- An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2′-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate
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5-Hydroxymethyl-2′-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are
- Chen, Zhen-Zhen,Chi, Mei,Dong, Ying-Ying,Pu, Shou-Zhi,Sun, Qi,Yang, Dong-Zhao
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- SYNTHESIS AND IMPROVEMENT OF A NUCLEOSIDE ANALOGUE AS AN ANTI-CANCER AND ANTI-VIRAL DRUG
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The invention is a drug for anticancer and antiviral therapy, comprising a nucleoside analogue (7) comprising a furan ring irreversibly bound to the RNA/DNA synthesis chain by phosphodiester bonds and having SP3 hybridization, and folic acid (A) bound to the nucleoside analogue (7) comprising furan ring. The synthesis method of the said nucleoside analogue is also contained within the scope of the invention. In this work, a nucleoside-analogue was transformed after converting the furan-ring hybridization from Sp2 to Sp3 to make it more selectivity with different enzymes and linking it via site 5 with the effective folic acid towards entering the substances inside the cells and to become the final compound possessing anti-cancer and anti- virus properties after controlling the replication and reproduction process in DNA.
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Page/Page column 7; 13
(2021/05/29)
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- Biochemical characterization of a recombinant acid phosphatase from Acinetobacter baumannii
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Genomic sequence analysis of Acinetobacter baumannii revealed the presence of a putative Acid Phosphatase (AcpA; EC 3.1.3.2). A plasmid construct was made, and recombinant protein (rAcpA) was expressed in E. coli. PAGE analysis (carried out under denaturing/ reducing conditions) of nickel-affinity purified protein revealed the presence of a nearhomogeneous band of approximately 37 kDa. The identity of the 37 kDa species was verified as rAcpA by proteomic analysis with a molecular mass of 34.6 kDa from the deduced sequence. The dependence of substrate hydrolysis on pH was broad with an optimum observed at 6.0. Kinetic analysis revealed relatively high affinity for PNPP (Km = 90 μM) with Vmax, kcat, and Kcat/Km values of 19.2 pmoles s-1, 4.80 s-1(calculated on the basis of 37 kDa), and 5.30 × 104 M-1s-1, respectively. Sensitivity to a variety of reagents, i.e., detergents, reducing, and chelating agents as well as classic acid phosphatase inhibitors was examined in addition to assessment of hydrolysis of a number of phosphorylated compounds. Removal of phosphate from different phosphorylated compounds is supportive of broad, i.e., 'nonspecific' substrate specificity; although, the enzyme appears to prefer phosphotyrosine and/or peptides containing phosphotyrosine in comparison to serine and threonine. Examination of the primary sequence indicated the absence of signature sequences characteristic of Type A, B, and C nonspecific bacterial acid phosphatases.
- Smiley-Moreno, Elizabeth,Smith, Douglas,Yu, Jieh-Juen,Cao, Phuong,Arulanandam, Bernard P.,Chambers, James P.
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- Meteorite-catalyzed intermoleculartrans-glycosylation produces nucleosides under proton beam irradiation
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Di-glycosylated adenines act as glycosyl donors in the intermoleculartrans-glycosylation of pyrimidine nucleobases under proton beam irradiation conditions. Formamide and chondrite meteorite NWA 1465 increased the yield and the selectivity of the reaction
- Bizzarri, Bruno Mattia,Fanelli, Angelica,Kapralov, Michail,Krasavin, Eugene,Saladino, Raffaele
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p. 19258 - 19264
(2021/06/03)
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- Spacer-Mediated Control of Coumarin Uncaging for Photocaged Thymidine
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Despite its importance in the design of photocaged molecules, less attention is focused on linker chemistry than the cage itself. Here, we describe unique uncaging properties displayed by two coumarin-caged thymidine compounds, each conjugated with (2) or without (1) an extended, self-immolative spacer. Photolysis of 1 using long-wavelength UVA (365 nm) or visible (420, 455 nm) light led to the release of free thymidine along with the competitive generation of a thymidine-bearing recombination product. The occurrence of this undesired side reaction, which is previously unreported, was not present with the photolysis of 2, which released thymidine exclusively with higher quantum efficiency. We propose that the spatial separation between the cage and the substrate molecule conferred by the extended linker can play a critical role in circumventing this unproductive reaction. This report reinforces the importance of linker selection in the design of coumarin-caged oligonucleosides and other conjugates.
- Baker, James R.,Cannon, Jayme,Choi, Seok Ki,Krummel, Matthew F.,Tang, Shengzhuang,Yang, Kelly
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- RETRACTED ARTICLE: Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases
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Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.
- Tran, Ai,Zheng, Song,White, Dawanna S.,Curry, Alyson M.,Cen, Yana
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p. 11818 - 11826
(2020/11/18)
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- Method for preparing beta-thymidine by adopting solid acid catalysis
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The invention relates to a method for preparing beta-thymidine by adopting solid acid catalysis. The method includes the following steps: the toluene feed liquid of intermediate bromide is obtained by5-methyluridine and [1] under the action of a solid acid and a phase transfer catalyst; and reduction reaction is performed on the toluene feed liquid of the intermediate bromide by using a palladium-carbon catalyst under characteristic environments, and the beta-thymidine is generated through post-treatment crystallization. The method is controllable in reaction condition, high in yield, low incost and suitable for industrial production, and has industrial application value.
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Paragraph 0016-0017
(2020/07/15)
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- Thermodynamic Reaction Control of Nucleoside Phosphorolysis
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Nucleoside analogs represent a class of important drugs for cancer and antiviral treatments. Nucleoside phosphorylases (NPases) catalyze the phosphorolysis of nucleosides and are widely employed for the synthesis of pentose-1-phosphates and nucleoside analogs, which are difficult to access via conventional synthetic methods. However, for the vast majority of nucleosides, it has been observed that either no or incomplete conversion of the starting materials is achieved in NPase-catalyzed reactions. For some substrates, it has been shown that these reactions are reversible equilibrium reactions that adhere to the law of mass action. In this contribution, we broadly demonstrate that nucleoside phosphorolysis is a thermodynamically controlled endothermic reaction that proceeds to a reaction equilibrium dictated by the substrate-specific equilibrium constant of phosphorolysis, irrespective of the type or amount of NPase used, as shown by several examples. Furthermore, we explored the temperature-dependency of nucleoside phosphorolysis equilibrium states and provide the apparent transformed reaction enthalpy and apparent transformed reaction entropy for 24 nucleosides, confirming that these conversions are thermodynamically controlled endothermic reactions. This data allows calculation of the Gibbs free energy and, consequently, the equilibrium constant of phosphorolysis at any given reaction temperature. Overall, our investigations revealed that pyrimidine nucleosides are generally more susceptible to phosphorolysis than purine nucleosides. The data disclosed in this work allow the accurate prediction of phosphorolysis or transglycosylation yields for a range of pyrimidine and purine nucleosides and thus serve to empower further research in the field of nucleoside biocatalysis. (Figure presented.).
