Mass spectrometric identification of modified urinary nucleosides used as potential biomedical markers by LC–ITMS coupling

In diseases accompanied by strong metabolic disorders, like cancer and AIDS, modifying enzymes are up- or down-regulated. As a result, many different types of metabolic end-products, including abnormal amounts of modified nucleosides, are found in urine. These nucleosides are degradation products of an impaired ribonucleic acid (RNA) metabolism, which affects the nucleoside pattern in urine. In several basic experiments we elucidated the fragmentation pathways of 16 characteristic nucleosides and six corresponding nucleic bases that occur in urine using electrospray ionization ion trap MS⁵ (ESI-ITMS) experiments operated in positive ionization mode. For urinary nucleoside analysis, we developed an auto-LC–MS³ method based on prepurification via boronate gel affinity chromatography followed by reversed phase chromatography. For this purpose, an endcapped LiChroCART Superspher RP 18 column with a gradient of ammonium formate and a methanol–water mixture was used. This method gives a limit of detection of between 0.1 and 9.6 pmol for 15 standard nucleosides, depending on the basicity of the nucleoside. Overall, the detection of 36 nucleosides from urine was feasible. It was shown that this auto-LC–MS³ method is a valuable tool for assigning nucleosides from complex biological matrices, and it may be utilized in the diagnosis of diseases associated with disorders in RNA metabolism.     

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.     

First synthesis of 2′-oxabicyclo[3.1.0]hexyl nucleosides with a north conformation

The first synthesis of 2′-oxabicyclo[3.1.0]hexyl nucleosides, a novel class of bicyclonucleosides, with a north conformation was successfully accomplished starting from (S)-epichlorohydrin via a tandem alkylation-lactonization, a less steric hindrance-dependent silylation in equilibrium and a coupling reaction with nucleobases under Vorbruggen conditions. Addition of acetic acid prevented a benzoyl group from migrating during desilylation with TBAF. ¹H NMR and X-ray crystallographic analysis indicated that the anomeric effect worked on the β-2′-oxabicyclo[3.1.0]hexyl nucleosides.     

Synthesis and Evaluation of Some Uracil Nucleosides as Promising Anti-Herpes Simplex Virus 1 Agents

Since herpes simplex virus type 1 (HSV-1) infection is so widespread, several antiviral drugs have been developed to treat it, among which are uracil nucleosides. However, there are major problems with the current medications such as severe side-effects and drug resistance. Here we present some newly synthesized cyclic and acyclic uracil nucleosides that showed very promising activity against HSV-1 compared to acyclovir.     

双环及三环核苷的合成

摘要综述了天然双环核苷、抗病毒构效研究中的双环核苷和反义寡核苷酸领域中双环及三环核苷的合成研究进展,介绍了常规官能团转化法及近年来出现的自由基环合、1,3-偶极环加成和烯烃复分解等新方法。     

Ab initio determination of the flexibility of 2'-aminoribonucleosides and 2'-aminoarabinonucleosides inserted in duplexes

The sugar puckering of adenosine and uridine nucleosides with an amino group at 2' in the ribo or arabino orientations are determined using high-level quantum mechanical calculations Only the conformations that have dihedrals compatible with their insertion into a duplex are retained. The amino group has always been found to be pyramidal and its orientation governs the conformation of the sugar. The energetically most favorable conformation of the 2'-aminoribonucleosides has the south puckering but must be discarded. For another orientation of the 2'-amino group, the conformation is energetically less favorable but has the north puckering. Calculations performed in the presence of a water molecule give similar results but with a smaller energy gap. The model then explains why the insertion of a 2'-aminoribonucleotide destabilizes double-stranded RNAs and also double-stranded DNAs. In the arabino orientation, an NH(2) substituent at 2' favors north puckering. In contrast to 2'-aminoribonucleosides, deoxynucleosides inserted into a duplex remain in the most energetically favorable conformation compatible with the canonical values of the torsion angles. The whole relaxed potential map, in the amplitude/pseudorotation space, shows that for natural deoxyadenosine there is only one valley in the east running from south to north puckering.     

Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine

5-Formylcytosine (fC or (5-CHO)dC) and 5-carboxylcytosine (caC or (5-COOH)dC) have recently been identified as constituents of mammalian DNA. The nucleosides are formed from 5-methylcytosine (mC or (5-Me)dC) via 5-hydroxymethylcytosine (hmC or (5-HOMe)dC) and are possible intermediates of an active DNA demethylation process. Here we show efficient syntheses of phosphoramidites which enable the synthesis of DNA strands containing these cytosine modifications based on Pd(0)-catalyzed functionalization of 5-iododeoxycytidine. The first crystal structure of fC reveals the existence of an intramolecular H-bond between the exocyclic amine and the formyl group, which controls the conformation of the formyl substituent. Using a newly designed in vitro mutagenicity assay we show that fC and caC are only marginally mutagenic, which is a prerequisite for the bases to function as epigenetic control units.     

