Detection and Sequence Identification of Dinucleotides Produced from N‐Phosphoryl Alanine and Four Nucleosides by HPLC‐ESI‐MS/MS

本文利用液相色谱质谱联用技术研究了N－磷酰化丙氨酸和四种核苷（腺苷,尿苷,胞苷和鸟苷）的模板反应产物。结果表明生成了不同类型的单核苷酸和二核苷酸,并且生成的二核苷酸序列也得到了确证。研究结果揭示,二核苷酸骨架裂解形成的c离子可以作为确证二核苷酸序列的诊断离子。本文首次证明不论是在正离子模式还是在负离子模式下,c离子都可以用来确定此反应体系中生成的二核苷酸产物的序列。     

Transfer ribonucleic acids

Transfer ribonucleic acids (tRNAs)

1 Abbreviations used according to IUPAC-IUB convention: tRNA = transfer ribonucleic acid; tRNA_yeast = mixture of tRNAs from yeast; tRNA^Phe = phenylalanine specific tRNA; Phe-tRNA = tRNA esterified (“charged”) with Phe; mRNA = messenger RNA; DNA = deoxyribonucleic acid; U = uridine; A = adenosine; C = cytidine; G = guanosine; pA = 5′-adenylic acid; Ap or A- = 3′-adenylic acid; m²′G = 2′-O-methyl guanosine; m⁷G = 7-methyl guanosine; mG = N(2)-dimethyl guanosine; other methylated nucleosides are abbreviated analogously; abbreviations of other odd nucleosides are given with Fig. 2; p or – signifies phosphate; RNase = ribonuclease; DEAE = diethylaminoethyl; fMet = N-formayl methionine.

occur in all living organisms. In biological protein synthesis they accept activated amino acids which are then transferred to growing peptide chains. With molecular weights lying between 25000 and 30000, tRNAs are easily within the reach of today's physical, chemical, and biochemical methods. The primary structures of several tRNAs as well as some relationships between structure and function have been elucidated. Three-dimensional structure, specificity, and mechanism of action are the subjects of present research efforts.     

Synthesis of Selectively 15N‐Labeled 2′‐O‐{[(Triisopropylsilyl)oxy]methyl}(=tom)‐Protected Ribonucleoside Phosphoramidites and Their Incorporation into a Bistable 32Mer RNA Sequence

We present optimized reaction conditions for the conversion of 2′‐O‐{[(triisopropylsilyl)oxy]methyl}(=tom) protected uridine and adenosine nucleosides into the corresponding protected (3‐¹⁵N)‐labeled uridine and cytidine and (1‐¹⁵N)‐labeled adenosine and guanosine nucleosides 4, 6, 12 , and 18 , respectively (Schemes 1–4). On a DNA synthesizer, the resulting ¹⁵N‐labeled 2′‐O‐tom‐protected phosphoramidite building blocks 19 – 22 were efficiently incorporated into five selected positions of a bistable 32mer RNA sequence 23 (known to adopt two different structures) (Fig. 1). By 2D‐HSQC and HNN‐COSY experiments in H₂O/D₂O 9 : 1, the ¹⁵N‐signals of all base‐paired ¹⁵N‐labeled nucleotides could be identified and attributed to one of the two coexisting structures of 23 .     

Targeted serum metabolite profiling of nucleosides in esophageal adenocarcinoma

Nucleosides are indicators of the whole‐body turnover of transfer RNA. Based on the activity of cancer cells these molecules could potentially be used as cancer biomarkers, and several studies have determined that the metabolic levels of nucleosides are significantly altered in cancer patients compared to control groups. Here we report a targeted metabolite investigation of serum nucleosides in esophageal adenocarcinoma specimens. We quantified eight nucleosides using high‐performance liquid chromatography/triple quadrupole mass spectrometry (HPLC/TQMS) and determined that the metabolic levels of 1‐methyladenosine (p <2.14 × 10^?7), N²,N²‐dimethylguanosine (p <2.78 × 10^?7), N²‐methylguanosine (p <2.48 × 10^?6) and cytidine (p <6.98 × 10^?4) were significantly elevated while the concentration of uridine (p <3.74 × 10^?3) was significantly lowered in serum samples from cancer patients compared to those of control group. Our results suggest that nucleosides could potentially serve as useful biomarkers to identify esophageal adenocarcinoma. Copyright © 2010 John Wiley & Sons, Ltd.     