- Kaspar, Felix,Giessmann, Robert T.,Neubauer, Peter,Wagner, Anke,Gimpel, Matthias
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p. 867 - 876
(2020/01/24)
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- RETRACTED ARTICLE: Convenient synthesis of pyrimidine 2′-deoxyribonucleoside monophosphates with important epigenetic marks at the 5-position
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Methyl groups of thymine and 5-methylcytosine (5mC) bases in DNA undergo endogenous oxidation damage. Additionally, 5mC residues can be enzymatically deaminated or oxidized through either genetic alterations or the newly identified epigenetic reprogramming pathway. Several methods have been developed to measure the formation of modified DNA nucleobases including 32P-postlabeling. However, the postlabeling method is often limited by the absence of authentic chemical standards. The synthesis of monophosphate standards of nucleotide oxidation products is complicated by the presence of additional functional groups on the modified bases that require complex protection and deprotection strategies. Due to the emerging interest in the pyrimidine oxidation products, the corresponding protected 3′-phosphoramidites needed for solid-phase oligonucleotide synthesis have been reported, and several are commercially available. We report here an efficient synthesis of 3′-monophosphates from 3′-phosphoramidites and the subsequent enzymatic conversion of 3′-monophosphates to the corresponding 5′-monophosphates using commercially available enzymes. This journal is
- Zheng, Song,Tran, Ai,Curry, Alyson M.,White, Dawanna S.,Cen, Yana
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p. 5164 - 5173
(2020/07/23)
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- Tuning the stability of alkoxyisopropyl protection groups
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Five different 2-alkoxypropan-2-yl groups are introduced as acid-labile protecting groups for the 5’- and 3’-hydroxy groups of a 2’-deoxynucleoside. All studied protecting groups were readily introduced with good to excellent yields using the appropriate enol ether as a reagent and 0.5 to 1 mol % p-toluenesulfonic acid as a catalyst. The protected compounds could be purified by silica gel column chromatography without degradation. The compatibility of these protecting groups in parallel use with benzoyl and silyl groups was verified. The stabilities of the different alkoxy acetal protecting groups were compared by following the kinetics of their hydrolysis at 25.0 °C in buffered solutions through an HPLC method. In the pH range 4.94 to 6.82 the hydrolysis reactions are of first order in the hydronium ion. The rate of hydrolysis correlates with the electron-donating or electron-withdrawing ability of the corresponding alkoxy group. The studied 2-alkoxypropan-2-yl groups and the relative rate constants for their cleavage from the 5’-hydroxy group of 2’-deoxythymidine were: cyclohexyloxy (krel = 7.7), isopropoxy (7.4), methoxy (1), benzyloxy (0.6) and 2,2,2-trifluoroethyloxy (0.04). The attachment of the same groups to the 3’-hydroxy group are from 1.3 to 1.9-fold more stable. The most reactive of these acetone-based acetal groups are faster removed than a dimethoxytrityl group, and they are easier to cleave completely in solution. The structural variation allows steering of the stability and lipophilicity of the compounds in some range.
- Liang, Zehong,Koivikko, Henna,Oivanen, Mikko,Heinonen, Petri
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p. 746 - 751
(2019/04/17)
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- ORTHOESTER COMPOSITIONS FOR AFFINITY PURIFICATION OF OLIGONUCLEOTIDES
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Compounds and methods for purifying oligonucleotides such as RNA and DNA. A target oligonucleotide is reacted with an orthoester linker comprising an affinity tag to form an orthoester oligonucleotide-orthoester linker conjugate which is subjected to a purification technique to separate the target oligonucleotide from impurities such as truncated oligonucleotides. The orthoester linker can be then removed under mild conditions to generate the target oligonucleotide in high purity.
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Paragraph 00298
(2019/03/05)
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- Identification of Flavin Mononucleotide as a Cell-Active Artificial N6-Methyladenosine RNA Demethylase
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N6-Methyladenosine (m6A) represents a common and highly dynamic modification in eukaryotic RNA that affects various cellular pathways. Natural dioxygenases such as FTO and ALKBH5 are enzymes that demethylate m6A residues in mRNA. Herein, the first identification of a small-molecule modulator that functions as an artificial m6A demethylase is reported. Flavin mononucleotide (FMN), the metabolite produced by riboflavin kinase, mediates substantial photochemical demethylation of m6A residues of RNA in live cells. This study provides a new perspective to the understanding of demethylation of m6A residues in mRNA and sheds light on the development of powerful small molecules as RNA demethylases and new probes for use in RNA biology.
- Xie, Li-Jun,Yang, Xiao-Ti,Wang, Rui-Li,Cheng, Hou-Ping,Li, Zhi-Yan,Liu, Li,Mao, Lanqun,Wang, Ming,Cheng, Liang
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supporting information
p. 5028 - 5032
(2019/03/17)
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- Hydrogen peroxide-Triggered gene silencing in mammalian cells through boronated antisense oligonucleotides
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Hydrogen peroxide (H2O2) is a reactive oxygen species (ROS) involved in various diseases, including neurodegeneration, diabetes, and cancer. Here, we introduce a new approach to use H2O2 to modulate specific gene expression in mammalian cells. H2O2-responsive nucleoside analogues, in which the Watson-Crick faces of the nucleobases are caged by arylboronate moieties, were synthesized. One of these analogues, boronated thymidine (dTB), was incorporated into oligodeoxynucleotides (ODNs) using an automated DNA synthesizer. The hybridization ability of this boronated ODN to complementary RNA was clearly switched in the off-To-on direction upon H2O2 addition. Furthermore, we demonstrated H2O2-Triggered gene silencing in mammalian cells using antisense oligonucleotides (ASOs) modified with dTB. Our approach can be used for the regulation of any gene of interest by the sequence design of boronated ASOs and will contribute to the development of targeted disease therapeutics.