微波促进的6-位磷功能化的非环嘌呤核苷类似物的合成

以2,6-二氯嘌呤核苷和亚磷酸酯为原料,通过微波促进的Arbuzov反应,一步合成6位磷酸酯取代的嘌呤核苷类化合物,然后再进一步衍生,得到6-位磷酸单酯和6-位磷酸取代的嘌呤核苷类新化合物.得到的非环嘌呤核苷类化合物通过核磁共振图谱、高分辨质谱和红外光谱进行了结构确认.     

Selenium‐Mediated Dehalogenation of Halogenated Nucleosides and its Relevance to the DNA Repair Pathway

Halogenated nucleosides can be incorporated into the newly synthesized DNA of replicating cells and therefore are commonly used in the detection of proliferating cells in living tissues. Dehalogenation of these modified nucleosides is one of the key pathways involved in DNA repair mediated by the uracil‐DNA glycosylase. Herein, we report the first example of a selenium‐mediated dehalogenation of halogenated nucleosides. We also show that the mechanism for the debromination is remarkably different from that of deiodination and that the presence of a ribose or deoxyribose moiety in the nucleosides facilitates the deiodination. The results described herein should help in understanding the metabolism of halogenated nucleosides in DNA and RNA.     

Synthesis and evaluation of hexitol nucleoside congeners as ambiguous nucleosides

A series of anhydrohexitol nucleoside congeners was synthesized as ambiguous or so-called universal nucleosides and was evaluated for their hybridization potential and discrimination properties. The 1,5-anhydro-2,3-dideoxy-2-(5-nitroindazol-1-yl)-d-arabino-hexitol 4e showed the lower spread in T_m values upon hybridization to the natural bases, with minimal destabilization, and therefore behaved as a true ambiguous nucleoside.     

Chemoselective Acylation of Nucleosides

Acylated nucleoside analogues play an important role in medicinal chemistry and are extremely useful precursors to various other nucleoside analogues. However, chemoselective acylation of nucleosides usually requires several protection and deprotection steps due to the competing nucleophilicity of hydroxy and amino groups. In contrast, direct protecting-group-free chemoselective acylation of nucleosides is a preferred strategy due to lower cost and fewer overall synthetic steps. Herein, a simple and efficient chemoselective acylation of nucleosides and nucleotides under mild reaction conditions, giving either O- or N-acylated products respectively with excellent chemoselectivity is reported.     

From cyclopentadiene to isoxazoline-carbocyclic nucleosides: a rapid access to biological molecules through nitrosocarbonyl chemistry

A rapid access to carbocyclic nucleosides containing a fused isoxazoline ring is proposed starting from cyclopentadiene. The route involves an hetero Diels-Alder cycloaddition reaction of nitrosocarbonylbenzene followed by a 1,3-dipolar cycloaddition of nitrile oxides, cleavage of the N-O tether and elaboration of the heterocyclic aminols into nucleosides via linear construction of purine and pyrimidine heterocycles.     

Dehalogenation of Halogenated Nucleobases and Nucleosides by Organoselenium Compounds

Halogenated nucleosides, such as 5-iodo-2′-deoxyuridine and 5-iodo-2′-deoxycytidine, are incorporated into the DNA of replicating cells to facilitate DNA single-strand breaks and intra- or interstrand crosslinks upon UV irradiation. In this work, it is shown that the naphthyl-based organoselenium compounds can mediate the dehalogenation of halogenated pyrimidine-based nucleosides, such as 5-X-2′-deoxyuridine and 5-X-2′-deoxycytidine (X=Br or I). The rate of deiodination was found to be significantly higher than that of the debromination for both nucleosides. Furthermore, the deiodination of iodo-cytidines was found to be faster than that of iodo-uridines. The initial rates of the deiodinations of 5-iodocytosine and 5-iodouracil indicated that the nature of the sugar moiety influences the kinetics of the deiodination. For both the nucleobases and nucleosides, the deiodination and debromination reactions follow a halogen-bond-mediated and addition/elimination pathway, respectively.     

Binding of nucleosides with the cytotoxic plant alkaloid sanguinarine: Spectroscopic and thermodynamic studies

