laboratories, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - David R W Hodgson
- Department of Chemistry, Science Laboratories, Durham University, South Road, Durham, DH1 3LE, United Kingdom
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