- Mori, Shohei,Morihiro, Kunihiko,Okuda, Takumi,Kasahara, Yuuya,Obika, Satoshi
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p. 1112 - 1118
(2018/02/09)
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- Potential of 4-thiothymidine as a molecular probe for H2O2 in systems related to PhotoDynamic therapy: A structuristic and mechanistic insight by UV–visible and FTIR-ATR spectroscopies and by ElectroSpray ionization mass spectrometry
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An investigation, based on the synergy between UV–Vis and FTIR-ATR spectroscopies and ElectroSpray Ionization Mass Spectrometry (ESI-MS), on the reactivity of 4-thiothymidine (S4-TdR) with H2O2, selected as a Reactive Oxyg
- Rizzi, Vito,Losito, Ilario,Abbattista, Ramona,Fini, Paola,Agostiano, Angela,Cataldi, Tommaso R.I.,Cosma, Pinalysa
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p. 398 - 409
(2018/05/28)
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- A Practical Method for Regioselective 5′-O-tert-Butyldimethylsilyl Deprotection of Persilylated Nucleosides by Methanolic Phosphomolybdic Acid
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In nucleoside/nucleotide chemistry, the regioselective cleavage of 5′-O-TBS groups of persilylated nucleosides is a desired approach for structural functionalization at the 5′-position. However, efficient and practical methods for this purpose are still limited. In our research, we found that homogeneous methanolic phosphomolybdic acid (PMA) efficiently catalyzes the regioselective deprotection of 5′- O -TBS groups of a diversity of persilylated nucleoside substrates and can be applied in practical synthesis at scales of up to 15 g. 31 P NMR results indicated that an anion cluster forms and the Lewis acidity of homogeneous PMA is organic-solvent dependent. The efficacy and pronounced regioselectivity of methanolic PMA occurs as a result of a lowering of the Lewis acid strength upon solvation of the molybdophosphate anions.
- Huang, Hua-Shan,Kong, Rui,Zheng, Xiu-An,Chen, Wei-Jie,Han, Shuai-Bo,Zeng, De-Yun,Gong, Shan-Shan,Sun, Qi
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supporting information
p. 2437 - 2443
(2018/11/23)
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- Photoredox-Catalyzed Deformylative 1,4-Addition of 2′-Deoxy-5′- O-phthalimidonucleosides for Synthesis of 5′-Carba Analogs of Nucleoside 5′-Phosphates
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A concise approach for the synthesis of the 5′-carba analogs of nucleoside 5′-phosphates from 2′-deoxy-5′-O-phthalimidonucleosides by a visible-light-mediated deformylative 1,4-addition was developed. This method enabled rapid and facile generation of 4′-carbon radicals of nucleosides. Moreover, this synthetic strategy was applicable to the 5′-carba analogs of nucleoside 5′-phosphates as well as other 5′-carba nucleosides bearing methoxycarbonyl, cyano, and N-methylsulfamoyl groups.
- Ito, Yuta,Kimura, Airi,Osawa, Takashi,Hari, Yoshiyuki
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p. 10701 - 10708
(2018/09/21)
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- REVERSIBLY BLOCKED NUCLEOSIDE ANALOGUES AND THEIR USE
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Reversibly blocked nucleoside analogues and methods of using such nucleoside analogues for sequencing of nucleic acids are provided.
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- AZIDOMETHYL ETHER DEPROTECTION METHOD
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The invention relates to a method of converting an azidomethyl ether substituent to a free hydroxyl group. The invention also relates tomethods of nucleic acid synthesis and sequencing comprising the use of nucleotide triphosphates having a 3'-O-azidomethyl substituent, to kitscomprising nucleotide triphosphates having a 3'-O-azidomethyl substituent and photoactivatable transition metal complex and to the use of said kits in methods of nucleic acid synthesis and sequencing.
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Page/Page column 15
(2017/02/09)
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- Enzymatic synthesis of ribo- and 2′-deoxyribonucleosides from glycofuranosyl phosphates: An approach to facilitate isotopic labeling
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Milligram quantities of α-D-ribofuranosyl 1-phosphate (sodium salt) (αR1P) were prepared by the phosphorolysis of inosine, catalyzed by purine nucleoside phosphorylase (PNPase). The αR1P was isolated by chromatography in >95% purity and characterized by 1H and 13C NMR spectroscopy. Aqueous solutions of αR1P were stable at pH 6.4 and 4 °C for several months. The isolated αR1P was N-glycosylated with different nitrogen bases (adenine, guanine and uracil) using PNPase or uridine phosphorylase (UPase) to give the corresponding ribonucleosides in high yield based on the glycosyl phosphate. This methodology is attractive for the preparation of stable isotopically labeled ribo- and 2′-deoxyribonucleosides because of the ease of product purification and convenient use and recycling of nitrogen bases. The approach eliminates the need for separate reactions to prepare individual furanose-labeled ribonucleosides, since only one ribonucleoside (inosine) needs to be labeled, if desired, in the furanose ring, the latter achieved by a high-yield chemical N-glycosylation. 2′-Deoxyribonucleosides were prepared from 2′-deoxyinosine using the same methodology with minor modifications.
- Zhang, Wenhui,Turney, Toby,Surjancev, Ivana,Serianni, Anthony S.
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p. 125 - 133
(2017/08/08)
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- Methyl ketone derivative, and preparation method and applications thereof
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The invention discloses a methyl ketone derivative, and a preparation method and applications thereof. The preparation method comprises following steps: a ketone derivative and an organic peroxide are dissolved in a solvent, and reaction is carried out at 80 to 130 DEG C so as to obtain methyl pyrimidone and a methyl pyrimidone derivative. According to the preparation method, the ketone derivative is taken as a starting material; the raw materials are easily and widely available; products of different kinds can be obtained via the preparation method, and can be used directly or used in other further reaction. No metal is involved, so that the preparation method is suitable to be applied in pharmaceutical preparation technology. The preparation method is short in route, mild in reaction conditions, simple in reaction operation and postprocessing process, and high in yield, and is suitable for large-scale production.