Simultaneous determination of nine nucleosides and nucleobases in different Fritillaria species by HPLC‐diode array detector

A sensitive and reliable HPLC‐diode‐array detector method was developed for the first time to simultaneously determine nine nucleosides and nucleobases including uracil, cytidine, guanine, uridine, thymine, inosine, guanosine, thymidine and adenosine in 13 different Fritillaria species. The analysis was performed on a BaseLine C18 column with a gradient of acetonitrile in water at a flow rate of 0.8 mL/min. The diode‐array detector wavelength was set at 260 nm for the UV detection of nucleosides and nucleobases. Satisfactory separation of these compounds was obtained in less than 40 min. The optimized method provided good linear relation (r² >0.9995 for all the investigated analytes), satisfactory precision (RSD <1.51%) and good recovery (from 97.64 to 101.16%). The established method was successfully applied to simultaneous determination of nine nucleosides and nucleobases in 61 batches of samples from 13 Fritillaria species collected from different habitats in China, which could be helpful to control the quality of Fritillaria bulbs.     

Separation and identification of purine nucleosides in the urine of patients with malignant cancer by reverse phase liquid chromatography/electrospray tandem mass spectrometry

Urinary‐modified nucleosides have a potential role as cancer biomarkers for a number of malignant diseases. High performance liquid chromatography (HPLC) was combined with full‐scan mass spectrometry, MS/MS analysis and accurate mass measurements in order to identify purine nucleosides purified from urine. Potential purine nucleosides were assessed by their evident UV absorbance in the HPLC chromatogram and then further examined by the mass spectrometric techniques. In this manner, numerous modified purine nucleosides were identified in the urine samples from cancer patients including xanthine, adenosine, N1‐methyladenosine, 5′‐deoxy‐5′‐methylthioadenosine, 2‐methyladenosine, N6‐threonylcarbamoyladenosine, inosine, N1‐methylinosine, guanosine, N1‐methylguanosine, N7‐methylguanine, N2‐methylguanosine, N2,N2‐dimethyguanosine, N2,N2,N7‐trimethylguanosine. Furthermore, a number of novel purine nucleosides were tentatively identified via critical interpretation of the combined mass spectrometric data including N3‐methyladenosine, N7‐methyladenine, 5′‐dehydro‐2′‐deoxyinosine, N3‐methylguanine, O6‐methylguanosine, N1,N2,N7‐trimethylguanosine, N1‐methyl‐N2‐ethylguanosine and N7‐methyl‐N1‐ethylguanosine. Copyright © 2009 John Wiley & Sons, Ltd.     

Nucleotides. Part LXXII

The synthesis of various N‐methylated nucleosides (m⁶A, m³C, m⁴C, m³U) is described. These minor nucleosides can be obtained by simple methylation with diazomethane of [2‐(4‐nitrophenyl)ethoxy]carbonyl(npeoc)‐protected nucleosides. These methylated compounds are easily further derivatized to fit into the scheme of the [2‐(dansyl)ethoxy]carbonyl (dnseoc) approach for RNA synthesis (dansyl=[5‐(dimethylamino)naphthalen‐1‐yl]sulfonyl). Various oligoribonucleotides containing N⁶‐methyladenosine were synthesized, underlining the usefulness of the dnseoc approach, especially for the synthesis of natural tRNA‐derived oligoribonucleotide sequences.     

Nucleosides. Part LXI. A Simple Procedure for the Monomethylation of Protected and Unprotected Ribonucleosides in the 2′-O- and 3′-O-Position Using Diazomethane and the Catalyst Stannous Chloride

Intensive studies on the diazomethane methylation of the common ribonucleosides uridine, cytidine, adenosine, and guanosine and its derivatives were performed to obtain preferentially the 2′-O-methyl isomers. Methylation of 5′-O-(monomethoxytrityl)-N²-(4-nitrophenyl)ethoxycarbonyl-O⁶-[2-(4-nitrophenyl)ethyl]-guanosine ( 1 ) with diazomethane resulted in an almost quantitative yield of the 2′- and 3′-O-methyl isomers which could be separated by simple silica-gel flash chromatography (Scheme 1). Adenosine, cytidine, and uridine were methylated with diazomethane with and without protection of the 5′ -O-position by a mono- or dimethoxytrityl group and the aglycone moiety of adenosine and cytidine by the 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) group (Schemes 2–4). Attempts to increase the formation of the 2′-O-methyl isomer as much as possible were based upon various solvents, temperatures, catalysts, and concentration of the catalysts during the methylation reaction.     

