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1.
Biochim Biophys Acta Proteins Proteom ; 1868(1): 140292, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31676450

RESUMO

Enzymatic transglycosylation, a transfer of the carbohydrate moiety from one heterocyclic base to another, is catalyzed by nucleoside phosphorylases (NPs) and is being actively developed and applied for the synthesis of biologically important nucleosides. Here, we report an efficient one-step synthesis of 5-substitited pyrimidine ribonucleosides starting from 7-methylguanosine hydroiodide in the presence of nucleoside phosphorylases (NPs).


Assuntos
Proteínas de Bactérias/química , Escherichia coli/enzimologia , Pentosiltransferases/química , Ribonucleosídeos/química , Uridina/química , Proteínas de Bactérias/genética , Catálise , Glicosilação , Pentosiltransferases/genética , Proteínas Recombinantes/química
2.
Nucleic Acids Res ; 47(19): 10296-10312, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31495891

RESUMO

Oxazinomycin is a C-nucleoside antibiotic that is produced by Streptomyces hygroscopicus and closely resembles uridine. Here, we show that the oxazinomycin triphosphate is a good substrate for bacterial and eukaryotic RNA polymerases (RNAPs) and that a single incorporated oxazinomycin is rapidly extended by the next nucleotide. However, the incorporation of several successive oxazinomycins or a single oxazinomycin in a certain sequence context arrested a fraction of the transcribing RNAP. The addition of Gre RNA cleavage factors eliminated the transcriptional arrest at a single oxazinomycin and shortened the nascent RNAs arrested at the polythymidine sequences suggesting that the transcriptional arrest was caused by backtracking of RNAP along the DNA template. We further demonstrate that the ubiquitous C-nucleoside pseudouridine is also a good substrate for RNA polymerases in a triphosphorylated form but does not inhibit transcription of the polythymidine sequences. Our results collectively suggest that oxazinomycin functions as a Trojan horse substrate and its inhibitory effect is attributable to the oxygen atom in the position corresponding to carbon five of the uracil ring.


Assuntos
RNA Polimerases Dirigidas por DNA/química , RNA/química , Transcrição Genética/efeitos dos fármacos , Uridina/análogos & derivados , RNA Polimerases Dirigidas por DNA/genética , Escherichia coli/genética , Oxigênio/química , Pseudomonas/química , RNA/genética , Clivagem do RNA/efeitos dos fármacos , Streptomyces/química , Especificidade por Substrato , Timidina/química , Timidina/genética , Transcrição Genética/genética , Fatores de Elongação da Transcrição/genética , Uracila/química , Uridina/síntese química , Uridina/química , Uridina/farmacologia
3.
PLoS Genet ; 15(8): e1008117, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31465447

RESUMO

The Elongator complex promotes formation of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) side-chains on uridines at the wobble position of cytosolic eukaryotic tRNAs. In all eukaryotic organisms tested to date, the inactivation of Elongator not only leads to the lack of mcm5/ncm5 groups in tRNAs, but also a wide variety of additional phenotypes. Although the phenotypes are most likely caused by a translational defect induced by reduced functionality of the hypomodified tRNAs, the mechanism(s) underlying individual phenotypes are poorly understood. In this study, we show that the genetic background modulates the phenotypes induced by the lack of mcm5/ncm5 groups in Saccharomyces cerevisiae. We show that the stress-induced growth defects of Elongator mutants are stronger in the W303 than in the closely related S288C genetic background and that the phenotypic differences are caused by the known polymorphism at the locus for the mRNA binding protein Ssd1. Moreover, the mutant ssd1 allele found in W303 cells is required for the reported histone H3 acetylation and telomeric gene silencing defects of Elongator mutants. The difference at the SSD1 locus also partially explains why the simultaneous lack of mcm5 and 2-thio groups at wobble uridines is lethal in the W303 but not in the S288C background. Collectively, our results demonstrate that the SSD1 locus modulates phenotypes induced by the lack of Elongator-dependent tRNA modifications.


