Characterization Of Nucleosides Research Articles

Characterization of nucleosides and nucleobases in natural Cordyceps by HILIC-ESI/TOF/MS and HILIC-ESI/MS.

A method combining hydrophilic interaction chromatography (HILIC) and electrospray ionization mass spectrometry (ESI-MS) was developed for the characterization and determination of natural Cordyceps. Separation was achieved on a Waters Xbridge Amide column with gradient elution. Identification of 15 target nucleosides and nucleobases was based on retention time, UV spectra and mass measurements of the protonated molecules ([M+H]+) and main fragment ions (ESI-TOF/MS). Eight non-target compounds were tentatively identified by ESI-TOF/MS. The 15 target compounds were quantified by HILIC-ESI-MS/MS using time-programmed selective ion monitoring or multiple reaction monitoring in positive-ion mode under optimized mass conditions. This technique showed good linearity, repeatability and recovery. This approach was also successfully implemented in the analysis of nucleosides and nucleobases in 12 batches of natural Cordyceps samples that were collected from different regions in China. The developed HILIC-ESI-MS method exhibited clear advantages in identifying and determining highly polar bioactive components in Cordyceps, as well as their quality control.

Characterization of Nucleosides and Nucleobases in Fruits of Ziziphus jujuba by UPLC-DAD-MS

The fruit of Ziziphus jujuba , named dazao in Chinese, has been utilized as food as well as crude drugs in China for thousands of years. To explore the profiles of the nucleosides and nucleobases in this fruit, an ultraperformance liquid chromatograph coupled with a photodiode array detector and electrospray ionization-mass spectrometer method (UPLC-DAD-MS) has been established and validated in this paper. The validated method was successfully applied for the simultaneous characterization and quantitation of 9 nucleosides and nucleobases in 49 dazao samples, which comprised 43 cultivars from 26 cultivation regions. Furthermore, principal component analysis (PCA) was performed to classify the samples on the basis of the contents of the nine analyzed compounds. The results showed that almost all of these dazao samples were rich in nucleosides and nucleobases, although their contents were obviously various, and the proposed method could serve as a prerequisite for quality control of jujube products.

Inhibitory Effect of 2′-Substituted Nucleosides on Hepatitis C Virus Replication Correlates with Metabolic Properties in Replicon Cells

Nucleosides have been widely used in the treatment of viral diseases, but relatively few have been identified as inhibitors of hepatitis C virus (HCV). The modified ribonucleosides, 2'-C-methyl-adenosine and 2'-O-methyl-cytidine, are potent inhibitors of HCV replication which specifically target the NS5B polymerase. Herein, a more extensive characterization of the effect of these compounds upon HCV replication in subgenomic replicons is reported. A highly selective antireplicative effect induced by the nucleosides in replicon-containing cell lines was maintained during an exponential growth period with potencies which paralleled the reduction of both positive- and negative-strand RNA replication. Moreover, the inhibitory effect closely correlated with the intrinsic metabolic properties of differing replicon clonal lines. Interestingly, while 2'-C-methyl-adenosine elicited similar inhibitory potencies in different cell lines, 2'-O-methyl-cytidine was found to be inactive in one replicon cell line tested, although the corresponding triphosphates comparably inhibited the in vitro activity of replication complexes isolated from these cells and the activity of NS5B polymerase using synthetic templates. The lack of antireplicative effect, attributed to poor intracellular conversion of the 2'-O-methyl-cytidine nucleoside to the active 5'-triphosphate, was reversed using a monophosphate prodrug. Thus, although replicon cells are useful for evaluating the effect of inhibitors upon HCV replication, these findings have important implications for their use in the identification and characterization of nucleosides and other chemotherapeutic agents requiring cellular metabolism.

Development of a Universal Nucleobase and Modified Nucleobases for Expanding the Genetic Code

This unit presents protocols for the synthesis and characterization of nucleosides with unnatural bases in order to develop bases for the expansion of the genetic alphabet or for nonselective pairing opposite natural bases. Protocols describe the design, synthesis, and characterization of unnatural base pairs involving 1-beta-D-2-deoxyribosyl-N- and -C-nucleosides. Determination of the thermodynamic and kinetic parameters of unnatural nucleosides is accomplished by incorporation into oligonucleotides and subsequent evaluation as described herein.

Synthesis and characterization of nucleosides and oligonucleotides with a benzo[a]pyren-6-ylmethyl adduct at adenine N6 or guanine N2.

Benzo[a]pyrene (1) can be converted to reactive electrophilic species by a number of metabolic pathways, of which the route to the mutagenic and carcinogenic diol epoxide(s) is the best studied. An alternative and interesting pathway to a highly genotoxic electrophile is through alkylation at the 6 position to 6-methylbenzo[a]pyrene (2) followed by oxidation of the methyl group to give 6-hydroxymethylbenzo[a]pyrene (3). Esterification of 3, especially to sulfate ester 4, gives compounds which are both mutagenic and carcinogenic. The major DNA adduct identified from exposure of rats and mice to 4 is the guanine N(2) adduct [2'-deoxy-N(2)-(benzo[a]pyren-6-ylmethyl)guanosine, 5] which is also formed via activation of 2 to a radical cation species by horseradish peroxidase/H(2)O(2) or iodine. To study the biological and structural properties of this adduct and the analogous adenine N(6) adduct (6), a nonbiomimetic synthesis of the adducted nucleosides 5 and 6 has been developed and has been extended to preparation of oligonucleotides containing 5 or 6 at a single site.

