- Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides
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The use of CuAAC chemistry to crosslink and stabilize oligonucleotides has been limited by the incompatibility of azides with the phosphoramidites used in automated oligonucleotide synthesis. Herein we report optimized reaction conditions to synthesize azide derivatives of thymidine and cytidine phosphoramidites. Investigation of the stability of the novel phosphoramidites using 31P NMR at room temperature showed less than 10% degradation after 6 h. The azide modified thymidine was successfully utilized as an internal modifier in the standard phosphoramidite synthesis of a DNA sequence. The synthesized azide and alkyne derivatives of pyrimidines will allow efficient incorporation of azide and alkyne click pairs into nucleic acids, thus widening the applicability of click chemistry in investigating the chemistry of nucleic acids.
- Lingala, Suresh,Nordstr?m, Lars Ulrik,Mallikaratchy, Prabodhika R.
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supporting information
p. 211 - 213
(2019/01/04)
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- Renewable amberlyst-15 catalyzed highly regioselective tritylation and deprotection of sugar-based diols
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Amberlyst-15 catalyzed highly regioselective tritylation of sugar-based diols was achieved under mild condition using 4,4′-dimethoxytrityl alcohol (DMTrOH). Deprotection of the corresponding DMTr group was also established by the variation to protic solvent. Meanwhile, the heterogeneous catalyst Amberlyst-15 was recycled 3 times with satisfactory retention of catalytic activity and proved its potential application in industry.
- Valeru, Anil,Luo, Zhibin,Penjarla, Srishylum,Khan, Imran,Liu, Bin,Sngepu, Bhavanarushi,Xu, Yin,Xie, Jimin
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p. 318 - 326
(2018/10/15)
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- Intermolecular 'cross-torque': The N4-cytosine propargyl residue is rotated to the 'CH'-edge as a result of Watson-Crick interaction
-
Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues attached to the exocyclic N4 may orient away from or toward the Watson-Crick face, ensuing dramatic alteration of base pairing properties. ROESY-NMR experiments suggest a uniform orientation toward the Watson-Crick face of N4-propargyl residues in derivatives of both deoxycytidine and 5-methyl-deoxycytidine. In oligodeoxynucleotides, however, UV-melting indicated that N4-propargyl-deoxycytidine undergoes standard base pairing. This implies a rotation of the propargyl moiety toward the 'CH'-edge as a result of base pairing on the Watson-Crick face. In oligonucleotides containing the corresponding 5-methyl-deoxycytidine derivative, dramatically reduced melting temperatures indicate impaired Watson-Crick base pairing. This was attributed to a steric clash of the propargyl moiety with the 5-methyl group, which prevents back rotation to the 'CH'-edge, consequently preventing Watson-Crick geometry. Our results emphasize the tendency of an opposing nucleic acid strand to mechanically rotate single N4-substituents to make way for Watson-Crick base pairing, providing no steric hindrance is present on the 'CH'-edge.
- Domingo, Olwen,Hellmuth, Isabell,J?schke, Andres,Kreutz, Christoph,Helm, Mark
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p. 5275 - 5283
(2015/07/15)
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- SUBSTITUTED NUCLEOSIDES, NUCLEOTIDES AND ANALOGS THEREOF
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Disclosed herein are nucleosides, nucleotides and nucleotide analogs, methods of synthesizing the same and methods of treating diseases and/or conditions such as a Coronaviridae virus, a Togaviridae virus, a Hepeviridae virus and/or a Bunyaviridae virus infection with one or more nucleosides, nucleotides and nucleotide analogs.
- -
-
Paragraph 1309; 1310
(2016/03/08)
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- SUBSTITUTED NUCLEOSIDES, NUCLEOTIDES AND ANALOGS THEREOF
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Disclosed herein are nucleosides, nucleotide analogs, methods of synthesizing nucleotide analogs and methods of treating diseases and/or conditions such as a Filoviridae virus infection with one or more nucleosides and/or nucleotide analogs.
- -
-
Paragraph 1252-1253
(2016/03/11)
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- Sensitized photochemistry of di(4-tetrazolouracil) dinucleoside monophosphate as a route to dicytosine cyclobutane photoproduct precursors
-
The DNA cis-syn cyclobutane photoproduct formed between two adjacent cytosine residues is highly mutagenic and responsible for the tandem CC to TT transition. However, its instability has prevented its in vitro study, so far. With a view to prepare oligodeoxynucleotides containing the CC cyclobutane lesion, we have synthesized in good yield a ditetrazolouracil cyclobutane dinucleotide photoproduct as a stable precursor of this photoproduct. Our approach also overcomes the low photochemical reactivity of the cytosine-cytosine deoxydinucleoside monophosphate.