Assuntos
Fatores de Alongamento de Peptídeos/genética , RNA de Transferência/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Expressão Gênica/genética , Genótipo , Histona Acetiltransferases/genética , Histona Acetiltransferases/metabolismo , Fatores de Alongamento de Peptídeos/metabolismo , Fenótipo , Processamento Pós-Transcricional do RNA/genética , RNA de Transferência/genética , Proteínas de Ligação a RNA/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/fisiologia , Uridina/análogos & derivados , Uridina/química
4.
Nucleic Acids Res ; 47(19): e113, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31361898

RESUMO

Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNA, and in yeast is found at position U54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. Here we developed a genome-wide single-nucleotide resolution mapping method, Fluorouracil-Induced-Catalytic-Crosslinking-Sequencing (FICC-Seq), in order to identify the relevant enzymatic targets. We demonstrate that TRMT2A is responsible for the majority of m5U present in human RNA, and that it commonly targets U54 of cytosolic tRNAs. By comparison to current methods, we show that FICC-Seq is a particularly robust method for accurate and reliable detection of relevant enzymatic target sites. Our associated finding of extensive irreversible TRMT2A-tRNA crosslinking in vivo following 5-Fluorouracil exposure is also intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of Fluorouracil-mediated cytotoxicity.


Assuntos
Desoxirribonucleases/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA/genética , Proteínas de Saccharomyces cerevisiae/genética , Uridina/genética , tRNA Metiltransferases/genética , Sobrevivência Celular/efeitos dos fármacos , Desoxirribonucleases/química , Fluoruracila/farmacologia , Células HEK293 , Humanos , RNA/química , RNA de Transferência , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Uridina/química , Leveduras/genética , tRNA Metiltransferases/química
5.
J Antibiot (Tokyo) ; 72(10): 769-774, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31341273

RESUMO

A novel sansanmycin analogue, sansanmycin Q (1), was identified by genome mining from the fermentation broth of Streptomyces sp. SS (CPCC 200442). In comparison with other sansanmycin compounds, sansanmycin Q has an extra glycine residue at the N-terminus of the pseudopeptide backbone. The additional glycine was proved to be assembled to sansanmycin A by SsaB, a tRNA-dependent aminoacyltransferase, based on the results of rescrutiny of sansanmycin biosynthetic gene cluster, and then overexpression and knockout of ssaB in the wild-type strain. The structure of sansanmycin Q was assigned by interpretation of NMR and mass spectral data. The results of the bioassay disclosed that sansanmycin Q exhibited more potency against Mycobacterium tuberculosis H37Rv and a rifampicin- and isoniazid-resistant strain than sansanmycin A.


Assuntos
Antituberculosos/metabolismo , Antituberculosos/farmacologia , Vias Biossintéticas/genética , Família Multigênica , Oligopeptídeos/biossíntese , Oligopeptídeos/farmacologia , Streptomyces/metabolismo , Uridina/análogos & derivados , Antituberculosos/química , Biologia Computacional , Fermentação , Genoma Bacteriano , Espectroscopia de Ressonância Magnética , Espectrometria de Massas , Testes de Sensibilidade Microbiana , Estrutura Molecular , Mycobacterium tuberculosis/efeitos dos fármacos , Oligopeptídeos/química , Streptomyces/crescimento & desenvolvimento , Uridina/biossíntese , Uridina/química , Uridina/farmacologia
6.
Adv Mater ; 31(32): e1902672, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31206855

RESUMO

Cancer theranostics holds potential promise for precision medicine; however, most existing theranostic nanoagents are simply developed by doping both therapeutic agents and imaging agent into one particle entity, and thus have an "always-on" pharmaceutical effect and imaging signals regardless of their in vivo location. Herein, the development of an organic afterglow protheranostic nanoassembly (APtN) that specifically activates both the pharmaceutical effect and diagnostic signals in response to a tumor-associated chemical mediator (hydrogen peroxide, H2 O2 ) is reported. APtN comprises an amphiphilic macromolecule and a near-infrared (NIR) dye acting as the H2 O2 -responsive afterglow prodrug and the afterglow initiator, respectively. Such a molecular architecture allows APtN to passively target tumors in living mice, specifically release the anticancer drug in the tumor, and spontaneously generate the uncaged afterglow substrate. Upon NIR light preirradiation, the afterglow initiator generates singlet oxygen to react and subsequently transform the uncaged afterglow substrate into an active self-luminescent form. Thus, the intensity of generated afterglow luminescence is correlated with the drug release status, permitting real-time in vivo monitoring of prodrug activation. This study proposes a background-free design strategy toward activatable cancer theranostics.