Oligodeoxynucleotides Containing 2′‐Deoxy‐1‐methyladenosine and Dimroth Rearrangement

2′‐Deoxy‐1‐methyladenosine was incorporated into synthetic oligonucleotides by phosphoramidite chemistry. Chloroacetyl protecting group and controlled anhydrous deprotection conditions were used to avoid Dimroth rearrangement. Hybridization studies of intramolecular duplexes showed that introduction of a modified residue into the loop region of the oligonucleotide hairpin increases the melting temperature. It was shown that modified oligonucleotides may be easily transformed into oligonucleotides containing 2′‐deoxy‐N⁶‐methyladenosine.     

Synthesis of Disaccharide Nucleosides by the O‐Glycosylation of Natural Nucleosides with Thioglycoside Donors

Disaccharide nucleosides constitute an important group of naturally‐occurring sugar derivatives. In this study, we report on the synthesis of disaccharide nucleosides by the direct O‐glycosylation of nucleoside acceptors, such as adenosine, guanosine, thymidine, and cytidine, with glycosyl donors. Among the glycosyl donors tested, thioglycosides were found to give the corresponding disaccharide nucleosides in moderate to high chemical yields with the above nucleoside acceptors using p‐toluenesulfenyl chloride (TolSCl) and silver triflate (AgOTf) as promoters. The interaction of these promoters with nucleoside acceptors was examined by ¹H NMR spectroscopic experiments.     

Synthesis of 2′‐O‐[(Triisopropylsilyl)oxy]methyl (= tom)‐Protected Ribonucleoside Phosphoramidites Containing Various Nucleobase Analogues

The first results of a study aiming at an efficient preparation of a large variety of 2′‐O‐[(triisopropylsilyl)oxy]methyl(= tom)‐protected ribonucleoside phosphoramidite building blocks containing modified nucleobases are reported. All of the here presented nucleosides have already been incorporated into RNA sequences by several other groups, employing 2′‐O‐tbdms‐ or 2′‐O‐tom‐protected phosphoramidite building blocks (tbdms = (tert‐butyl)dimethylsilyl). We now optimized existing reactions, developed some new and shorter synthetic strategies, and sometimes introduced other nucleobase‐protecting groups. The 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides N²‐acetylisocytidine 5 , O²‐(diphenylcarbamoyl)‐N⁶‐isobutyrylisoguanosine 8 , N⁶‐isobutyryl‐N²‐(methoxyacetyl)purine‐2,6‐diamine ribonucleoside (= N⁸‐isobutyryl‐2‐[(methoxyacetyl)amino]adenosine) 11 , 5‐methyluridine 13 , and 5,6‐dihydrouridine 15 were prepared by first introducing the nucleobase protecting groups and the dimethoxytrityl group, respectively, followed by the 2′‐O‐tom group (Scheme 1). The other presented 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides inosine 17 , 1‐methylinosine 18 , N⁶‐isopent‐2‐enyladenosine 21 , N⁶‐methyladenosine 22 , N⁶,N⁶‐dimethyladenosine 23 , 1‐methylguanosine 25 , N²‐methylguanosine 27 , N²,N²‐dimethylguanosine 29 , N⁶‐(chloroacetyl)‐1‐methyladenosine 32 , N⁶‐{{{(1S,2R)‐2‐{[(tert‐butyl)dimethylsilyl]oxy}‐1‐{[2‐(4‐nitrophenyl)ethoxy]carbonyl}propyl}amino}carbonyl}}adenosine 34 (derived from L ‐threonine) and N⁴‐acetyl‐5‐methylcytidine 36 were prepared by nucleobase transformation reactions from standard, already 2′‐O‐tom‐protected ribonucleosides (Schemes 2–4). Finally, all these nucleosides were transformed into the corresponding phosphoramidites 37 – 52 (Scheme 5), which are fully compatible with the assembly and deprotection conditions for standard RNA synthesis based on 2′‐O‐tom‐protected monomeric building blocks.     