- Peyrane, Frederic,Clivio, Pascale
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p. 1366 - 1374
(2013/08/23)
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- Delivery of floxuridine derivatives to cancer cells by water-soluble organometallic cages
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The self-assembly of 2,4,6-tris(pyridin-4-yl)-1,3,5-triazine (tpt) triangular panels with p-cymene (pPriC6H4Me) ruthenium building blocks and 2,5-dioxydo-1,4-benzoquinonato (dobq) or 5,8-dioxydo-1,4-naphthoquinonato (donq) bridges, in the presence of a pyrenyl-nucleoside derivatives (pyreneR), affords the triangular prismatic host-guest compounds [(pyrene-R)?Ru6(pPriC 6H4Me)6(tpt)2(dobq) 3]6+ ([(pyrene-R)?1]6+) and [(pyrene-R)?Ru6(pPriC6H4Me) 6(tpt)2(donq)3]6+ ([(pyrene-R)?2]6+), respectively. The inclusion of six monosubstitutedpyrenyl-nucleosides (pyrene-R1 = 5′-(1-pyrenyl butanoate)-2′-deoxyuridine, pyrene-R2 = 5-fluoro-5′-(1-pyrenyl butanoate)-2′-deoxyuridine, pyrene-R3 = 5′-{N-[1-oxo-4-(1-pyrenyl) butyl]-glycyl}-2′-deoxyuridine, pyrene-R4 = 5-fluoro-5′-{N-[1-oxo-4- (1-pyrenyl)butyl]-glycyl}-2′-deoxyuridine, pyrene-R5 = 5-fluoro-5′-{N-[1-oxo-4-(1-pyrenyl)butyl]-phenylalanyl} -2′-deoxyvuridine, pyrene-R6 = 5-fluoro-5′-{N-[1-oxo-4-(1-pyrenyl) butyl]-phenylalanyl}-2′-deoxyuridine) has been accomplished. The carceplex nature of [(pyrene-R)?1]6+ with the pyrenyl moiety firmly encapsulated in the hydrophobic cavity of the cage with the nucleoside groups pointing outward was confirmed by NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS), while the host-guest nature of [(pyrene-R)?2] 6+ was studied in solution by NMR techniques. In contrast to the floxuridine compounds used in the clinic, the host-guest complexes are highly water-soluble. Consequently, the cytotoxicities of these water-soluble compounds have been established using human ovarian A2780 and A2780cisR cancer cells. All the host-guest systems are more cytotoxic than the empty cages alone [1][CF3SO3]6 (IC50 = 23 μM) and [2][CF3SO3]6 (IC50 = 10 μM), the most active compound [pyrene-R4?1][CF3SO3] 6being 2 orders of magnitude more cytotoxic (IC50 = 0.3 μM) on these human ovarian cancer cell lines (A2780 and A2780cisR).
- Yi, Jeong Wu,Barry, Nicolas P. E.,Furrer, Mona A.,Zava, Olivier,Dyson, Paul J.,Therrien, Bruno,Kim, Byeang Hyean
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experimental part
p. 461 - 471
(2012/06/04)
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- Improved synthesis of 5-hydroxymethyl-2′-deoxycytidine phosphoramidite using a 2′-deoxyuridine to 2′-deoxycytidine conversion without temporary protecting groups
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5-Hydroxymethylcytosine has recently been characterized as the 'sixth base' in human DNA. To enable research on this DNA modification, we report an improved method for the synthesis of 5-hydroxymethyl-2′-deoxycytidine (5-HOMedC) phosphoramidite for site-specific incorporation into oligonucleotides. To minimize manipulations we employed a temporary protecting group-free 2′-deoxyuridine to 2′-deoxycytidine conversion procedure that utilizes phase transfer catalysis. The desired 5-HOMedC phosphoramidite is obtained in six steps and 24% overall yield from 2′-deoxyuridine.
- Hansen, Anders S.,Thalhammer, Armin,El-Sagheer, Afaf H.,Brown, Tom,Schofield, Christopher J.