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Paragraph 0046; 0047
(2017/08/28)
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- Synthesis method of beta-thymidine
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The invention discloses a synthesis method of beta-thymidine. The synthesis method takes trimethylchlorosilane and 5-methyluracil as raw materials to react; in a reaction line process, tetraacetylribose, trifluoromethanesulfonic acid, N,N-dimethylformamide and acetylchloride are introduced; then hydrogenation reaction and hydrolysis reaction are carried out to finally obtain a beta-thymidine finished product and the yield is 89 percent. Compared with an existing synthesis method, the synthesis method of the beta-thymidine has the advantages that the price of raw materials is low, the content of the beta-thymidine in the final product is high, and pollution to the environment in a production process is small; in a synthesis process, the content of generated impurities is less. According to the synthesis method disclosed by the invention, an obtained result is stable and the operation is simple; demands on equipment and preparation environments are not strict so that large-scale popularization is facilitated.
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- Method for preparing β-thymidine
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The invention relates to a preparation method of beta-thymidine, and specifically discloses a method of preparing beta-thymidine from the formula II compound. The method comprises following steps: subjecting the compound represented as the formula II to carry out dehalogenation reactions, in a hydrogen atmosphere, in the presence of a catalyst, and in a buffer system with a pH value of 6.5 to 8.0, so as to obtain beta-thymidine represented as the formula I, wherein X represents Cl or Br. The dehalogenation reactions are carried out under atmospheric pressure, and the preparation method has the advantages of environment-friendliness, economy, high product yield, good product purity, and suitability for industrial production.
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Paragraph 0102-0107
(2018/02/04)
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- Method for preparing Thymidine
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The invention discloses a method for preparing Thymidine as shown in a formula (IV). The method comprises the following step of performing a three-step reaction of dehydration, halogenation and reduction on ribothymidine as shown in a formula (I) according to the following chemical equation so as to obtain the Thymidine as shown in a formula (IV), wherein the three-step reaction of dehydration, halogenation and reduction is completed by a one-pot method. The method for preparing the Thymidine disclosed by the invention is simple to operate, low in cost of human resources and low in equipment investment, the production cycle is substantially shortened, and the method is suitable for industrialized mass production and has wide application prospects.
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Paragraph 0025; 0026; 0027; 0028; 0029; 0030; 0031-0037
(2017/02/24)
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- Efficient and green approach for the complete deprotection of O-acetylated biomolecules
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A simple, efficient and mild strategy for the complete O-deacetylation of different per-acetylated biomolecules in aqueous media has been described. Different lipases were tested but only the commercial Amano lipase A from Aspergillus Niger catalyzed the complete deprotection of peracetylated α-glucose to glucose in excellent yield. The experimental conditions were tested, in particular the pH effect. The reaction was performed at different pHs considering the only enzymatic process was evaluated at pH 5 and the combination of enzymatic and chemical migration process was evaluated at higher pHs. Finally pH 7 and 25 °C were selected as best conditions. Thus this lipase fully hydrolyzed different peracetylated α-glycopyranosides (glucose, mannose, glucal, galactal) with >99% yields, whereas very good deprotecting yields (75-80%) were achieved for different acetylated β-glycopyranosides (galactose, ribofuranose) under these mild conditions. This strategy was successfully extended to the fully O-selective deprotection of acetylated nucleosides where >99% yield was rapidly obtained. No selectivity was observed for the N-deacetylation in amino acids and peptides.
- Dunne, Anthony,Palomo, Jose M.
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p. 88974 - 88978
(2016/10/03)
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- Method for preparing high-purity telbivudine compound
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The invention belongs to the technical field of medicine and provides a method for preparing a high-purity telbivudine compound. The method includes the steps that an LTD-4 compound serves as the raw material and reacts with thymine subjected to silicification protection, and an intermediate, namely an LTD-5 compound, can be obtained; then, through deprotection reaction, the telbivudine compound is obtained after post-processing, wherein MeONa serves as an alkaline reagent of the deprotection reaction, and strong-acidity resin serves as a dealkalization reagent. The method simplifies the production process, the yield of each step is high, and a target product high in purity and yield is obtained. Please see the structural formula in the description.
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Paragraph 0046; 0047
(2017/01/02)
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- METHODS FOR THE TREATMENT OF HEPATITIS B AND HEPATITIS D VIRUS INFECTIONS
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It is disclosed a method for treating hepatitis B virus infection or hepatitis B virus/hepatits delta virus co-infection, the method comprising administering to a subject in need of such treatment a first pharmaceutically acceptable agent that comprises at least one phosphorothioated nucleic acid polymer and a second pharmaceutically acceptable agent that comprises at least one nucleoside/nucleotide analog HBV polymerase inhibitor.
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- Method for preparing telbivudine
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The invention relates to a method for preparing telbivudine. The reaction mechanism is as shown in the specification specifically. Compared with a method of the prior art, the method provided by the invention has the advantages that firstly, all raw materials are low in cost and can be easily obtained from the market; secondly, reaction of different steps is normal reaction, and the reaction steps are simple and easy to implement; and thirdly, production requirements can be met by using normal preparation equipment, the production is easy to control, and industrial production can be achieved.
