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Gong Y, Chen L, Zhang W, Salter R. Transglycosylation in the Modification and Isotope Labeling of Pyrimidine Nucleosides. Org Lett 2020; 22:5577-5581. [PMID: 32628494 DOI: 10.1021/acs.orglett.0c01941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transglycosylation of pyrimidine nucleosides is demonstrated in a one-pot synthesis of uridine derivatives under microwave irradiation. Inductive activation of 2',3',5'-tri-O-acetyl uridine with a 5-nitro group produces a more-reactive glycosyl donor. Under optimized Vorbrüggen conditions, the 5-nitrouridine facilitates a reversible nucleobase exchange with a series of 5-substituted uracils. The protocol is also exemplified in a gram-scale reaction under thermal heating. The strategy provides easy access to isotopically labeled uridine.
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Affiliation(s)
- Yong Gong
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Lu Chen
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Wei Zhang
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Rhys Salter
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
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2
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Akula HK, Lakshman MK. Facile Modifications at the C4 Position of Pyrimidine Nucleosides via In Situ Amide Activation with 1H-Benzotriazol-1-yloxy-tris(dimethyl-amino)phosphonium Hexafluorophosphate. ACTA ACUST UNITED AC 2019; 76:e73. [PMID: 30688408 DOI: 10.1002/cpnc.73] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Two approaches for C4 modifications of silyl-protected thymidine, 2'-deoxyuridine, and 3'-azido-2',3'-dideoxythymidine (AZT) are described. In both, nucleoside amide activation with 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and DBU yields O4 -(benzotriazol-1-yl) derivatives. These in situ-formed intermediates are reacted with various nucleophiles, resulting in C4 modifications. In the two-step, one-pot approach, the O4 -(benzotriazol-1-yl) nucleoside intermediates are initially produced by reactions of the nucleosides with BOP and DBU in THF. This step is fast and typically complete within 30 min. Subsequently, the O4 -(benzotriazol-1-yl) derivatives are reacted with nucleophiles, such as aliphatic and aromatic amines, thiols, and alcohols, under appropriate conditions. Workup, isolation, and purification lead to the desired C4-modified pyrimidine nucleosides in good to excellent yields. In the one-step approach, the nucleosides are reacted with BOP and DBU, in the presence of the nucleophile (only aliphatic and aromatic amines, and thiols have been tested). Where comparisons are possible, the one-step approach is generally superior. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Hari K Akula
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York
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Abstract
This review highlights the use of the bisphosphine ligand group in homogeneous catalysis.
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4
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Akula HK, Kokatla H, Andrei G, Snoeck R, Schols D, Balzarini J, Yang L, Lakshman MK. Facile functionalization at the C4 position of pyrimidine nucleosides via amide group activation with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and biological evaluations of the products. Org Biomol Chem 2017; 15:1130-1139. [PMID: 28054092 PMCID: PMC5367150 DOI: 10.1039/c6ob02334g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of O-t-butyldimethylsilyl-protected thymidine, 2'-deoxyuridine, and 3'-azidothymidine (AZT) with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) leads to activation of the C4 amide carbonyl by formation of putative O4-(benzotriazol-1-yl) derivatives. Subsequent substitution with alkyl and aryl amines, thiols, and alcohols leads to facile functionalization at this position. Reactions with amines and thiols were conducted either as a two-step, one-pot transformation, or as a one-step conversion. Reactions with alcohols were conducted as two-step, one-pot transformations. In the course of these investigations, the formation of 1-(4-pyrimidinyl)-1H-benzotriazole-3-oxide derivatives from the pyrimidine nucleosides was identified. However, these too underwent conversion to the desired products. Products obtained from AZT were converted to the 3'-amino derivatives by catalytic reduction. All products were assayed for their abilities to inhibit cancer cell proliferation and for antiviral activities. Many were seen to be active against HIV-1 and HIV-2, and one was active against herpes simplex virus-1 (HSV-1).