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p. 1181 - 1184
(2011/04/16)
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- Modified 5'-Trityl Nucleosides as Inhibitors of Plasmodium falciparum dUTPase
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2'-Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) is a potential drug target for the treatment of malaria. We previously reported the discovery of 5'-tritylated analogues of deoxyuridine as selective inhibitors of this Plasmodium falciparum enzyme. Herein we report further structure-activity studies; in particular, variations of the 5'-trityl group, the introduction of various substituents at the 3'-position of deoxyuridine, and modifications of the base. Compounds were tested against both the enzyme and the parasite. Variations of the 5'-trityl group and of the 3'-substituent were well tolerated and yielded active compounds. However, there is a clear requirement for the uracil base for activity, because modifications of the uracil ring result in loss of enzyme inhibition and significant decreases in antiplasmodial action. Fewer trips to the dUMP: dUTPase is a potential drug target for the treatment of malaria. We previously reported the discovery of 5'-tritylated analogues of deoxyuridine as selective inhibitors of this P.falciparum enzyme. Herein we report further structure-activity studies of the 5'-trityl group, the introduction of various substituents at the 3'-position of deoxyuridine, and modifications of the base.
- Ruda, Gian Filippo,Nguyen, Corinne,Ziemkowski, Przemyslaw,Felczak, Krzysztof,Kasinathan, Ganasan,Musso-Buendia, Alexander,Sund, Christian,Zhou, Xiao Xiong,Kaiser, Marcel,Ruiz-Perez, Luis M.,Brun, Reto,Kulikowski, Tadeusz,Johansson, Nils Gunnar,Gonzalez-Pacanowska, Dolores,Gilbert, Ian H.
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experimental part
p. 309 - 320
(2012/01/12)
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- PROCESS FOR PREPARING DISULPHIDES AND THIOSULPHINATES AND COMPOUNDS PREPARED
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Process for preparing a compound of the formula (I) R1-S(O)x—S(O)yR2 in which R1 represents a molecular hydrocarbon radical which can be substituted and/or interrupted by one or more atoms and/or by one or more groups containing one or more atoms, said atoms being selected from N, O, P, S, Si and X, where X represents a halogen; R2, independently of R1, represents a carbon-containing group or a molecular hydrocarbon radical which can be substituted and/or interrupted by one or more atoms and/or by one or more groups containing one or more atoms, said atoms being selected from N, O, P, S, Si and X, where X represents a halogen, and x and y are selected from 0 and 1 in such a way that the sum of x and y is not more than 1, characterized in that a compound of formula (II) R1-S(O)x—R3-Si(R4)(R5)(R6) in which R3 represents a hydrocarbon chain of two carbon atoms, which is optionally unsaturated and/or substituted, and R4, R5 and R6, which are identical or different, each represent, independently of one another, a hydrocarbon group, is reacted with a compound of formula (VII) R2-S(O)y—X in which X represents a halogen, intermediate compounds, and compounds prepared.
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-
Page/Page column 29
(2009/10/30)
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- Anti-retroviral and cytostatic activity of 2′,3′-dideoxyribonucleoside 3′-disulfides
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Herein, we report the synthesis, antiviral and cytostatic effects of nucleosides bearing a 3′-disulfide function as prodrugs of potentially active 3′-mercaptonucleotides. The lack of the anti-HIV effects in mutant CEM/TK-cells for most of the thymidine disulfides suggests that a phosphorylation step involving thymidine kinase is necessary for the eventual antiviral activity of the thymidine nucleosides. The comparable anti-HIV activities of most of the disulfides and their rapid reduction in CEM cell extracts imply an inhibitory effect of the 2′,3′-dideoxy-3′-mercaptothymidine 5′-triphosphate metabolite. The cytostatic effects of the disulfides in CEM/0 and Molt4/C8 cells appeared to be strongly dependent on the nature of the non-nucleosidic disulfide moiety and were decreased in preserving the anti-retroviral activity.