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-
Paragraph 0052; 0053; 0054
(2016/10/09)
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- PRODUCTION METHOD OF NUCLEOSIDE COMPOUND
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PROBLEM TO BE SOLVED: To provide a production method of a nucleoside compound by which an isotopic labeled nucleoside compound can be produced efficiently. SOLUTION: A production method of a nucleoside compound comprises obtaining a target nucleoside compound by the base exchange reaction of a raw material nucleoside compound and a base in the solution containing a phosphoric acid ion by a nucleoside phosphorylase, wherein the target nucleoside compound is labeled with a stable isotope or a radioisotope. COPYRIGHT: (C)2015,JPOandINPIT
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- Rose Bengal-photosensitized oxidation of 4-thiothymidine in aqueous medium: evidence for the reaction of the nucleoside with singlet state oxygen
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The photoreactivity of 4-thiothymidine (S4TdR) under visible light in the presence of Rose Bengal (RB), acting as a photosensitizer, was investigated in aqueous solutions at pH 7 and 12, using UV-vis, FTIR-ATR and 1H-NMR spectroscopic techniques, time resolved absorption spectroscopy and electrospray ionization mass spectrometry (ESI-MS). Evidence for the generation of thymidine (TdR) as the main product, after one hour of irradiation, was obtained from UV-Vis data, that suggested 4-thiothymidine photodegradation to be faster at basic pH, and confirmed by FTIR-ATR and 1H-NMR data. Clues for the presence of a further product, likely corresponding to a dimeric form of S4TdR, were obtained from the latter techniques. Besides indicating the presence of thymidine, the ESI-MS and MS/MS spectra of the reaction mixtures enabled the identification of the additional product as a S-S bridged covalent dimer of 4-thiothymidine. The concentration of the dimeric species could be estimated with the aid of 1H-NMR data and was found to be lower than that of thymidine in pH 7 reaction mixtures and almost negligible in the pH 12 ones. From a mechanistic point of view, time-resolved absorption spectroscopy measurements provided direct evidence that the formation of the two products cannot be ascribed to a photoinduced electron transfer involving S4TdR and the excited triplet state of RB. Rather, their generation can be interpreted as the result of a bimolecular reaction occurring between singlet state oxygen (1O2), photogenerated by RB, and S4TdR, as demonstrated by the direct detection of 1O2 through IR luminescence spectroscopy. More specifically, a sequential reaction pathway, consisting in the generation of an electrophilic hydroxylated form of S4TdR and its subsequent, rapid reaction with S4TdR, was hypothesized to explain the presence of the S-S bridged covalent dimer of 4-thiothymidine in the reaction mixtures. The described processes make S4TdR an interesting candidate in the role of molecular probe for the detection of 1O2 under different pH conditions.
- Rizzi, Vito,Losito, Ilario,Ventrella, Andrea,Fini, Paola,Fraix, Aurore,Sortino, Salvatore,Agostiano, Angela,Longobardi, Francesco,Cosma, Pinalysa
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p. 26307 - 26319
(2015/10/12)
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- Nucleotides and nucleosides and methods for their use in DNA sequencing
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The present invention relates generally to labeled and unlabled cleavable terminating groups and methods for DNA sequencing and other types of DNA analysis. More particularly, the invention relates in part to nucleotides and nucleosides with chemically cleavable, photocleavable, enzymatically cleavable, or non-photocleavable groups and methods for their use in DNA sequencing and its application in biomedical research.
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Page/Page column 147
(2015/12/18)
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- Efficacy and site specificity of hydrogen abstraction from DNA 2-deoxyribose by carbonate radicals
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The carbonate radical anion CO3?- is a potent reactive oxygen species (ROS) produced in vivo through enzymatic one-electron oxidation of bicarbonate or, mostly, via the reaction of CO2 with peroxynitrite. Due to the vitally essential role of the carbon dioxide/bicarbonate buffer system in regulation of physiological pH, CO3?- is arguably one of the most important ROS in biological systems. So far, the studies of reactions of CO3?- with DNA have been focused on the pathways initiated by oxidation of guanines in DNA. In this study, low-molecular products of attack of CO3?- on the sugar-phosphate backbone in vitro were analyzed by reversed phase HPLC. The selectivity of damage in double-stranded DNA (dsDNA) was found to follow the same pattern C4′ > C1′ > C5′ for both CO3?- and the hydroxyl radical, though the relative contribution of the C1′ damage induced by CO3?- is substantially higher. In single-stranded DNA (ssDNA) oxidation at C1′ by CO3?- prevails over all other sugar damages. An approximately 2000-fold preference for 8-oxoguanine (8oxoG) formation over sugar damage found in our study identifies CO3?- primarily as a one-electron oxidant with fairly low reactivity toward the sugar-phosphate backbone.
- Roginskaya, Marina,Moore,Ampadu-Boateng,Razskazovskiy
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p. 1431 - 1437
(2015/11/09)
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- Nucleoside 2′-deoxyribosyltransferase from psychrophilic bacterium Bacillus psychrosaccharolyticus - Preparation of an immobilized biocatalyst for the enzymatic synthesis of therapeutic nucleosides
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Nucleoside 2′-deoxyribosyltransferase (NDT) from the psychrophilic bacterium Bacillus psychrosaccharolyticus CECT 4074 has been cloned and produced for the first time. A preliminary characterization of the recombinant protein indicates that the enzyme is an NDT type II since it catalyzes the transfer of 2′-deoxyribose between purines and pyrimidines. The enzyme (BpNDT) displays a high activity and stability in a broad range of pH and temperature. In addition, different approaches for the immobilization of BpNDT onto several supports have been studied in order to prepare a suitable biocatalyst for the one-step industrial enzymatic synthesis of different therapeutic nucleosides. Best results were obtained by adsorbing the enzyme on PEI-functionalized agarose and subsequent cross-linking with aldehyde-dextran (20 kDa and 70% oxidation degree). The immobilized enzyme could be recycled for at least 30 consecutive cycles in the synthesis of 2′-deoxyadenosine from 2′-deoxyuridine and adenine at 37 °C and pH 8.0, with a 25% loss of activity. High conversion yield of trifluridine (64.4%) was achieved in 2 h when 20 mM of 2′-deoxyuridine and 10 mM 5-trifluorothymine were employed in the transglycosylation reaction catalyzed by immobilized BpNDT at 37 °C and pH 7.5.
- Fresco-Taboada, Alba,Serra, Immacolata,Fernandez-Lucas, Jesus,Acebal, Carmen,Arroyo, Miguel,Terreni, Marco,De La Mata, Isabel
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p. 11231 - 11249
(2014/11/08)
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- Photogenerator of trichloroacetic acid as a promising detritylation agent for oligonucleotide microarray synthesis
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[[4-(4-Methoxyphenyl)-2,6-dinitro-phenyl](phenyl)methyl]-2,2,2-trichloroacetate, which generates trichloroacetic acid when irradiated with light of 405 nm wavelength, has been studied as a detritylation agent in the oligonucleotide microarray synthesis. This agent was shown to be suitable for the deprotection of the 4,4'-dimethoxytrityl group during the solid phase oligonucleotide synthesis.
