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Ren S, Fier PS, Ren H, Hoover AJ, Hesk D, Marques R, Mergelsberg I. 34S: A New Opportunity for the Efficient Synthesis of Stable Isotope Labeled Compounds. Chemistry 2018; 24:7133-7136. [DOI: 10.1002/chem.201801494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Sumei Ren
- Department of Process Research & Development, Merck Research Laboratories (MRL); Merck Sharp & Dohme Corp; Rahway NJ 07065 USA
| | - Patrick S. Fier
- Department of Process Research & Development, Merck Research Laboratories (MRL); Merck Sharp & Dohme Corp; Rahway NJ 07065 USA
| | - Hong Ren
- Department of Process Research & Development, Merck Research Laboratories (MRL); Merck Sharp & Dohme Corp; Rahway NJ 07065 USA
| | - Andrew J. Hoover
- Department of Process Research & Development, Merck Research Laboratories (MRL); Merck Sharp & Dohme Corp; Rahway NJ 07065 USA
| | - David Hesk
- Department of Process Research & Development, Merck Research Laboratories (MRL); Merck Sharp & Dohme Corp; Rahway NJ 07065 USA
| | - Rosemary Marques
- Department of Process Research & Development, Merck Research Laboratories (MRL); Merck Sharp & Dohme Corp; Rahway NJ 07065 USA
| | - Ingrid Mergelsberg
- Department of Process Research & Development, Merck Research Laboratories (MRL); Merck Sharp & Dohme Corp; Rahway NJ 07065 USA
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Szlenkier M, Kamel K, Boryski J. Regioselective Mitsunobu Reaction of Partially Protected Uridine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:410-25. [PMID: 27351239 DOI: 10.1080/15257770.2016.1188943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Mitsunobu reaction of partially acylated uridine proceeds with high regioselectivity for intramolecular SN2 anhydro linkage closuring. Under the reaction conditions, an isomeric mixture of diacyl uridine derivatives with either free 2'- or 3'-hydroxyl group was transformed into a single cyclonucleosidic product, 2,2'-anhydro-3',5'-di-O-acyluridine. This paper presents a possible mechanism of the reactions, the explanation of observed phenomenon based on semiempirical and density functional theory (DFT) calculations and possible utility of this synthetic pathway.
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Affiliation(s)
- Maurycy Szlenkier
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
| | - Karol Kamel
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
| | - Jerzy Boryski
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
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3
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Qu H, Sun W, Zhang Y, Sollogoub M, Zhang Y. Synthesis and NMR elucidation of four novel 2-(trimethylsilyl)ethyl glycosides. RESEARCH ON CHEMICAL INTERMEDIATES 2014. [DOI: 10.1007/s11164-013-1060-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Silva S, V. M. Silva F, Justino J, Pilar Rauter A, Rollin P, Tatibouët A. Synthesis and Antimicrobial Evaluation of Oxazole-2(3H)-thione and 2-Alkylsulfanyl-1,3-oxazole Derivatives. HETEROCYCLES 2014. [DOI: 10.3987/com-13-s(s)56] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Wunderlich CH, Spitzer R, Santner T, Fauster K, Tollinger M, Kreutz C. Synthesis of (6-(13)C)pyrimidine nucleotides as spin-labels for RNA dynamics. J Am Chem Soc 2012; 134:7558-69. [PMID: 22489874 DOI: 10.1021/ja302148g] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present a (13)C-based isotope labeling protocol for RNA. Using (6-(13)C)pyrimidine phosphoramidite building blocks, site-specific labels can be incorporated into a target RNA via chemical oligonucleotide solid-phase synthesis. This labeling scheme is particularly useful for studying milli- to microsecond dynamics via NMR spectroscopy, as an isolated spin system is a crucial prerequisite to apply Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion type experiments. We demonstrate the applicability for the characterization and detection of functional dynamics on various time scales by incorporating the (6-(13)C)uridine and -cytidine labels into biologically relevant RNAs. The refolding kinetics of a bistable terminator antiterminator segment involved in the gene regulation process controlled by the preQ(1) riboswitch class I was investigated. Using (13)C CPMG relaxation dispersion NMR spectroscopy, the milli- to microsecond dynamics of the HIV-1 transactivation response element RNA and the Varkud satellite stem loop V motif was addressed.
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Affiliation(s)
- Christoph H Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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6
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Fürtig B, Buck J, Richter C, Schwalbe H. Functional dynamics of RNA ribozymes studied by NMR spectroscopy. Methods Mol Biol 2012; 848:185-199. [PMID: 22315070 DOI: 10.1007/978-1-61779-545-9_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Catalytic RNA motifs (ribozymes) are involved in various cellular processes. Although functional cleavage of the RNA phosphodiester backbone for self-cleaving ribozymes strongly differs with respect to sequence specificity, the structural context, and the underlying mechanism, these ribozyme motifs constitute evolved RNA molecules that carry out identical chemical functionality. Therefore, they represent ideal systems for detailed studies of the underlying structure-function relationship, illustrating the diversity of RNA's functional role in biology. Nuclear magnetic resonance (NMR) spectroscopic methods in solution allow investigation of structure and dynamics of functional RNA motifs at atomic resolution. In addition, characterization of RNA conformational transitions initiated either through addition of specific cofactors, as e.g. ions or small molecules, or by photo-chemical triggering of essential RNA functional groups provides insights into the reaction mechanism. Here, we discuss applications of static and time-resolved NMR spectroscopy connected with the design of suitable NMR probes that have been applied to characterize global and local RNA functional dynamics together with cleavage-induced conformational transitions of two RNA ribozyme motifs: a minimal hammerhead ribozyme and an adenine-dependent hairpin ribozyme.