Reliable Synthesis of Various Nucleoside Diphosphate Glycopyranoses

A reliable and high yielding synthetic pathway for the synthesis of the biologically highly important class of nucleoside diphosphate sugars (NDP‐sugars) was developed by using various cycloSal‐nucleotides 1 and 9 as active ester building blocks. The reaction with anomerically pure pyranosyl‐1‐phosphates 2 led to the target NDP‐sugars 20 – 45 in a nucleophilic displacement reaction, which cleaves the cycloSal moiety in anomerically pure forms. As nucleosides cytidine, uridine, thymidine, adenosine, 2′‐deoxy‐guanosine and 2′,3′‐dideoxy‐2′,3′‐didehydrothymidine were used while the phosphates of D ‐glucose, D ‐galactose, D ‐mannose, D ‐NAc‐glucosamine, D ‐NAc‐galactosamine, D ‐fucose, L ‐fucose as well as 6‐deoxy‐D ‐gulose were introduced.     

Rapid Sample Pretreatment,Identification and Determination of Active Constitutents in Water‐soluble Radix isatidis Extract via MAE,ESI‐MS and RODWs‐HPLC

In this study, we successfully studied water‐soluble extract from Radix isatidis. Optimized conditions of MAE were listed, the sample can be extracted completely in 10 minutes under microwave power of 400W and solid/liquid ratio of 1:80. Active compounds in water‐soluble extract from R. isatidis were identified with HPLC‐DAD/ESI‐MS, these compounds followed by cytidine, uridine, guanosine, (R,S)‐goitrin and adenosine. RODWs–HPLC as a new sensitive chromatography were also first proposed and investigated, we favoringly used this method for simultaneous determination of these active constitutents in water‐soluble R. isatidis extract. Chromatographic separation was performed on a Diamonsil C18 column (5 μm, 150 mm × 4.6 mm) with a mobile phase gradient consisting of methanol and water at a flow‐rate of 1.0 mL/min, detection wavelengths 240, 250, 260 and 270 nm, the retention times of the tested five compounds were about 4.2, 5.8, 11.1, 14.2 and 20.8 min respectively, the limits of detection were 15, 12, 20, 5.8 and 24 ng/mL for cytidine, uridine, guanosine, (R,S)‐goitrin and adenosine respectively, their linear ranges were between 0.045 and 350 μg/mL with correlation coefficient (R) of 0.9998‐0.9999. The relative standard deviations (RSDs) of intra‐day and inter‐day assays were 0.30‐2.36% and 0.86‐2.54% respectively. Extraction recoveries were 94.25‐106.21%. This novel analytical method was shown to be simple, low‐cost, sensitive and reliable for multiple components in complex or undeveloped materials via MAE, ESI‐MS and RODWs‐HPLC.     

The “Speedy” Synthesis of Atom‐Specific 15N Imino/Amido‐Labeled RNA

Although numerous reports on the synthesis of atom‐specific ¹⁵N‐labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid‐phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of ¹⁵N(1) adenosine and ¹⁵N(1) guanosine amidites, which are the much needed counterparts of the more straightforward‐to‐achieve ¹⁵N(3) uridine and ¹⁵N(3) cytidine amidites in order to tap full potential of ¹H/¹⁵N/¹⁵N‐COSY experiments for directly monitoring individual Watson–Crick base pairs in RNA. Demonstrated for two preQ₁ riboswitch systems, we exemplify a versatile concept for individual base‐pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered.     