- Sinyakov, A. N.,Nikolaenkova, E. B.,Os'Kina, I. A.,Savel'Ev, V. A.,Samsonov, V. A.,Tikhonov, A. Y.,Palatkina, M. Yu.,Zaytsev, D. E.
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p. 586 - 588
(2015/02/18)
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- Reductive removal of methoxyacetyl protective group using sodium borohydride
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Herein, we have developed a mild and selective reductive deprotection method for the MAc protected alcohols using sodium borohydride. The new deprotection conditions provide a complete orthogonality between O-MAc and other protecting groups such as tert-butyl ester, N-Boc, Fmoc, Cbz, O-TBDMS, N-benzyl, O-benzyl, O-acetyl, N-acetyl, N-MAc, etc. In addition to O-MAc deprotection, this method is also applicable for S-MAc deprotection.
- Gadekar, Pradip K.,Hoermann, Maryann,Corbo, Faith,Sharma, Rajiv,Sarveswari,Roychowdhury, Abhijit
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p. 503 - 506
(2014/01/06)
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- Mapping structurally defined guanine oxidation products along DNA duplexes: Influence of local sequence context and endogenous cytosine methylation
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DNA oxidation by reactive oxygen species is nonrandom, potentially leading to accumulation of nucleobase damage and mutations at specific sites within the genome. We now present the first quantitative data for sequence-dependent formation of structurally defined oxidative nucleobase adducts along p53 gene-derived DNA duplexes using a novel isotope labeling-based approach. Our results reveal that local nucleobase sequence context differentially alters the yields of 2,2,4-triamino-2H-oxal-5-one (Z) and 8-oxo-7,8-dihydro-2′- deoxyguanosine (OG) in double stranded DNA. While both lesions are overproduced within endogenously methylated MeCG dinucleotides and at 5′ Gs in runs of several guanines, the formation of Z (but not OG) is strongly preferred at solvent-exposed guanine nucleobases at duplex ends. Targeted oxidation of MeCG sequences may be caused by a lowered ionization potential of guanine bases paired with MeC and the preferential intercalation of riboflavin photosensitizer adjacent to MeC:G base pairs. Importantly, some of the most frequently oxidized positions coincide with the known p53 lung cancer mutational hotspots at codons 245 (GGC), 248 (CGG), and 158 (CGC) respectively, supporting a possible role of oxidative degradation of DNA in the initiation of lung cancer.
- Ming, Xun,Matter, Brock,Song, Matthew,Veliath, Elizabeth,Shanley, Ryan,Jones, Roger,Tretyakova, Natalia
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p. 4223 - 4235
(2014/04/03)
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- Regioselective mono-deprotection of di-ferf-butylsilylene acetal derived from 1,3-diol with ammonium fluoride
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Here we report a novel and efficient method for the regioselective mono-deprotection of di-terf-butylsilylene acetals derived from 1,3-diols consisting of primary and secondary alcohols. The ammonium fluoride-mediated reactions of pyripyropene A derivative, thymidine and uridine derivatives, methyl β-D-glucofuranoside, and pyranoside derivatives each gave the corresponding primary alcohol with high regioselectivity.
- Ohtawa, Masaki,Tomoda, Hiroshi,Nagamitsu, Tohru
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p. 113 - 118
(2014/02/14)
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- 4-Acetylthio-2,2-dimethyl-3-oxobutyl group as an esterase- And thermo-labile protecting group for oligomeric phosphodiesters
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(4-Acetylthio-2,2-dimethyl-3-oxobutyl)-protected oligomeric phosphodiesters 1 and 2 were synthesized and removal of the protecting groups in the presence and absence of hog liver esterase was followed at pH 7.5 and 37 °C. Phosphotriesters 1 and 2 were successfully converted into the desired fully deprotected phosphodiesters 3 and 4, respectively. Some cleavage of internucleosidic P-O bonds took place, which reduced the yield of 3 and 4. Non-enzymatic removal of the protecting group was only modestly retarded by accumulation of negative charge on the molecule. With 1, the half-lives for the departure of the first and second protecting groups were 7.8 and 10.7 h, respectively, and with 2, 6.2 and 7.2 h, respectively. After 4 d, 70% of both starting materials 1 and 2 were converted into the unprotected phosphodiester. The presence of hog liver esterase (2.6 units mL-1) resulted in fast removal of the first protecting group (τ1/2 2.7 min and 36 min with 1 and 2, respectively), but the appearance of fully deprotected 3 and 4 was accelerated only by a factor of 2, consistent with dramatic retardation of the enzymatic reaction upon accumulation of the negative charge.
- Leisvuori, Anna,L?nnberg, Harri,Ora, Mikko
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p. 5816 - 5826
(2014/10/16)
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- Deamination, oxidation, and C-C bond cleavage reactivity of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine
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Three new cytosine derived DNA modifications, 5-hydroxymethyl-2′- deoxycytidine (hmdC), 5-formyl-2′-deoxycytidine (fdC) and 5-carboxy-2′-deoxycytidine (cadC) were recently discovered in mammalian DNA, particularly in stem cell DNA. Their function is currently not clear, but it is assumed that in stem cells they might be intermediates of an active demethylation process. This process may involve base excision repair, C-C bond cleaving reactions or deamination of hmdC to 5-hydroxymethyl-2′- deoxyuridine (hmdU). Here we report chemical studies that enlighten the chemical reactivity of the new cytosine nucleobases. We investigated their sensitivity toward oxidation and deamination and we studied the C-C bond cleaving reactivity of hmdC, fdC, and cadC in the absence and presence of thiols as biologically relevant (organo)catalysts. We show that hmdC is in comparison to mdC rapidly oxidized to fdC already in the presence of air. In contrast, deamination reactions were found to occur only to a minor extent. The C-C bond cleavage reactions require the presence of high concentration of thiols and are acid catalyzed. While hmdC dehydroxymethylates very slowly, fdC and especially cadC react considerably faster to dC. Thiols are active site residues in many DNA modifiying enzymes indicating that such enzymes could play a role in an alternative active DNA demethylation mechanism via deformylation of fdC or decarboxylation of cadC. Quantum-chemical calculations support the catalytic influence of a thiol on the C-C bond cleavage.