Assuntos
Antineoplásicos/síntese química , Substâncias Luminescentes/química , Nanopartículas/química , Neoplasias/diagnóstico por imagem , Neoplasias/tratamento farmacológico , Pró-Fármacos/síntese química , Animais , Antineoplásicos/administração & dosagem , Linhagem Celular Tumoral , Dimerização , Sistemas de Liberação de Medicamentos , Floxuridina/química , Peróxido de Hidrogênio/metabolismo , Raios Infravermelhos , Camundongos , Polietilenoglicóis/química , Pró-Fármacos/farmacologia , Nanomedicina Teranóstica , Distribuição Tecidual , Microambiente Tumoral , Uridina/análogos & derivados , Uridina/química
7.
Curr Protoc Nucleic Acid Chem ; 77(1): e86, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31125509

RESUMO

This unit describes the detailed preparation of 5-alkynyl-2'-halogenated arabinosyl uridine nucleosides (2'-halo-ara-EdU) from uridine. These compounds were synthesized as prospective chemical probes for the detection of DNA synthesis in proliferating cells. Currently, this is the only synthetic methodology reported to access these compounds. The key to success of the synthetic approach was to employ a 3-N-nitro-protecting group to stabilize the required 2'-triflate nucleoside precursor toward nucleophilic substitution. Several synthetic challenges were overcome to accommodate the combination of a 5-alkyne and 3-N-nitro functional group, including facile introduction and removal of the N-nitro group, and removal of the sugar acetyl groups under acidic conditions. © 2019 by John Wiley & Sons, Inc.


Assuntos
Alquinos/química , Halogênios/química , Nucleosídeos/síntese química , Uridina/química , Sondas Moleculares , Nucleosídeos/química , Análise Espectral/métodos
8.
Eur J Med Chem ; 171: 462-474, 2019 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-30933853

RESUMO

The present status of antibiotic resistant requires an urgent invention of novel agents that act on clinically unexplored antibacterial targets. The enzyme MraY (phospho-MurNAc-pentapeptide translocase), essential for bacterial cell wall synthesis, fulfils this criterion as it has not been explored as a target in a clinical context. Specifically, the enzyme is involved in the lipid-linked cycle of peptidoglycan biosynthesis and is reportedly targeted by naturally-occurring nucleoside antibiotics. The antimicrobial 'caprazamycin' class of nucleoside antibiotics targets Mycobacterium tuberculosis and clinically relevant Gram-negative bacteria such as Pseudomonas aeruginosa besides various drug resistant strains and is therefore an eligible starting point for the development of novel agents. In this review, we aim to summarise the structure-activity relationships of the natural, semi-synthetic as well as synthetic analogues of nucleoside antibiotic caprazamycins. This review highlights caprazamycins as promising lead structures for development of potent and selective antimicrobial agents that target MraY, the bacterial enzyme involved in the first membrane-dependent step in bacterial peptidoglycan assembly.


