Comparative studies on the mechanism of uridine phosphorolysis

We have used quantum mechanical method to study the transition states(TSs) of uridine phosphorolysis reaction. Comparing the four different reaction pathways and the five transition states obtained, we conclude that enzymatic uridine phosphorolysis takes place mainly according to acid-catalyzed SN2 mechanism. The proposed reaction pathway is consistent with many experimental results.     

Synthesis of 5‐Radioiodoarabinosyl Uridine Analog for Probing the HSV‐1 Thymidine Kinase Gene

Tumor cells transduced with herpes simplex virus thymidine kinase gene have been intensively applied to the field of positron emission tomography via imaging of its substrate. As a pilot synthesis approach, a facile preparation of 5‐[¹²⁵I] iodoarabinosyl uridine starting from commercially available uridine is reported herein.     

The Synthesis of Amino Acid Methyl Ester 5′-Phosphoamidates of Protected Uridine

In this article, we used the Atherton–Todd reaction to synthesize amino acid methyl ester 5′-phosphoamidates of uridine as prodrugs. Their structures were confirmed by ¹H NMR, ³¹P NMR, ¹³C NMR, IR, and mass spectrometry.

Supplemental materials are available for this article. Go to the publisher′s online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.     

微波辅助快速制备核-壳型尿苷印迹聚合物及其在线富集应用研究

采用微波辅助加热,以尿苷为模板分子,丙烯酰胺(AA)为功能单体,乙二醇二甲基丙烯酸酯(EGDMA)为交联剂,快速制备尿苷印迹聚合物,聚合时间大大缩短,仅为传统加热的1/8.采用红外光谱和扫描电镜对印迹聚合物进行表征,结果表明二氧化硅表面成功包覆尿苷印迹壳层;该印迹聚合物颗粒分散均匀,印迹壳层厚度约为100 nm.将该印...     

高效液相色谱/二极管阵列检测/质谱/质谱(HPLC/DAD/MS2)联用在板蓝根注射液成分鉴定中的应用

用HPLC/DAD/MS2联用仪,鉴定了板蓝根注射液中含有的核苷类物质。色谱条件:Luna C18 色谱柱(250 mm×4.6 mm i.d., 5 μm);甲醇-水梯度洗脱,流量0.8 mL/min; 柱温25 ℃。用二极管阵列检测器记录各个色谱峰的紫外吸收光谱,色谱检测波长254 nm。质谱条件:电喷雾离子源(ESI);正离子检测;扫描范围m/z 50-800。记录质量色谱图和各个色谱峰的一级、二级质谱图,并对质谱结果进行解析,通过与对照品比较,确定板蓝根注射液样品中含有腺苷、鸟苷、尿苷、胞苷及腺     

Monitoring of metabolic profiling and water status of Hayward kiwifruits by nuclear magnetic resonance

The metabolic profiling of kiwifruit (Actinidia deliciosa, Hayward cultivar) aqueous extracts and the water status of entire kiwifruits were monitored over the season (June-December) using nuclear magnetic resonance (NMR) methodologies. The metabolic profiling of aqueous kiwifruit extracts was investigated by means of high field NMR spectroscopy. A large number of water-soluble metabolites were assigned by means of 1D and 2D NMR experiments. The change in the metabolic profiles monitored over the season allowed the kiwifruit development to be investigated. Specific temporal trends of aminoacids, sugars, organic acids and other metabolites were observed.The water status of kiwifruits was monitored directly on the intact fruit measuring the T₂ spin-spin relaxation time by means of a portable unilateral NMR instrument, fully non-invasive. Again, clear trends of the relaxation time were observed during the monitoring period.The results show that the monitoring of the metabolic profiling and the monitoring of the water status are two complementary means suitable to have a complete view of the investigated fruit.     

Analysis of nucleotides binding to chromatography supports provided by nuclear magnetic resonance spectroscopy

The epitope mapping of nucleotides bound to three chromatography supports is accomplished using saturation transfer difference (STD)-NMR spectroscopy. This experiment involves subtracting a spectrum in which the support was selectively saturated from one recorded without support saturation. In the difference spectrum only the signals of the ligands that bind to the support and received saturation transfer remain. The nucleotide protons in closer contact with the support have more intense signals due to a more efficient transfer of saturation. We investigate the effects on the binding to the nucleotides by the introduction of a spacer arm between l-histidine and Sepharose. Our NMR experiments evidence a clear contribution of the spacer to the interaction with all the nucleotides, increasing the mobility of the amino acid and giving different STD responses. This enhanced mobility originates the reinforcement of the interactions with the sugar moiety and phosphate group of 5'-CMP and 5'-TMP or the base of 5'-GMP and 5'-UMP. Hence, with this study we show that by using STD NMR technique on chromatographic systems it is possible to provide a fast, robust and efficient way of screening the atoms involved in the binding to the supports.     

Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment

Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions.     

Combined use of Overhauser spectroscopy and NMR diffusion experiments for mapping the hydration structure of nucleosides: structure and dynamics of uridine in water

Complementary results from 13C intermolecular nuclear Overhauser effects (NOE), 1H-13C heteronuclear Overhauser spectroscopy (HOSEY) and 1H-NMR diffusion measurements were used for probing the structure of the first solvation shell of uridine in water. It is demonstrated that a cyclic dihydrate is formed. The two water molecules produce two hydrogen bonds with the two oxygen atoms from the pyrimidine ring and accept only one hydrogen bond from the amide proton. The dihydrate has only a short lifetime as compared with the rotational correlation time of the free nucleoside. The chemical exchange constant of the amide proton with water is then estimated by diffusion experiments. The results are consistent with previous data obtained for uracil in water and provide interesting information about water accessibility in nucleic acid bases.     

Interaction between N-Phospho-Amino Acids and Nucleoside in Aqueous Medium

Thebiosynthesisofnucleicacid,oneofthemostimportantbio-macromolecules,isahighlyelegantprocess,whichinvolvestheparticipationofmanyenzymesandenergycarriers,suchasATP',whilechemicalsynthesisofoligonucleotidesgenerallyinvolvescomplicatedprotectinganddeprotectingprocesses'.Inthepreviouswork,nucleotidesandoligonucleotidesweredirectlyformedacthereaction,,-ofN-(O,O-diisopropyl)phosphorylthreonineanduridineinanhydrouspyridine'.SoN-(O,O-diisopropyl)phospho-aminoacid(DIPP-aa)wasproposedasamodelcompou…