- Schiesser, Stefan,Pfaffeneder, Toni,Sadeghian, Keyarash,Hackner, Benjamin,Steigenberger, Barbara,Schroeder, Arne S.,Steinbacher, Jessica,Kashiwazaki, Gengo,Hoefner, Georg,Wanner, Klaus T.,Ochsenfeld, Christian,Carell, Thomas
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supporting information
p. 14593 - 14599
(2013/10/22)
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- Continuous flow photochemistry for the rapid and selective synthesis of 2′-deoxy and 2′,3′-dideoxynucleosides
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A new photochemical flow reactor has been developed for the photo-induced electron-transfer deoxygenation reaction to produce 2′-deoxy and 2′,3′-dideoxynucleosides. The continuous flow format significantly improved both the efficiency and selectivity of the reaction, with the streamlined multi-step sequence directly furnishing the highly desired unprotected deoxynucleosides.
- Shen, Bo,Jamison, Timothy F.
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p. 157 - 164
(2013/04/10)
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- Developing a collection of immobilized nucleoside phosphorylases for the preparation of nucleoside analogues: Enzymatic synthesis of arabinosyladenine and 2',3'-dideoxyinosine
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The use of nucleoside phosphorylases (NPs; EC 2.4.2.n) represents a convenient alternative to the chemical route for the synthesis of natural and modified nucleosides. We purified four recombinantly expressed nucleoside phosphorylases from the bacterial pathogens Citrobacter koseri, Clostridium perfringens, and Streptococcus pyogenes (CkPNPI, CkPNPII, CpUP, SpUP) and their substrate specificity was investigated towards either natural pyrimidine or purine nucleosides and some analogues, namely, arabinosyladenine (araA) and 2',3'-dideoxyinosine (ddI). A 2-3 % activity towards these latter compounds (compared to the natural substrates) was observed. Enzyme activities were compared to the specificities obtained for the enzymes pyrimidine nucleoside phosphorylase from Bacillus subtilis (BsPyNP) and purine nucleoside phosphorylase from Aeromonas hydrophila (AhPNPII) previously reported by some of the authors. The enzymes displaying the suitable specificity for the synthesis of araA and ddI were immobilized on aldehyde-agarose. The immobilized preparations were highly stable at alkaline pH and in the presence of methanol or acetonitrile as cosolvent. They were used in the synthesis of araA and ddI by a one-pot, bienzymatic transglycosylation achieving 74 and 44 % conversion, respectively. Something different: Nucleoside phosphorylases are a convenient alternative to the chemical route for the synthesis of natural and modified nucleosides. Four new nucleoside phosphorylases have been prepared, characterized, and tested for their use in biocatalyzed syntheses of araA and ddI (see scheme). A generally applicable immobilization technique has been found to provide active and stable biocatalysts.
- Serra, Immacolata,Ubiali, Daniela,Piskur, Jure,Christoffersen, Stig,Lewkowicz, Elizabeth S.,Iribarren, Adolfo M.,Albertini, Alessandra M.,Terreni, Marco
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p. 157 - 165
(2013/04/24)
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- Synthesis and hydrolytic properties of thymidine boranomonophosphate
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Detailed synthetic procedures of thymidine 5′-O-(P-borano) monophosphate (TMPB) via an H-phosphonate approach are reported. The hydrolytic properties of TMPB in pH 1.8 and 6.76 buffers at 22 or 37 C were studied using LC-MS. One nucleoside product, thymid
- Xu, Zhihong,Sergueeva, Zinaida A.,Shaw, Barbara Ramsay
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p. 2882 - 2885
(2013/06/26)
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- Oxidation and reduction of the 5-(2-Deoxyuridinyl)methyl radical
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Sleeping beauty: The 5-(2-Deoxyuridinyl)methyl radical 1 is a key intermediate in the thymine oxidative reaction mediated by reactive oxygen species. Evidence is presented that 1 is prone to both oxidation and reduction reactions at the absence of O2. These results question the current paradigm and suggest that the redox chemistry of 1, which has been largely overlooked in the past, may play a major role in determining the fate of 1. Copyright
- Lin, Gengjie,Li, Lei
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p. 5594 - 5598
(2013/06/27)
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- A straightforward diphenylmethyl protection method and deprotection of some pyrimidine nucleosides
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Benzhydryl protection of primary and secondary alcohols has been reported previously via reaction with metal alcoholates. Our aim was to find generally useful and very mild conditions for the alcoholic protection and deprotection of nucleosides with the diphenylmethyl group. This was accomplished for some pyrimidine nucleosides using PdCl2 as the transition metal catalyst, and with optimization yields of 70-90% have been achieved. A lack of solubility of other nucleosides hampers its more general use.
- Saudi, Milind,Van Aerschot, Arthur
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p. 8524 - 8534
(2013/08/23)
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- Photochemical Control of DNA Structure through Radical Disproportionation
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Photolysis of an aryl sulfide-containing 5,6-dihydropyrimidine (1) at 350 nm produces high yields of thymidine and products resulting from trapping of a 5,6-dihydrothymidin-5-yl radical by O2 or thiols. Thymidine is believed to result from disproportionation of the radical pair originally generated from C-S bond homolysis of 1 on the microsecond timescale, which is significantly shorter than other photochemical transformations of modified nucleotides into their native forms. Duplex DNA containing 1 is destabilized, presumably due to disruption of π-stacking. Incorporation of 1 within the binding site of the restriction endonuclease EcoRV provides a photochemical switch for turning on the enzyme's activity. In contrast, 1 is a substrate for endonuclease VIII and serves as a photochemical off switch for this base excision repair enzyme. Modification 1 also modulates the activity of the 10-23 DNAzyme, despite its incorporation into a nonduplex region. Overall, dihydropyrimidine 1 shows promise as a tool to provide spatiotemporal control over DNA structure on the miscrosecond timescale.
- San Pedro, Joanna Maria N.,Greenberg, Marc M.