Assuntos
Antibacterianos/farmacologia , Azepinas/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Produtos Biológicos/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Transferases/antagonistas & inibidores , Uridina/análogos & derivados , Antibacterianos/química , Azepinas/química , Proteínas de Bactérias/metabolismo , Produtos Biológicos/química , Relação Dose-Resposta a Droga , Estrutura Molecular , Mycobacterium tuberculosis/enzimologia , Relação Estrutura-Atividade , Transferases/metabolismo , Uridina/química , Uridina/farmacologia
9.
Bull Environ Contam Toxicol ; 102(6): 854-860, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30989281

RESUMO

Photodegradation is an important non-biodegradation process of pesticide degradation in aquatic environments. In this study, the effect of different forms of nitrogen on the photodegradation kinetics of penoxsulam was investigated. The photodegradation of penoxsulam was accelerated by NO3- and NO2- but was not affected by NH4+. Ultra-high-performance liquid chromatography coupled with time-of-flight mass spectrometry was used to separate and identify the transformation products (TPs)converted by photodegradation of penoxsulam in an aqueous solution under UV-Vis (290-800 nm) irradiation. Seven major transformation products were identified based on mass spectral data. The structure was determined by elemental composition calculations, comparison of structural analogs, and existing literature. The main pathways of photodegradation were found to be sulfonamide bond cleavage, rearrangement, triazole ring cleavage, and hydroxylation. These findings are critical to elucidate the environmental fate of penoxsulam in aquatic ecosystems and provide a basis for further environmental risk assessment.


Assuntos
Herbicidas/química , Fotólise , Sulfonamidas/química , Uridina/análogos & derivados , Poluentes Químicos da Água/química , Amônia/química , Cromatografia Líquida de Alta Pressão , Herbicidas/análise , Cinética , Espectrometria de Massas/métodos , Óxido Nítrico/química , Medição de Risco , Sulfonamidas/análise , Raios Ultravioleta , Uridina/análise , Uridina/química , Água/química , Poluentes Químicos da Água/análise
10.
Methods Mol Biol ; 1973: 251-260, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31016707

RESUMO

A robust, fluorescence-based analysis and discovery platform is described for bacterial A-site binders. The assay relies on an incorporated isomorphic fluorescent uridine analog, which substitutes the A-site's U1406 and serves as a FRET donor to an A-site bound coumarin-labeled aminoglycoside that serves as the FRET acceptor. Binding efficiency of unlabeled A-site ligands can be determined by competition experiments, where the acceptor-labeled aminoglycoside is displaced. The replacement efficiency is gauged by the concentration-dependent loss of the sensitized FRET acceptor's signal with concomitant restoration of the donor's emission. Plotting the relative emission intensity of both the donor and acceptor as a function of ligand concentration followed by fitting of the data points to a dose-response curve yields IC50 values, one possible measure of the antibiotic potency of new A-site binders.


Assuntos
Aminoglicosídeos/metabolismo , Cumarínicos/metabolismo , Transferência Ressonante de Energia de Fluorescência/métodos , Fluorescência , RNA Bacteriano/metabolismo , Uridina/metabolismo , Aminoglicosídeos/química , Cumarínicos/química , Ligantes , RNA Bacteriano/química , Uridina/química
11.
Molecules ; 24(6)2019 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-30901934

RESUMO

Tick-borne encephalitis virus (TBEV) is a causative agent of tick-borne encephalitis (TBE), one of the most important human infections involving the central nervous system. Although effective vaccines are available on the market, they are recommended only in endemic areas. Despite many attempts, there are still no specific antiviral therapies for TBEV treatment. Previously, we synthesized a series of uridine derivatives of 2-deoxy sugars and proved that some compounds show antiviral activity against viruses from the Flaviviridae and Orthomyxoviridae families targeting the late steps of the N-glycosylation process, affecting the maturation of viral proteins. In this study, we evaluated a series of uridine derivatives of 2-deoxy sugars for their antiviral properties against two strains of the tick-borne encephalitis virus; the highly virulent TBEV strain Hypr and the less virulent strain Neudoerfl. Four compounds (2, 4, 10, and 11) showed significant anti-TBEV activity with IC50 values ranging from 1.4 to 10.2 µM and low cytotoxicity. The obtained results indicate that glycosylation inhibitors, which may interact with glycosylated membrane TBEV E and prM proteins, might be promising candidates for future antiviral therapies against TBEV.