- Gerland, Beatrice,Desire, Jerome,Balzarini, Jan,Decout, Jean-Luc
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p. 6824 - 6831
(2008/12/22)
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- Synthesis of 3′-S-phosphorothiolate oligonucleotides for their potential use in RNA interference
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The potency of RNA interference (RNAi) undoubtedly can be improved through chemical modifications to the small interfering RNAs (siRNA). By incorporation of the 3′-S-phosphorothiolate modification into strands of RNA, it is hoped that specific regions of a siRNA duplex can be stabilised to enhance the target binding affinity of a selected antisense strand into the activated RNA-induced silencing complex (RISC*). Oligonucleotides composed entirely of this modification are desirable so unconventional 5′ → 3′synthesis is investigated, with initial solution-phase testing proving successful. The phosphoroamidite monomer required for solid-phase synthesis has also been produced. Copyright Taylor & Francis Group, LLC.
- Gaynor, James W.,Brazier, John,Cosstick, Rick
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p. 709 - 712
(2008/03/27)
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- Synthesis and mutagenesis of the butadiene-derived N3 2′-deoxyuridine adducts
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1,3-Butadiene is a known carcinogen and mutagen that acts through a variety of metabolic intermediates that react with DNA, forming stable and unstable lesions on dG, dA, dC, and dT. The N3 2′-deoxyuridine adducts are a highly stable, stereoisomeric mixture of adducts derived from the reaction of cytosine with the monoepoxide metabolite of butadiene, followed by spontaneous deamination. In this study, the phosphoramidites and subsequent oligodeoxynucleotides containing the N3 2′-deoxyuridine adducts have been constructed and characterized. Using a single-stranded shuttle vector DNA, the mutagenic potential of these adducts has been tested following replication in mammalian cells. Replication past the N3 2′-deoxyuridine adducts was found to be highly mutagenic with an overall mutation yield of ～97%. The major mutations that were observed were C to T transitions and C to A transversions. In vitro, these adducts posed a complete block to both the Klenow fragment of Escherichia coli polymerase I and polymerase ε, while these lesions significantly blocked polymerase δ. These data suggested a possible involvement of bypass polymerases in the in vivo replication of these lesions. Overall, these findings indicate that the N3 2′-deoxyuridine adducts are highly mutagenic lesions that may contribute to butadiene-mediated carcinogenesis.
- Fernandes, Priscilla H.,Hackfeld, Linda C.,Kozekov, Ivan D.,Hodge, Richard P.,Lloyd, R. Stephen
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p. 968 - 976
(2008/01/27)
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- Stereospecific syntheses of 3'-deuterated pyrimidine nucleosides and their site-specific incorporation into DNA.
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[reaction: see text] 2'-Deoxy-3'-deutero pyrimidines have been synthesized in high yields and incorporated into deoxyoligonucleotides using standard phosphoramidite chemistry. A key synthetic step is a stereospecific reduction of 3'-keto nucleosides using sodium triacetoxyborodeuteride to give 3'-deuterated thymidine and 2'-deoxy uridine nucleosides. Conversion of the corresponding phorphoramidites 7a and 7b to 4-triazolo derivatives has, for the first time, enabled incorporation of 2'-deoxy-3'-deutero cytidine and 2'-deoxy-3'-deutero-5-methyl cytidine into oligonucleotides.
- Chirakul, Panadda,Sigurdsson, Snorri Th
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p. 917 - 919
(2007/10/03)
-
- Synthesis and characterization of DNA duplexes containing an N4C-ethyl-N4C interstrand cross-link
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Short DNA duplexes containing an N4C-ethyl-N4C interstrand cross-link, C-C, were synthesized on controlled pore glass supports. Duplexes having two, three, or four A/T base pairs on either side of the C-C cross-link and terminating with a C4 overhang at their 5′-ends were prepared. The cross-link was introduced using a convertible nucleoside approach. Thus, an oligonucleotide terminating at its 5′-end with O4-triazoyl-2′-deoxyuridine was first prepared on the support. The triazole group of support-bound oligomer was displaced by the aminoethyl group of 5′-dimethoxytrityl-3′-O-tert-butyldimethylsilyl-N4- (2-aminoethyl)deoxycytidine to give the cross-link. The dimethoxytrityl group was removed, and the upper and lower strands of the duplex were extended from two 5′-hydroxyl groups of the cross-link using protected nucleoside 3′-phosphoramidites. The tert-butyldimethylsilyl group of the resulting partial duplex was then removed, and the chain was extended in the 3′-direction from the resulting 3′-hydroxyl of the cross-link using protected nucleoside 5′-phosphoramidites. The cross-linked duplexes were purified by HPLC and characterized by enzymatic digestion and MALDITOF mass spectrometry. Duplexes with three or four A/T base pairs on either side of the C-C cross-link gave sigmoidal shaped A260 profiles when heated, a behavior consistent with cooperative denaturation of the A/T base pairs. Each cross-linked duplex could be ligated to an acceptor duplex using T4 DNA ligase, a result that suggests that the C-C cross-link does not interfere with the ligation reaction, even when it is located only two base pairs from the site of ligation. The ability to synthesize duplexes with a defined interstrand cross-link and to incorporate these duplexes into longer pieces of DNA should enable preparation of substrates that can be used for a variety of biophysical and biochemical experiments, including studies of DNA repair.