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p. 1590 - 1596
(2013/09/23)
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- A comparison between immobilized pyrimidine nucleoside phosphorylase from Bacillus subtilis and thymidine phosphorylase from Escherichia coli in the synthesis of 5-substituted pyrimidine 2′-deoxyribonucleosides
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Pyrimidine nucleoside phosphorylase from Bacillus subtilis (BsPyNP, E.C. 2.4.2.3) and thymidine phosphorylase from Escherichia coli (EcTP, E.C. 2.4.2.4) were used, as immobilized enzymes, in the synthesis of 5-halogenated pyrimidine 2′-deoxyribonucleosides (14-18) by transglycosylation in fully aqueous medium. From the comparative study of the two biocatalysts, no remarkable differences emerged about their substrate specificity, bioconversion yield, stability in organic cosolvents (DMF and MeCN). Moreover, both biocatalysts could be recycled for at least 5 times with no loss of the productivity. Both enzymes do not accept arabinonucleosides and 2′,3′- dideoxynucleosides as substrates, whereas they catalyze bioconversions involving 5′-deoxyribonucleosides and 5-halogenated uracils. The synthesis of compounds 14-18 proceeded at a similar conversion (33-68% for BsPyNP and 25-62% for EcTP, respectively). Immobilization was found to exert, for both the biocatalysts, a dramatic enhancement of stability upon incubation in MeCN. Optimization of 5-fluoro-2′-deoxyuridine (14) synthesis (pH 7.5, 10 mM phosphate buffer, nucleoside/nucleobase 3:1 molar ratio) and subsequent scale-up afforded the target compound in 73% (EcTP) or 76% (BsPyNP) conversion (about 9 g/L).
- Serra, Immacolata,Bavaro, Teodora,Cecchini, Davide A.,Daly, Simona,Albertini, Alessandra M.,Terreni, Marco,Ubiali, Daniela
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- Synthesis and stability of a 2′-O-[N-(aminoethyl)carbamoyl] methyladenosine-containing dinucleotide
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Working towards the synthesis of 2′-O-[N-(aminoethyl)carbamoyl] methyl-modified di- and oligonucleotides, we have synthesised a protected 2′-O-[N-(aminoethyl)carbamoyl]methyl-modified adenosine where the modification is introduced in a convenient one-pot three-step procedure. The corresponding H-phosphonate building block was also synthesised, and from this intermediate, a 2′-O-[N-(aminoethyl)carbamoyl]methyl-containing dinucleotide could be made. We also performed studies on the chemical and enzymatic stability of this dinucleotide. The dinucleotide was subjected to different ammonolysis and other basic conditions, and HPLC analysis showed that the modification was intact to most conditions, but that there was some minor hydrolysis when NH3 (concd. aq.) was used at 55 °C. Under several other sets of conditions, including saturated NH3 in methanol, and ethylenediamine, the amide remained intact. Treatment of the dinucleotide with Phosphodiesterase I from Crotalus adamanteus venom and Phosphodiesterase II from bovine spleen showed that the N-(aminoethyl)carbamoylmethyl moiety gives the phosphodiester linkage substantial protection against enzymatic degradation; the phosphodiester was not degraded by PDE II at all after seven days. A 2′-O-[N-(aminoethyl)carbamoyl]methyl-modified adenosine and a corresponding dinucleotide were synthesised. Hydrolysis (1-2 %) was observed in concentrated aqueous NH3 at 55°C, but under several other sets of reaction conditions, the amide remained intact. The N-(aminoethyl) carbamoylmethyl moiety gave substantial protection against enzymatic degradation by nucleases from snake venom and bovine spleen. Copyright
- Milton, Stefan,Ander, Charlotte,Honcharenko, Dmytro,Honcharenko, Malgorzata,Yeheskiely, Esther,Stroemberg, Roger
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p. 7184 - 7192
(2013/11/06)
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- Phosphorylating reagent-free synthesis of 5′-phosphate oligonucleotides by controlled oxidative degradation of their 5′-end
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The 5′-phosphorylated oligonucleotides (5′-pONs) are currently synthesized using expensive and sensitive modified phosphoramidite reagents. In this work, a simple, cost-effective, efficient, and automatable method is presented, based on the controlled oxidation of the 5′-terminal alcohol followed by a β-elimination reaction. The latter reaction leads to the removal of the terminal 5′-nucleoside and subsequent formation of the 5′-phosphate moiety. Thus, chemical phosphorylation of oligonucleotides (DNA or RNA) is achieved without using modified phosphoramidites.
- Sallamand, Corinne,Miscioscia, Audrey,Lartia, Remy,Defrancq, Eric
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supporting information; body text
p. 2030 - 2033
(2012/06/18)
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- Continuous flow photocatalysis enhanced using an aluminum mirror: Rapid and selective synthesis of 2′-deoxy and 2′,3′-dideoxynucleosides
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A unique photochemical flow reactor featuring quartz tubing, an aluminum mirror and temperature control has been developed for the photo-induced electron-transfer deoxygenation reaction to produce 2′-deoxy and 2′,3′-dideoxynucleosides. The continuous flow format significantly increased the efficiency and selectivity of the reaction.
- Shen, Bo,Bedore, Matthew W.,Sniady, Adam,Jamison, Timothy F.
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supporting information; experimental part
p. 7444 - 7446
(2012/10/08)
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- Development of hydrophilic photolabile hydroxyl protecting groups
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Hydrophilic photolabile protecting groups (PPGs) for hydroxyl protection have been developed. The new PPGs are derived from 3-(dimethylamino)trityl (DMATr) by replacing the two methyl groups with two hydrophilic butyryl groups. The new PPG reagents can be readily prepared and installed. They are stable in the dark but can be removed cleanly and efficiently in aqueous environments upon irradiation with a UV lamp or sunlight.
- Yang, Haishen,Zhou, Lei,Wang, Pengfei
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scheme or table
p. 514 - 517
(2012/06/30)
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- Semisynthetic peptide-lipase conjugates for improved biotransformations
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An efficient chemoselective method for the creation of semisynthetic lipases by site-specific incorporation of tailor-made peptides on the lipase-lid site was developed. These new enzymes showed excellent improved specificity and regio- or enantioselectivity in different biotransformations.
- Romero, Oscar,Filice, Marco,Guisan, Jose M.,Palomo, Jose M.,De Las Rivas, Blanca,Carrasco-Lopez, Cesar,Hermoso, Juan A.,Klett, Javier,Morreale, Antonio,Abian, Olga
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supporting information
p. 9053 - 9055,3
(2020/08/31)
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