Assuntos
Antivirais/farmacologia , Desoxiaçúcares/farmacologia , Vírus da Encefalite Transmitidos por Carrapatos/efeitos dos fármacos , Uridina/farmacologia , Antivirais/química , Linhagem Celular Tumoral , Células Cultivadas , Desoxiaçúcares/química , Relação Dose-Resposta a Droga , Vírus da Encefalite Transmitidos por Carrapatos/fisiologia , Humanos , Testes de Sensibilidade Microbiana , Estrutura Molecular , Biossíntese de Proteínas/efeitos dos fármacos , Uridina/análogos & derivados , Uridina/química , Ensaio de Placa Viral
12.
Molecules ; 24(4)2019 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-30781738

RESUMO

A P(V)-N activation method based on nucleoside phosphoropiperidate/DCI system has been developed for improved synthesis of diverse UDP-furanoses. The reaction conditions including temperature, amount of activator, and reaction time were optimized to alleviate the degradation of UDP-furanoses to cyclic phosphates. In addition, an efficient and facile phosphoramidite route was employed for the preparation of furanosyl-1-phosphates.


Assuntos
Arabinose/análogos & derivados , Imidazóis/química , Imino Furanoses/síntese química , Arabinose/síntese química , Arabinose/química , Imino Furanoses/química , Nucleosídeos/química , Fosfatos/química , Piperidinas/química , Uridina/química
13.
Molecules ; 24(3)2019 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-30678171

RESUMO

As an abundant post-transcriptional modification, dihydrouridine (D) has been found in transfer RNA (tRNA) from bacteria, eukaryotes, and archaea. Nonetheless, knowledge of the exact biochemical roles of dihydrouridine in mediating tRNA function is still limited. Accurate identification of the position of D sites is essential for understanding their functions. Therefore, it is desirable to develop novel methods to identify D sites. In this study, an ensemble classifier was proposed for the detection of D modification sites in the Saccharomyces cerevisiae transcriptome by using heterogeneous features. The jackknife test results demonstrate that the proposed predictor is promising for the identification of D modification sites. It is anticipated that the proposed method can be widely used for identifying D modification sites in tRNA.


Assuntos
RNA de Transferência/química , Saccharomyces cerevisiae/química , Máquina de Vetores de Suporte , Uridina/química , Algoritmos , Fenômenos Químicos , Conformação de Ácido Nucleico , Reprodutibilidade dos Testes , Uridina/análogos & derivados
14.
RNA ; 25(1): 121-134, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30341177

RESUMO

Uridine tetrads (U-tetrads) are a structural element encountered in RNA G-quadruplexes, for example, in the structures formed by the biologically relevant human telomeric repeat RNA. For these molecules, an unexpectedly strong stabilizing influence of a U-tetrad forming at the 3' terminus of a quadruplex was reported. Here we present the high-resolution solution NMR structure of the r(UGGUGGU)4 quadruplex which, in our opinion, provides an explanation for this stabilization. Our structure features a distinctive, abrupt chain reversal just prior to the 3' uridine tetrad. Similar "reversed U-tetrads" were already observed in the crystalline phase. However, our NMR structure coupled with extensive explicit solvent molecular dynamics (MD) simulations identifies some key features of this motif that up to now remained overlooked. These include the presence of an exceptionally stable 2'OH to phosphate hydrogen bond, as well as the formation of an additional K+ binding pocket in the quadruplex groove.


Assuntos
Quadruplex G , Estabilidade de RNA , RNA/química , Sequência de Bases , Sítios de Ligação , Cátions/química , Humanos , Simulação de Dinâmica Molecular , Ressonância Magnética Nuclear Biomolecular , Potássio/química , Espalhamento a Baixo Ângulo , Sódio/química , Uridina/química , Água/química , Difração de Raios X
15.
J Mol Graph Model ; 86: 66-83, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30336453