Radiolysis and radioracemization of RNA ribonucleosides: implications for the origins of life

The RNA nucleosides, namely adenosine, cytidine, guanosine and uridine were γ-radioyzed in solid state and in vacuo at room temperature to a total dose of 3.2 MGy. Through electronic absorption spectroscopy, differential scanning calorimetry and through polarimetry and optical rotatory dispersion spectroscopy, it was found that the purine-based nucleosides (adenosine and guanosine) show a much higher radiolysis resistance than the pyrimidine-based nucleosides (cytidine and uridine). In an astrochemical/astrobiological context, these results may explain why purine nucleobases are found in practically all carbonaceous chondrite meteorites while the pyrimidine nucleobases are absent or below the detection limits of the current analytical techniques. In the hypothesis that both purines and pyrimidines nucleobases were present in certain bodies at the beginning of the solar system 4.6?×?10⁹ years ago, the radiolysis due to radionuclides decay has destroyed more easily and completely the pyrimidine bases due to their much lower radiolysis resistance than the purine bases.     

An effective method for the preparation of O6 -substituted guanosine and n3-substituted uridine derivatives via the corresponding stannylated intermediates

O₆-substituted guanosine and N³-substituted uridine derivatives were obtained in high yields by stannylation of the corresponding unsubstituted nucleosides with bis(tributyltin)-oxide followed by treatment with various electrophiles.     

Synthesis of Thymidine,Uridine, and 5‐Methyluridine Nucleolipids: Tools for a Tuned Lipophilization of Oligonucleotides

Three pyrimidine nucleosides, uridine ( 1 ), 5‐methyluridine ( 6 ), and 2′‐deoxythymidine ( 11 ), were converted to amphiphilic nucleolipids. Compounds 1 and 6 were lipophilized by introduction of symmetric ketal moieties with various carbon chain lengths (i.e., 5–17). Two ketal derivatives, 2b and 7a , were additionally further hydrophobized by N(3)‐farnesylation. 2′‐Deoxythymidine was alkylated at N(3) with a cetyl (=hexadecyl) residue, either directly or, after complete orthogonal protection of the sugar OH groups, by Mitsunobu reaction with hexadecan‐1‐ol. Some of the nucleolipids were subsequently converted to their 2‐cyanoethyl phosphoramidites (5′ or 3′), one of which was used for an exemplary synthesis of a lipo‐oligonucleotide. The sequence of this lipo‐oligonucleotide is an encoded manifestation of Pythagoras' law, created with a key table in which the letters of the alphabet, the numbers from 0 to 9 as well as the mostly used mathematical symbols are allocated to a ribonucleic acid triplet of the genetic code.     

Nucleotides. Part XLII. The 2-dansylethoxycarbonyl (= 2-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}ethoxycarbonyl; dnseoc) group for protection of the 5′-hydroxy function in oligoribonucleotide synthesis

The 2-dansylethoxycarbonyl (Dnseoc) group was employed for protection of the 5′-hydroxy function in oligoribonucleotide synthesis by the phosphoramidite approach using the acid-labile tetrahydro-4-methoxy-2H-pyran-4-yl (Thmp) group for 2′-protection. The syntheses of monomeric building blocks, both phosphoramidites and nucleoside-functionalized supports, are described for the four common nucleosides adenosine, guanosine, cytidine, and uridine, and for the two modified minor nucleosides ribothymidine (= ribosylthymine) and pseudouridine.     

7‐Iodo‐5‐aza‐7‐deazaguanine: Syntheses of Anomeric D‐ and L‐Configured 2‐Deoxyribonucleosides

Iodination of N²‐isobutyryl‐5‐aza‐7‐deazaguanine ( 7 ) with N‐iodosuccinimide (NIS) gave 7‐iodo‐N²‐isobutyryl‐5‐aza‐7‐deazaguanine ( 8 ) in a regioselective reaction (Scheme 1). Nucleobase‐anion glycosylation of 8 with 2‐deoxy‐3,5‐di‐O‐toluoyl‐α‐D ‐ or α‐L ‐erythro‐pentofuranosyl chloride furnished anomeric mixtures of D ‐ and L ‐nucleosides. The anomeric D ‐nucleosides were separated by crystallization to give the α‐D ‐anomer and β‐D ‐anomer with excellent optical purity. Deprotection gave the 7‐iodo‐5‐aza‐7‐deazaguanine 2′‐deoxyribonucleosides 3 (β‐D ; ≥99% de) and 4 (α‐D ; ≥99% de). The reaction sequence performed with the D ‐series was also applied to L ‐nucleosides to furnish compounds 5 (β‐L ; ≥99% de) and 6 (α‐L ; ≥95% de).