In spite of a large number of studies of the interaction of the cytotoxic plant alkaloid sanguinarine(SAN) with nucleic acids,the anticancer mechanism of SAN is still not clear.In contrast to the large number of studies of the interaction mechanism of SAN with DNA,there have been relatively few studies of the interaction of SAN with nucleosides.In this work,the interaction of SAN with three nucleosides-thymidine(T),uridine(U),and adenosine(A)-was investigated using a combination of conventional fluorescence and UV-vis spectroscopic techniques;thermodynamic calculations were also carried out at physiological pH 7.2.The binding processes of SAN with the different nucleosides were characterized by hypochromic and bathochromic effects in the absorption spectra of SAN and by the quenching of the fluorescence intensity of SAN.The measurements of fluorescence lifetime,the variations of the absorption spectra of the fluorophore,and the dependence of the quenching on the temperature indicated that the fluorescence quenching is static.The Stern-Volmer plot is nonlinear and approximately quadratic showing that,in this process,one SAN molecule can bind with two nucleoside molecules.These studies,together with our earlier studies of the binding of SAN with cytidine(C) and guanosine(G),showed that the binding constants of SAN with the five nucleosides at T = 308.15,318.15,and 328.15 K decreased in the order C > G > T > U > A and at T = 298.15 K decreased in the order G > C > T > U > A,and that the binding of SAN with the various nucleosides is not only slightly exothermic but also entropy-driven.All these results together with fluorescence quenching experiments advance good evidence concerning the interaction of SAN with various nucleosides.Such studies of the interaction mechanism of alkaloids with DNA may promote the development of new drugs.     

A new protecting group for the exocyclic amino groups of nucleosides

A new protecting group has been developed for the exocyclic amino groups of nucleosides that occur in DNA. 3-Phenyl-[{N-(2-trimethylsilyl-ethoxycarbonyl)-2-amino}]-propanoic acid used as the protective agent.     

Direct determination of nucleosides in the urine of patients with breast cancer using column-switching liquid chromatography-tandem mass spectrometry

We developed an analytical method for a simple, sensitive and simultaneous determination of oxidized nucleosides in urine using column-switching liquid chromatography-electrospray/tandem mass spectrometry (LC-ESI/MS/MS). We connected two columns through a six-way switching valve and effectively separated nucleosides in the urine from the interference by column-switching liquid chromatography. We monitored separated nucleosides using positive ionization tandem mass spectrometry in selective reaction monitoring (SRM) mode. The calibration ranges of nucleosides were 0.2-100 nmol/mL. The linearity of the method was 0.994-0.999, and the limits-of-detection (LOD) at a signal-to-noise (S/N) ratio of 3 were 0.1-0.2 nmol/mL. The coefficients of variation were in the range 2.28-11.74% for within-day variation and 4.36-11.15% for day-to-day variation, respectively. To explore the relationship between breast cancer and the nucleosides level in human urine, we measured the concentrations of nucleosides in female patients with breast cancer (n = 30) and in normal female subjects (n = 30). The concentration of nucleosides was significantly increased in patients with breast cancer when compared with the normal controls (1-methyladenosine; p < 0.005, N(2),N(2)-dimethylguanosine; p < 0.01, 5-hydroxymethyl-2'-deoxyuridine; p < 0.001, 8-hydroxy-2-deoxyguanosine; p < 0.001). Therefore, the elevated levels of nucleosides could be used as an important biomarker for breast-cancer research.     

A new method for inversion of hydroxyl group of carbocyclic nucleosides

The hydroxyl group of carbocyclic nucleosides was inversed when the compounds were treated with Me_3SiCl,KCN and a catalytic amount of NaI in DMF/CH_3CN.     

Solvent- and environment-dependent fluorescence of modified nucleobases

Fluorescent nucleosides with modified nucleobases are useful tools for detecting nucleic acids and probing their structures and functions. Nucleobases are suitable for modification because 1) intrinsically light-absorbing nucleobases can be converted to fluorescent chromophores by simple chemical modification, 2) attaching substituents to nucleobases at appropriately selected positions does not inhibit base pairing or duplex formation, and 3) duplex formation and protein interactions affect the environment of nucleobases, causing changes in their fluorescence intensities and/or wavelengths. This review summarizes recent fluorescent nucleosides and their photophysical properties, such as absorption wavelength, emission wavelength, and fluorescence quantum yield together with their solvent dependency.     

整体柱高效液相色谱法测定尿中核苷的方法研究

尿中修饰核苷已被研究用作可能的肿瘤标记物,目前最常用的分析方法为反相高效液相色谱法,其不足之处是分析周期太长。为此,建立了应用整体柱的高效液相色谱方法对尿中修饰核苷进行分析,所用缓冲液为25 mmol/L磷酸二氢钾溶液(pH 4.55)和60%(体积分数）的甲醇水溶液,线性梯度洗脱,检测波长为260 nm。12种目标核苷可被完全分离。所建立的方法在分离度、线性、重现性、灵敏度及回收率等指标上与普通反相液相色谱法相近,但分析周期大大缩短,仅为23 min,适合于大量临床样品的分析。     

Efficient synthesis of extended guanine analogues designed for recognition of an A·T inverted base pair in triple helix based-strategy

We report herein an efficient synthesis of new nucleosides N1, N2, and N3 as extended guanine analogues, derived from aminobenzimidazole and thymine or 5-substituted uracil. These nucleosides were devised for the recognition of an A·T inverted base pair by three hydrogen bonds, in triple helix-based technology.