RESUMO

A quantum chemical semi-empirical RM1 approach was used to deduce the structural role of hypermodified nucleoside 5-carboxymethylaminomethyluridine 5'-monophosphate (pcmnm5U) from 'wobble' (34th) position of mitochondrial tRNAs. The energetically preferred pcmnm5U(34) adopted a 'skew' conformation for C5-substituted side chain (-CH2-NH2+-CH2-COO-) moiety that orient towards the 5'-ribose-phosphate backbone, which support 'anti' orientation of glycosyl (χ34) torsion angle. Preferred conformation of pcmnm5U(34) was stabilized by O(4) … HC(10), O1P⋯HN(11), O(15) … HN(11), O(15) … HC(10), O4' … HC(6) and O(2) … HC2' hydrogen bonding interactions. The high flexibility of side chain moiety displayed different structural properties for pcmnm5U(34). Three different conformations of pcmnm5U(34) were observed in molecular dynamics simulations and Markov state model studies. The unmodified uracil revealed 'syn' and 'anti' orientations for glycosyl (χ34) torsion angle that substantiate the role of "-CH2-NH2+-CH2-COO-" moiety in maintaining the 'anti' orientation of pcmnm5U(34). The preferred conformation of pcmnm5U(34) helps to recognize Guanosine more proficiently than Adenosine from the third position of codons. The role of pcmnm5U(34) in tRNA biogenesis paves the way to understand its structural significance in usual mitochondrial metabolism and respiration.


Assuntos
Cadeias de Markov , Conformação Molecular , Simulação de Dinâmica Molecular , RNA Mitocondrial/química , RNA de Transferência/química , Uridina/análogos & derivados , Ligações de Hidrogênio , Análise Espectral , Uridina/química
16.
Methods ; 156: 60-65, 2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30308313

RESUMO

Well over a hundred types of naturally occurring covalent modifications can be made to ribonucleotides in RNA molecules. Moreover, several types of such modifications are each known to be catalysed by multiple enzymes which largely appear to modify distinct sites within the cellular RNA. In order to aid functional investigations of such multi-enzyme RNA modification types in particular, it is important to determine which enzyme is responsible for catalysing modification at each site. Two methods, Aza-IP and methylation-iCLIP, were developed and used to map genome-wide locations of methyl-5-cytosine (m5C) RNA modifications inherently in an enzyme specific context. Though the methods are quite distinct, both rely on capturing catalytic intermediates of RNA m5C methyltransferases in a state where the cytosine undergoing methylation is covalently crosslinked to the enzyme. More recently the fundamental methylation-iCLIP principle has also been applied to map methyl-2-adenosine sites catalysed by the E. coli RlmN methylsynthase. Here I describe the ideas on which the two basic methods hinge, and summarise what has been achieved by them thus far. I also discuss whether and how such principles may be further exploited for profiling of other RNA modification types, such as methyl-5-uridine and pseudouridine.


Assuntos
Proteínas de Escherichia coli/metabolismo , Imunoprecipitação/métodos , Metiltransferases/metabolismo , Complexos Multienzimáticos/metabolismo , Processamento Pós-Transcricional do RNA , RNA Mensageiro/química , Transcriptoma , Animais , Azacitidina/química , Azacitidina/metabolismo , Biocatálise , Reagentes para Ligações Cruzadas/química , Proteínas de Escherichia coli/genética , Fluoruracila/química , Fluoruracila/metabolismo , Humanos , Metilação , Metiltransferases/genética , Complexos Multienzimáticos/genética , Pseudouridina/química , Pseudouridina/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Uridina/análogos & derivados , Uridina/química , Uridina/metabolismo
17.
Rapid Commun Mass Spectrom ; 33(5): 482-490, 2019 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-30430683

RESUMO

RATIONALE: Charge transfer via DNA plays an important role in physical and chemical processes in biological systems, and is used in biomolecular electronics. The present study considers the resonant interaction of free electrons with nucleosides, which is important for an understanding of the processes of electron transport in DNA. METHODS: Resonant electron capture negative ion mass spectrometry was used to study the processes of low-energy electron attachment to two uracil nucleosides, uridine and deoxyuridine, while density functional theory (DFT) calculations were used to analyze the energy aspects of ion formation and decay. RESULTS: Short-lived molecular ions, formed via mechanisms of π* shape resonances, were found in the energy region below 5 eV. The fragmentation channels of these resonances and the structures of the charged and neutral products formed were determined. CONCLUSIONS: These results suggest that the formation of some fragment negative ions occurs through intramolecular charge transfer.