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Affiliation(s)
- Hari K Akula
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA. and The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - Hariprasad Kokatla
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Jan Balzarini
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Lijia Yang
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA. and The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
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5
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Mamais M, Kouloumoundra V, Smyrli E, Grammatopoulos P, Chrysina ED, Gimisis T. Synthesis of N4-aryl-β-d-glucopyranosylcytosines: a methodology study. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.08.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Weissman BP, Li NS, York D, Harris M, Piccirilli JA. Heavy atom labeled nucleotides for measurement of kinetic isotope effects. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1737-45. [PMID: 25828952 DOI: 10.1016/j.bbapap.2015.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/06/2015] [Accepted: 03/18/2015] [Indexed: 02/01/2023]
Abstract
Experimental analysis of kinetic isotope effects represents an extremely powerful approach for gaining information about the transition state structure of complex reactions not available through other methodologies. The implementation of this approach to the study of nucleic acid chemistry requires the synthesis of nucleobases and nucleotides enriched for heavy isotopes at specific positions. In this review, we highlight current approaches to the synthesis of nucleic acids enriched site specifically for heavy oxygen and nitrogen and their application in heavy atom isotope effect studies. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Darrin York
- Center for Integrative Proteomics Research, Biology at the Interface with the Mathematical and Physical Sciences (BioMaPS) Institute for Quantitative Biology, The State University of New Jersey, Piscataway, NJ, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Michael Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Joseph A Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
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7
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Bosch L, Delelis O, Subra F, Deprez E, Witvrow M, Vilarrasa J. Thymidine- and AZT-linked 5-(1,3-dioxoalkyl)tetrazoles and 4-(1,3-dioxoalkyl)-1,2,3-triazoles. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2011.11.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Battenberg OA, Nodwell MB, Sieber SA. Evaluation of α-pyrones and pyrimidones as photoaffinity probes for affinity-based protein profiling. J Org Chem 2011; 76:6075-87. [PMID: 21726094 DOI: 10.1021/jo201281c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
α-Pyrones and pyrimidones are common structural motifs in natural products and bioactive compounds. They also display photochemistry that generates high-energy intermediates that may be capable of protein reactivity. A library of pyrones and pyrimidones was synthesized, and their potential to act as photoaffinity probes for nondirected affinity-based protein profiling in several crude cell lysates was evaluated. Further "proof-of-principle" experiments demonstrate that a pyrimidone tag on an appropriate scaffold is equally capable of proteome labeling as a benzophenone.
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Affiliation(s)
- Oliver A Battenberg
- Department Chemie, Center for Integrated Protein Science CIPSM, Institute of Advanced Studies, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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9
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Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR. Enzymatic de novo pyrimidine nucleotide synthesis. J Am Chem Soc 2011; 133:297-304. [PMID: 21166398 PMCID: PMC3134529 DOI: 10.1021/ja1059685] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of stable isotope labeling has revolutionized NMR studies of nucleic acids, and there is a need for methods of incorporation of specific isotope labels to facilitate specific NMR experiments and applications. Enzymatic synthesis offers an efficient and flexible means to synthesize nucleoside triphosphates from a variety of commercially available specifically labeled precursors, permitting isotope labeling of RNAs prepared by in vitro transcription. Here, we recapitulate de novo pyrimidine biosynthesis in vitro, using recombinantly expressed enzymes to perform efficient single-pot syntheses of UTP and CTP that bear a variety of stable isotope labeling patterns. Filtered NMR experiments on (13)C, (15)N, (2)H-labeled HIV-2 TAR RNA demonstrate the utility and value of this approach. This flexible enzymatic synthesis will make implementing detailed and informative RNA stable isotope labeling schemes substantially more cost-effective and efficient, providing advanced tools for the study of structure and dynamics of RNA molecules.
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Affiliation(s)
- Heather L Schultheisz
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB33, La Jolla, California 92037, USA
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10
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Ono A, Torigoe H, Tanaka Y, Okamoto I. Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev 2011; 40:5855-66. [DOI: 10.1039/c1cs15149e] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Caner J, Vilarrasa J. (15)N Double-labeled guanosine from inosine through ring-opening-ring-closing and one-pot Pd-catalyzed C-O and C-N cross-coupling reactions. J Org Chem 2010; 75:4880-3. [PMID: 20550202 DOI: 10.1021/jo100808w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
[N,1-(15)N(2)]-Guanosine, or [1,NH(2)-(15)N(2)]-guanosine, and derivatives were prepared from tri-O-acetylinosine, via N-nitration and reaction with (15)NH(2)OH, followed by conversion of the (15)N-labeled 1-hydroxyinosine to the corresponding 2,6-dichloropurine riboside. The sequential one-pot C-O and C-N key couplings of this dichloro derivative with PhCH(2)OH and PhCO(15)NH(2) or (i)PrCO(15)NH(2) was achieved in good overall yields, with Pd(0)-Xantphos as the best choice of five different catalytic systems examined.