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Affiliation(s)
- Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
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7
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Synthesis and molecular modelling of unsaturated exomethylene pyranonucleoside analogues with antitumor and antiviral activities. Eur J Med Chem 2008; 43:1366-75. [DOI: 10.1016/j.ejmech.2007.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 10/12/2007] [Indexed: 11/17/2022]
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8
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Honcharenko D, Zhou C, Chattopadhyaya J. Modulation of pyrene fluorescence in DNA probes depends upon the nature of the conformationally restricted nucleotide. J Org Chem 2008; 73:2829-42. [PMID: 18331060 DOI: 10.1021/jo702747w] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The DNA probes (ODNs) containing a 2'-N-(pyren-1-yl)-group on the conformationally locked nucleosides [2'-N-(pyren-1-yl)carbonyl-azetidine thymidine, Aze-pyr (X), and 2'-N-(pyren-1-yl)carbonyl-aza-ENA thymidine, Aza-ENA-pyr (Y)], show that they can bind to complementary RNA more strongly than to the DNA. The Aze-pyr (X) containing ODNs with the complementary DNA and RNA duplexes showed an increase in the fluorescence intensity (measured at lambda em approximately 376 nm) depending upon the nearest neighbor at the 3'-end to X [dA ( approximately 12-20-fold) > dG ( approximately 9-20-fold) > dT ( approximately 2.5-20-fold) > dC ( approximately 6-13-fold)]. They give high fluorescence quantum yields (Phi F = 0.13-0.89) as compared to those of the single-stranded ODNs. The Aza-ENA-pyr (Y)-modified ODNs, on the other hand, showed an enhancement of the fluorescence intensity only with the complementary DNA (1.4-3.9-fold, Phi F = 0.16-0.47); a very small increase in fluorescence is also observed with the complementary RNA (1.1-1.7-fold, Phi F = 0.17-0.22), depending both upon the site of the Y modification introduced as well as on the chemical nature of the nucleobase adjacent to the modification site into the ODN. The fluorescence properties, thermal denaturation experiments, absorption, and circular dichroism (CD) studies with the X- and Y-modified ODNs in the form of matched homo- and heteroduplexes consistently suggested (i) that the orientation of the pyrene moiety is outside the helix of the nucleic acid duplexes containing a dT-d/rA base pair at the 3'-end of the modification site for both X and Y types of modifications, and (ii) that the microenvironment around the pyrene moiety in the ODN/DNA and ODN/RNA duplexes is dictated by the chemical nature of the conformational constraint in the sugar moiety, as well as by the nature of neighboring nucleobases. The pyrene fluorescence emission in both X and Y types of the conformationally restricted nucleotides is found to be sensitive to a mismatched base present in the target RNA: (i) The X-modified ODN showed a decrease ( approximately 37-fold) in the fluorescence intensity (measured at lambda em approximately 376 nm) upon duplex formation with RNA containing a G nucleobase mismatch (dT-rG pair instead of dT-rA) opposite to the modification site. (ii) In contrast, the Y-modified ODN in the heteroduplex resulted in a approximately 3-fold increase in the fluorescence intensity upon dT-rG mismatch, instead of matched dT-rA pair, in the RNA strand. Our data corroborate that the pyrene moiety is intercalated in the X-modified mismatched ODN/RNA (G mismatch) heteroduplex as compared to that of the Y-modified ODN/RNA (G mismatch) heteroduplex, in which it is located outside the helix.
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Affiliation(s)
- Dmytro Honcharenko
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, SE-75123 Uppsala, Sweden
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Dai Q, Frederiksen JK, Anderson VE, Harris ME, Piccirilli JA. Efficient synthesis of [2'-18O]uridine and its incorporation into oligonucleotides: a new tool for mechanistic study of nucleotidyl transfer reactions by isotope effect analysis. J Org Chem 2007; 73:309-11. [PMID: 18052189 DOI: 10.1021/jo701727h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lack of sufficient quantities of isotopically labeled materials has precluded the use of heavy atom isotope effects to investigate mechanisms of nucleotidyl transfer reactions in nucleic acids. Here we achieve regioselective opening of 2,2'-cyclouridine with [(18)O2]benzoic acid/potassium hydride, allowing an efficient "one-pot" synthesis of [2'-18O]uridine in 88% yield. Conversion to the corresponding phosphoramidite enables solid-phase synthesis of [2'-(18)O] RNA substrates for isotope effect studies with nucleotidyl transferases and hydrolases.