Assuntos
Desoxiuridina/química , Espectrometria de Massas/métodos , Uridina/química , Ânions/química , Transporte de Elétrons , Elétrons , Íons/química
18.
J Pharm Pharmacol ; 71(3): 329-337, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30456846

RESUMO

OBJECTIVES: Uridine was conjugated with fatty acids to improve the drug lipophilicity and the interaction with phospholipid bilayers. METHODS: The esterification reaction using carbodiimides compounds as coupling agents and a nucleophilic catalyst allowed us to synthesize tri-acyl ester derivatives of uridine with fatty acids. Analysis of molecular interactions between these tri-acyl ester derivatives and l-α-dimyristoylphosphatidylcholine (DMPC) multilamellar vesicles (MLV) - as a mammalian cell membrane model - have been performed by differential scanning calorimetry (DSC). KEY FINDINGS: The DSC thermograms suggest that nucleoside and uridine triacetate softly interact with phospholipidic multilamellar vesicles which are predominantly located between the polar phase, whereas the tri-acyl ester derivatives with fatty acids (myristic and stearic acids) present a strongly interaction with the DMPC bilayer due to the nucleoside and aliphatic chains parts which are oriented towards the polar and lipophilic phases of the phospholipidic bilayer, respectively. However, the effects caused by the tri-myristoyl uridine and tri-stearoyl uridine are different. CONCLUSIONS: We show how the structural changes of uridine modulate the calorimetric behaviour of DMPC shedding light on their affinity with the phospholipidic biomembrane model.


Assuntos
Acetatos/química , Dimiristoilfosfatidilcolina/química , Ésteres/química , Membranas/química , Nucleosídeos/química , Uridina/análogos & derivados , Varredura Diferencial de Calorimetria/métodos , Ácidos Graxos/química , Modelos Teóricos , Fosfolipídeos/química , Uridina/química
19.
Methods ; 155: 88-103, 2019 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-30529548

RESUMO

Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only giving information on the (presumed steady-state) abundances of transcripts. Through the combination of metabolic labeling and high-throughput sequencing, several groups have been able to measure both transcription rates and decay rates of the entire transcriptome of an organism in a single experiment. This review focuses on the methodology used to specifically measure RNA decay at a global level. By comparing and contrasting approaches and describing the experimental protocols in a modular manner, we intend to provide both experienced and new researchers to the field the ability to combine aspects of various protocols to fit the unique needs of biological questions not addressed by current methods.


Assuntos
Química Click/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA Mensageiro/metabolismo , Coloração e Rotulagem/métodos , Transcriptoma , Animais , Biotina/análogos & derivados , Biotina/química , Linhagem Celular , Humanos , Estabilidade de RNA , RNA Mensageiro/genética , Tiouracila/análogos & derivados , Tiouracila/química , Tiouracila/metabolismo , Tiouridina/química , Tiouridina/metabolismo , Uracila/análogos & derivados , Uracila/química , Uracila/metabolismo , Uridina/análogos & derivados , Uridina/química , Uridina/metabolismo
20.
Org Biomol Chem ; 17(3): 461-466, 2019 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-30570639

RESUMO

The natural product A-94964 is a uridine-derived nucleoside antibiotic isolated from Streptomyces sp. SANK 60404. In this study, we propose a biosynthetic pathway for A-94964 using gene deletion experiments coupled with in silico analysis of the biosynthetic gene cluster. This study provides insights into the unique biosynthetic pathway for A-94964.


Assuntos
Antibacterianos/biossíntese , Produtos Biológicos/metabolismo , Dissacarídeos/biossíntese , Nucleotídeos de Pirimidina/biossíntese , Uridina/metabolismo , Antibacterianos/química , Produtos Biológicos/química , Dissacarídeos/química , Dissacarídeos/genética , Estrutura Molecular , Família Multigênica , Nucleotídeos de Pirimidina/química , Nucleotídeos de Pirimidina/genética , Uridina/química
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