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Affiliation(s)
- Joaquim Caner
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona, Av. Diagonal 647, 08028 Barcelona, Catalonia, Spain
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El Ashry ESH, Nadeem S, Shah MR, Kilany YE. Recent Advances in the Dimroth Rearrangement. ADVANCES IN HETEROCYCLIC CHEMISTRY 2010. [DOI: 10.1016/s0065-2725(10)01005-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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13
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Bilbille Y, Vendeix FAP, Guenther R, Malkiewicz A, Ariza X, Vilarrasa J, Agris PF. The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs. Nucleic Acids Res 2009; 37:3342-53. [PMID: 19324888 PMCID: PMC2691828 DOI: 10.1093/nar/gkp187] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3′-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5′-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNALys3. The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s2U34, and pseudouridine, Ψ39, appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U162•Ψ39 and G163•A38, that maintained a reasonable A-form helix diameter. The tRNA's s2U34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Ψ39 stabilized the adjacent mismatched pairs.
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Affiliation(s)
- Yann Bilbille
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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14
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Mahto SK, Chow CS. Synthesis and solution conformation studies of the modified nucleoside N(4),2'-O-dimethylcytidine (m(4)Cm) and its analogues. Bioorg Med Chem 2008; 16:8795-800. [PMID: 18805697 DOI: 10.1016/j.bmc.2008.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 08/29/2008] [Accepted: 09/05/2008] [Indexed: 11/24/2022]
Abstract
The dimethylated ribosomal nucleoside m(4)Cm and its monomethylated analogues Cm and m(4)C were synthesized. The conformations (syn vs anti) of the three modified nucleosides and cytidine were determined by CD and 1D NOE difference spectroscopy. The ribose sugar puckers were determined by the use of proton coupling constants. The position of modification (e.g., O vs N methylation) was found to have an effect on the sugar pucker of cytidine.
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Affiliation(s)
- Santosh K Mahto
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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15
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Zhong M, Strobel SA. Synthesis of isotopically labeled P-site substrates for the ribosomal peptidyl transferase reaction. J Org Chem 2007; 73:603-11. [PMID: 18081346 DOI: 10.1021/jo702070m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Isotopomers of the ribosomal P-site substrate, the trinucleotide peptide conjugate CCA-pcb (Zhong, M.; Strobel, S. A. Org. Lett. 2006, 8, 55-58), have been designed and synthesized in 26-35 steps. These include individual isotopic substitution at the alpha-hydrogen, carbonyl carbon, and carbonyl oxygen of the amino acid, the O2' and O3' of the adenosine, and a remote label in the N3 and N4 of both cytidines. These isotopomers were synthesized by coupling cytidylyl-(3',5')-cytidine phosphoramidite isotopomers as the common synthetic intermediates, with isotopically substituted A-Phe-cap-biotin (A-pcb). The isotopic enrichment is higher than 99% for 1-13C (Phe), 2-2H (Phe), and 3,4-15N2 (cytidine), 93% for 2'/3'-18 O (adenosine), and 64% for 1-18 O (Phe). A new synthesis of highly enriched [1-18 O2]phenylalanine has been developed. The synthesis of [3'-18 O]adenosine was improved by Lewis acid aided regioselective ring opening of the epoxide and by an economical SN2-SN2 method with high isotopic enrichment (93%). Such substrates are valuable for studies of the ribosomal peptidyl transferase reaction by complete kinetic isotope effect analysis and of other biological processes catalyzed by nucleic acid related enzymes, including polymerases, reverse transcriptases, ligases, nucleases, and ribozymes.
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Affiliation(s)
- Minghong Zhong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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16
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Jensen SS, Ariza X, Nielsen P, Vilarrasa J, Kirpekar F. Collision-induced dissociation of cytidine and its derivatives. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:49-57. [PMID: 17149798 DOI: 10.1002/jms.1136] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The collision-induced dissociation of adenosine, uridine and guanosine, and their corresponding nucleobases has been published previously.1-3 Here we report the collision-induced dissociation of cytidine and the elucidation of its fragmentation pathways using stable isotope-labeled cytidines, through a quadrupole ion trap for tandem mass spectrometry up to MS(4). Furthermore, we investigated the collision-induced dissociation of five cytidine derivatives: 3-methylcytidine, N(4)-methyl-2'-deoxycytidine, 5-methylcytidine, 2-thiocytidine and N(4)-acetylcytidine. The primary fragmentation pathway was the neutral loss of ribose. MS(3) on the retained nucleobase generally resulted in an intense signal from the elimination of ammonia, but also in fragment ions characteristic of the different cytosine derivatives. On the basis of the MS(n) data, fragmentation pathways and plausible mechanisms are suggested.