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Affiliation(s)
- Qing Dai
- Department of Biochemistry & Molecular Biology, Department of Chemistry, and Howard Hughes Medical Institute, The University of Chicago, MC 1028, Chicago, Illinois 60637, USA
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Zhou C, Pathmasiri W, Honcharenko D, Chatterjee S, Barman J, Chattopadhyaya J. High-quality oligo-RNA synthesis using the new 2′-O-TEM protecting group by selectively quenching the addition of p-tolyl vinyl sulphone to exocyclic amino functions. CAN J CHEM 2007. [DOI: 10.1139/v07-025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During the F–-promoted deprotection of the oligo–RNA, synthesized using our 2′-O-(4-tolylsulfonyl)ethoxymethyl (2′-O-TEM) group [Org. Biomol. Chem. 5, 333 (2007)], p-tolyl vinyl sulphone (TVS) is formed as a by-product. The TVS formed has been shown to react with the exocyclic amino functions of adenosine (A), guanosine (G), and cytidine (C) of the fully deprotected oligo–RNA to give undesirable adducts, which are then purified by HPLC and unambiguously characterized by 1H, 13C Heteronuclear Multiple Bond Correlation (HMBC) NMR and mass spectroscopic analysis. The relative nucleophilic reactivities of the nucleobases toward TVS have been found to be the following: N6–A > N4–C > N2–G > > N3–U. This reactivity of TVS toward RNA nucleobases to give various Michael adducts could, however, be suppressed by using various amines as scavengers. Among all these amines, morpholine and piperidine are the most efficient scavenger for TVS, which gave highly pure oligo–RNA even in the crude form and can be used directly in RNA chemical biology studies.Key words: RNA synthesis, RNA alkylation, p-tolyl vinyl sulphone, Michael addition.
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11
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Zhou C, Honcharenko D, Chattopadhyaya J. 2-(4-Tolylsulfonyl)ethoxymethyl (TEM)-a new 2'-OH protecting group for solid-supported RNA synthesis. Org Biomol Chem 2006; 5:333-43. [PMID: 17205178 DOI: 10.1039/b614210a] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 2-(4-tolylsulfonyl)ethoxymethyl (TEM) as a new 2'-OH protecting group is reported for solid-supported RNA synthesis using phosphoramidite chemistry. The usefulness of the 2'-O-TEM group is exemplified by the synthesis of 12 different oligo-RNAs of various sizes (14-38 nucleotides long). The stepwise coupling yield varied from 97-99% with an optimized coupling time of 120 s. The synthesis of all four pure phosphoramidite building blocks is also described. Two new reliable parameters, delta(C2')-delta(C3') and delta(H2')-delta(H3'), have been suggested for the characterization of isomeric 2'-O-TEM and 3'-O-TEM as well as other isomeric mono 2'/3'-protected ribonucleoside derivatives. The most striking feature of this strategy is that the crude RNA prepared using our 2'-O-TEM strategy is sufficiently pure (>90%) for molecular biology research without any additional purification step, thereby making oligo-RNAs easily available at a relatively low cost, saving both time and lab resources.
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Affiliation(s)
- Chuanzheng Zhou
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, S-751 23, Uppsala, Sweden
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12
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Zhu XF, Williams HJ, Ian Scott A. Aqueous Trichloroacetic Acid: Another Useful Reagent for Highly Selective 5′-Desilylation of Multisilylated Nucleosides. SYNTHETIC COMMUN 2003. [DOI: 10.1081/scc-120021027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Saito Y, Zevaco TA, Agrofoglio LA. Chemical synthesis of 13C labeled anti-HIV nucleosides as mass-internal standards. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)01246-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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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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15
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Milecki J, Földesi A, Fischer A, Adamiak RW, Chattopadhyaya J. Synthesis of multiply labelled ribonucleosides for sequence-specific labelling of oligo-RNA. J Labelled Comp Radiopharm 2001. [DOI: 10.1002/jlcr.503] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Földesi A, Trifonova A, Kundu MK, Chattopadhyaya J. The synthesis of deuterionucleosides. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1615-56. [PMID: 11200263 DOI: 10.1080/15257770008045450] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The synthesis of deuterionucleosides for site-specific incorporation into oligo-DNA or -RAA is herein reviewed for NMR or biological studies. The review covers the following aspects: (i) deuteration of the aglycone; (ii) single-site chemical deuteration of the sugar residues; (iii) multiple-site chemical deuteration of the sugar residues; (iv) enzymatic synthesis of deuterated nucleosides or nucleotides; and (v) synthesis of labelled nucleosides with multiple isotopes
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Affiliation(s)
- A Földesi
- Department of Bioorganic Chemistry, Biomedical Center, University of Uppsala, Sweden.
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Földesi A, Trifonova A, Dinya Z, Chattopadhyaya J. Selective cleavage of the O6-diphenylcarbamoyl group from sugar-modified guanosines for incorporation into oligo-RNA. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)01524-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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