Synthesis and characterization of nucleosides and oligonucleotides bearing adducts of butadiene epoxides on adenine n(6) and guanine n(2).

Butadiene is a major industrial chemical whose genotoxic effects are attributed to the reaction of its oxidized metabolites, butadiene monoepoxide (BDO) and butadiene diepoxide (BDO2), with DNA. Nucleosides and oligonucleotides containing regio- and stereochemically specific adducts of BDO and the BDO2-related compound, butene 3,4-diol 1,2-epoxide (BDE), on guanine [(2R)- and (2S)-N(2)-(1-hydroxy-3-buten-2-yl) and (2R,3R)- and (2S,3S)-N(2)-(2,3,4-trihydroxybut-1-yl), respectively] and on adenine [(2R)- and (2S)-N(6)-(1-hydroxy-3-buten-2-yl) and (2R,3R)- and (2S,3S)-N(6)-(2,3,4-trihydroxybut-1-yl), respectively] have been prepared by nonbiomimetic routes. For guanine adducts, 2-fluoro-O(6)-(trimethylsilylethyl)-2'-deoxyinosine was treated with (2R)- and (2S)-2-amino-3-buten-1-ol to give the BDO adducts and with (2R,3R)- and (2S,3S)-1-amino-2,3,4-butanetriol to produce the BDE adducts; the adducted oligonucleotides were prepared from 11-mer oligonucleotides containing the halopurine. Adenine adducts were prepared in a similar fashion using 6-chloropurine 2'-deoxyriboside as the reactive purine component.

The study and characterization of nucleosides by mass spectrometry. 3. Comparison between the mass spectra of trimethylsilyl derivatives of purine 2'-and 3'-linked anhydro, thioanhydro, and aminoanhydro nucleosides.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization of nucleosides by mass spectrometry. III. Comparison between the mass spectra of trimethylsilyl derivatives of purine 2'- and 3'-linked anhydrothionanhydro, and aminoanhydro nucleosidesDenis C. K. Lin, L. Slotin, K. K. Ogilvie, and J. B. WestmoreCite this: J. Org. Chem. 1973, 38, 6, 1118–1123Publication Date (Print):March 1, 1973Publication History Published online1 May 2002Published inissue 1 March 1973https://doi.org/10.1021/jo00946a012RIGHTS & PERMISSIONSArticle Views58Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (738 KB) Get e-Alerts Get e-Alerts

The study and characterization of nucleosides by mass spectrometry—II: Comparisons between the mass spectra of 3′,5′‐substituted, isomeric pairs of 2,2′‐anhydrouridines

AbstractThe mass spectra of 2,2′‐anhydrouridines substituted in the 3′ and 5′ positions were studied. When the substituents were acetyl, pivaloyl, trifluoroacetyl or trimethylsilyl, it was found that specific fragmentations occured which could identify the position of the substituent. The specific fragmentations often resolve earlier ambiguities in the interpretation of mass spectra of 2,2′‐anhydropyrimidine derivatives. Mono‐acetyl and mono‐pivaloyl 2,2′‐anhydrouridines are not easily distinguished because of thermal reactions in the sample probe. They may be readily distinguished, however, by acetylation (with acetic anhydride‐d6 for the mono‐acetyl isomers), trifluoroacetylation or trimethylsilylation, followed by mass spectral analysis of the reaction product.

The study and characterization of nucleosides by mass spectrometry—I: The mass spectra of pyrimidine 2,2′‐anhydronucleosides and their derivatives

AbstractThe mass spectra of 2,2′‐anhydrouridine, 2,2′‐anhydrothymidine and 2,2′‐anhydro‐4‐thiouridine are reported. The acetyl, trifluoroacetyl, trityl, pivaloyl and trimethylsilyl ether derivatives were also studied. Deuterium labeling in acetyl and trimethylsilyl groups aided characterization of many ions in the spectra, as well as helping to clarify hydrogen migration processes. The anhydronucleosides and their derivatives are readily distinguished from natural nucleosides by the presence of an ion containing the base moiety plus the anhydro‐ring plus one hydrogen atom from the rest of the molecule. As for natural nucleosides the [base + H]+ and [base + 2H]+ ions are usually prominent, but in contrast to natural nucleosides, ions characteristic of the sugar moiety do not retain the 2′‐oxygen atom (i.e. the oxygen atom of the anhydro‐ring). The mass spectra of deuterium labeled derivatives suggest a test for the presence of a 3′‐O‐acetyl function (the O‐acetyl group is lost from the molecular ion much more readily from the 3′‐ than from the 5′‐carbon atom). The trimethylsilyl derivatives showed evidence in their mass spectra for migration of trimethylsilyl groups in addition to hydrogen atoms.