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Affiliation(s)
- Søren S Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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17
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Bdour HM, Kao JLF, Taylor JS. Synthesis and characterization of a [3-15N]-labeled cis-syn thymine dimer-containing DNA duplex. J Org Chem 2006; 71:1640-6. [PMID: 16468818 PMCID: PMC2580729 DOI: 10.1021/jo0524167] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cis-syn thymine dimers are the major photoproducts of DNA and are the principal cause of mutations induced by sunlight. To better understand the nature of base pairing with cis-syn thymine dimers, we have synthesized a decamer oligodeoxynucleotide (ODN) containing a cis-syn thymine dimer labeled at the N3 of both T's with 15N by two efficient routes from [3-15N]-thymidine phosphoramidite. In the postsynthetic irradiation route, an ODN containing an adjacent pair of [3-15N]-labeled T's was irradiated and the cis-syn dimer-containing ODN isolated by HPLC. In the mixed building block route, a mixture of cis-syn and trans-syn dimer-containing ODNs was synthesized from a mixture of [3-15N]-labeled thymine dimer phosphoramidites after which the cis-syn dimer-containing ODN was isolated by HPLC. The N3-nitrogen and imino proton signals of an (15)N-labeled thymine dimer-containing decamer duplex were assigned by 2D 1H-15N heterocorrelated HSQC NMR spectroscopy, and the 15N-1H coupling constant was found to be 1.8 Hz greater for the 5'-T than for the 3'-T. The larger coupling constant is indicative of weaker H-bonding that is consistent with the more distorted nature of the 5'-base pair found in solution state NMR and crystallographic structures.
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18
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Miyata K, Kobori A, Tamamushi R, Ohkubo A, Taguchi H, Seio K, Sekine M. Conformational Studies of 4-N-Carbamoyldeoxycytidine Derivatives and Synthesis and Hybridization Properties of Oligodeoxyribonucleotides Incorporating these Modified Bases. European J Org Chem 2006. [DOI: 10.1002/ejoc.200501006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Terrazas M, Ariza X, Vilarrasa J. Advantages of the Ns group in the reactions of N1-SO2R inosines with benzylamine and with 15NH3. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.05.137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Okuda K, Seila AC, Strobel SA. Synthesis of isotopically labeled puromycin derivatives for kinetic isotope effect analysis of ribosome catalyzed peptide bond formation. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Sako M, Kawada H. A New and Efficient Synthetic Method for 15N3-Labeled Cytosine Nucleosides: Dimroth Rearrangement of Cytidine N3-Oxides. J Org Chem 2004; 69:8148-50. [PMID: 15527310 DOI: 10.1021/jo0486241] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The treatment of (15)N(4)-labeled cytidine N(3)-oxide and (15)N(4)-labeled 2'-deoxycytidine N(3)-oxide, prepared from the appropriate unprotected uridines in three reaction steps, with benzyl bromide in the presence of excess lithium methoxide allowed the smooth occurrence of their Dimroth rearrangement even under mild conditions leading to the corresponding (15)N(3)-labeled uridine 4-O-benzyloximes which can easily undergo the reductive N-O bond cleavage to give the desirable (15)N(3)-labeled cytosine nucleosides in high total yields.
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Affiliation(s)
- Magoichi Sako
- Gifu Pharmaceutical University, 5-6-1, Mitahora-higashi, Gifu 502-8585, Japan.
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22
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Abstract
[reaction: see text]. A procedure for the chemical synthesis of [3-15N]-labeled pseudouridine and a methylated derivative was developed. A suitably protected pseudouridine precursor was nitrated at N3 followed by treatment with 15NH4Cl to afford the 15N-labeled product in six steps with a 20% yield. This methodology will allow for the production of RNAs with [3-15N]pseudouridine and [3-15N-methyl]pseudouridine at specific locations.
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Affiliation(s)
- Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry, Innrain 52a, Innsbruck, Austria.
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Gorchs O, Hernández M, Garriga L, Pedroso E, Grandas A, Farràs J. A new method for the preparation of modified oligonucleotides. Org Lett 2002; 4:1827-30. [PMID: 12027624 DOI: 10.1021/ol025643t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction-see text] N-Nitrothymidine can be transformed into a phosphoramidite building block suitable for oligonucleotide synthesis using the standard phosphite triester solid-phase approach. The N-nitrothymidine residues remain stable during the elongation cycles and react smoothly with primary amines, furnishing oligonucleotides containing N3-modified thymidines. A number of N3-substituted oligonucleotides have been prepared using this methodology, some of them incorporating aminoalkyl or hydroxyalkyl groups.