- Noll,Noronha,Miller
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p. 3405 - 3411
(2007/10/03)
-
- New carbamate supports for the preparation of 3'-amino-modified oligonucleotides
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A novel approach for the preparation of oligonucleotides carrying amino groups at the 3'-end is described. Several CPG supports having aminoalkyl groups and 3'-amino-2',3'-dideoxynucleosides linked through base-labile carbamate linkages such as 2-(2- nitrophenyl)ethoxycarbonyl and fluorenylmethoxycarbonyl were prepared using two different strategies. These supports are compatible to the standard solid phase phosphite-triester methodology and yield oligonucleotides containing amino groups at the 3'-end. Several properties of the 3'-amino oligonucleotides, such as nuclease resistance, hybridization, and preparation of oligonucleotide conjugates are discussed.
- Avino, Anna,Garcia, Ramon Gueimil,Albericio, Fernando,Mann, Matthias,Wilm, Matthias,Neubauer, Gitte,Eritja, Ramon
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p. 1649 - 1658
(2007/10/03)
-
- Oligodeoxyribonucleotides covalently linked via nucleic bases with 3'-5' and 5'-5' polarities
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The solid-phase preparation of oligodeoxyribonucleotides covalently linked via nucleic bases with normal (3'-5') or inverted (5'-5') polarities is reported. The key-step of these syntheses is the preparation of the tethered dimers.
- Asseline,Thuong
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p. 889 - 893
(2007/10/02)
-
- 5'-5' tethered oligonucleotides via nucleic bases: A potential new set of compounds for alternate strand triple-helix formation
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The solid-phase synthesis of 5'-5'-linked oligonucleotides tethered via nucleic bases and with opposite polarities has been performed using a modified dinucleoside bearing a phosphoramidite group at the 3'-position of one nucleoside and a dimethoxytrityl group at the 3'-position of the second nucleoside.
- Asseline,Thuong
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p. 5221 - 5224
(2007/10/02)
-
- Synthesis of 4'-cyanothymidine and analogs as potent inhibitors of HIV
-
4'-Cyanothymidine inhibits HIV in A301 (Alex) cells with an IC50 of 0.002 μM. The uridine and cytidine analogs show similar potencies.
- O-Yang,Wu,Fraser-Smith,Walker
-
-
- Synthesis and Properties of Phosphoramidite Derivatives of Modified Nucleosides
-
Protected N6-methyl-2'-deoxyadenosine (d-m6A), 2-amino-2'-deoxyadenosine (d-a2A), 2'-deoxyinosine (dI), 5-methyl-2'-deoxycytidine (d-m5C) and deoxyuridine (dU) were reacted with bis(diisopropylamino)methoxyphosphine in the presence of diisopropylammonium tetrazolide as the activating reagent to give the corresponding phosphoramidite derivatives in yields of 100, 65, 90, 78 and 65 percent respectively.The 31P-nuclear magnetic resonance spectra of the products were measured.Using these compounds, dinucleotides and trinucleotides were synthesized on a longchain alkylamine controlled pore glass (LCA-CPG) in quantitative yields.The stability of 6-methyldeoxyadenosine and N,N-diisobutyryl-2-aminodeoxyadenosine to acid was examined.When protected di- and trinucleotides (m6A-T, a2A-T, T-m6A-T, T-a2A-T) bound to the support (LCA-CPG) were treated with 3 percent trichloroacetic acid in dichloromethane, depurination was negligible within 10 min (dinucleotide) or 60 min (trinucleotide).Keywords - phosphoramidite; solid-phase synthesis; phosphite method; acid treatment; enzyme degradation
- Tanaka, Toshiki,Tamatsukuri, Sigeru,Ikehara, Morio
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p. 2044 - 2048
(2007/10/02)
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