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Affiliation(s)
- Olga Gorchs
- Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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Ouwerkerk N, Steenweg M, de Ruijter M, Brouwer J, van Boom JH, Lugtenburg J, Raap J. One-pot two-step enzymatic coupling of pyrimidine bases to 2-deoxy-D-ribose-5-phosphate. A new strategy in the synthesis of stable isotope labeled deoxynucleosides. J Org Chem 2002; 67:1480-9. [PMID: 11871876 DOI: 10.1021/jo0107249] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic synthesis of thymidine from 2-deoxy-D-ribose-5-phosphate is achieved, in a one-pot two-step reaction using phosphoribomutase (PRM) and commercially available thymidine phosphorylase (TP). In the first step the sugar-5-phosphate is enzymatically rearranged to alpha-2-deoxy-D-ribose-1-phosphate. Highly active PRM is easily obtained from genetically modified overproducing E. coli cells (12,000 units/84 mg protein) and is used without further purification. In the second step thymine is coupled to the sugar-1-phosphate. The thermodynamically unfavorable equilibrium is shifted to the product by addition of MnCl(2) to precipitate inorganic phosphate. In this way the overall yield of the beta-anomeric pure nucleoside increases from 14 to 60%. In contrast to uracil, cytosine is not accepted by TP as a substrate. Therefore, 2'-deoxy-cytidine is obtained by functional group transformations of the enzymatically prepared 2'-deoxy-uridine. The method has been demonstrated by the synthesis of [2',5'-(13)C(2)]- and [1',2',5'-(13)C(3)]thymidine as well as [1',2',5'-(13)C(3)]2'-deoxyuridine and [3',4'-(13)C(2)]2'-deoxycytidine. In addition the nucleoside bases thymine and uracil are tetralabeled at the (1,3-(15)N(2),2,4-(13)C(2))-atomic positions. All compounds are prepared without any scrambling or dilution of the labeled material and are thus obtained with a very high isotope enrichment (96-99%). In combination with the methods that have been developed earlier it is concluded that each of the (13)C- and (15)N-positions and combination of positions of the pyrimidine deoxynucleosides can be efficiently labeled starting from commercially available and highly (13)C- or (15)N-enriched formaldehyde, acetaldehyde, acetic acid, potassium cyanide, methylamine hydrochloride, and ammonia.
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Affiliation(s)
- N Ouwerkerk
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Kobori A, Miyata K, Ushioda M, Seio K, Sekine M. A new method for the synthesis of oligodeoxyribonucleotides containing 4-N-alkoxycarbonyldeoxycytidine derivatives and their hybridization properties. J Org Chem 2002; 67:476-85. [PMID: 11798320 DOI: 10.1021/jo010813l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligodeoxyribonucleotides incorporating 4-N-alkoxycarbonyldeoxycytidine derivatives were synthesized on polystyrene-type ArgoPore resins having a new benzyloxy(diisopropyl)silyl linker, by use of ZnBr(2) as the detritylating agent. The first 3'-terminal thymidine could be attached to the resin by successive in situ reactions of 5'-O-DMTr-thymidine with diisopropylsilanediyl ditriflate and an ArgoPore resin containing hydroxyl groups. The use of this new silanediyl-type linker allowed release of the DNA chain from the resin by treatment with TBAF under neutral conditions. The T(m) experiments apparently showed that incorporation of 4-N-alkoxycarbonyldeoxycytidines into DNA strands resulted in higher hybridization affinity with the complementary DNA strands than that of 4-N-acyldeoxycytidines. In addition, comparable T(m) studies using oligodeoxyribonucleotides incorporating acyl (RC(O)-) groups and alkoxyacyl (RO(CH(2))(n)C(O)-) groups having the same chain length show that the latter tend to exhibit higher T(m) values than the former. It turned out that 4-N-alkoxycarbonyldeoxycytidines can form base pairs not only with deoxyguanosine but also with deoxyadenosine. Based on the ab initio calculations of the hydrogen bond energies of the possible base pairs formed between 4-N-methoxycarbonyl-1-methylcytosine and 9-methyladenine and the NMR analysis of the base-pairs of (15)N-labeled 4-N-alkoxycarbonyldeoxycytidines with deoxyadenosine derivatives, we conclude that the base pair involves two unique hydrogen bonds between the cytosyl 4-NH group and the adenyl N(1) atom and between the O atom of the ester group and the adenyl 6-NH group.
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Affiliation(s)
- Akio Kobori
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Milecki J. Specific labelling of nucleosides and nucleotides with13C and15N. J Labelled Comp Radiopharm 2002. [DOI: 10.1002/jlcr.553] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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