BIOTECHNOLOGY LETTERS
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2017
·Vol. 39
·期 12
·1903-1910
·
IF 1.73
Liu Ke,Zhou Youzhi,Zhang Jinsong,Chu Jianlin,Zhang Yewei,He Bingfang
Objective To isolate a thermostable pyrimidine nucleoside phosphorylase (PyNP) from mesophilic bacteria by gene mining. Results
Bb PyNP from Brevibacillus borstelensis LK01 was isolated by gene mining. Bb PyNP had a highest 60% identity with that of reported PyNPs. Bb PyNP could catalyze the phosphorolysis of thymidine, 2′-deoxyuridine, uridine and 5-methyuridine. Bb PyNP had good thermostability and retained 73% of its original activity after 2 h incubation at 50 °C. Bb PyNP had the highest activity at an optimum alkaline pH of 8.5. Bb PyNP was stable from pH 7 to 9.8. Under preliminary optimized conditions, the biosynthesis of various 5-halogenated pyrimidine nucleosides by Bb PyNP reached the yield of 61–84%. Conclusion An efficient approach was estimated in isolating thermostable PyNP from mesophilic bacteria.
研究领域:
生物化学
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酶学
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生物技术
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PubMed
高影响因子
CHROMATOGRAPHIA
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2024
·
IF 1.2
Xiang Yuqian,Huang Yu,Yan Xiaohui,Zhu Zhipeng,Wu Dapeng,Gao Peng,Li Jiulong
In this work, in order to investigate retention and selectivity mechanism on hydrophilic interaction liquid chromatography (HILIC), one of the most common hydrophilic stationary phases, polyethylene glycols (PEG) of different molecular weights (200, 400, 800 and 2000 Dalton) were covalently bonded to porous silica spheres via isocyanate silane. The PEG stationary phase was then characterized in detail by infrared spectroscopy, scanning electron microscope, nitrogen adsorption–desorption isotherms, and thermogravimetric analysis, and the PEG bonding density was determined as 2.7, 2.3, 1.4, 0.26 μmol m −2 , respectively. The HILIC retention mechanism was systematically conducted by quantitative evaluation of the effect of partitioning and adsorption, hydrogen bonding and hydrophilicity, and temperature on the retention of nucleosides and nucleobases. It was found that the retention was highly relevant on the partitioning, hydrogen bonding between solutes and PEG, and strong electrostatic interactions (attractive/repulsive) between solutes and silica. To further assess the separation performance, three kinds of polar compounds (nucleosides and nucleobases, organic acids and β-blockers) were chosen as probe compounds. Among the four PEG stationary phases, it was found that the higher PEG ligand density generally resulted into more superior separation performance to these polar compounds, that is, PEG200-bonded stationary phase with highest ligand density of 2.7 μmol m −2 generated better resolution. Furthermore, higher ligand bonding mass would increase the retention of nucleosides, nucleobases and organic acids except β-blockers. Generally, the HILIC stationary phase with continuous and dense hydrophilic layer is beneficial to the separation of polar analytes. Graphical Abstract
研究领域:
分析化学
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色谱学
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高影响因子
MICROCHEMICAL JOURNAL
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2025
·
IF 5.1
Zhipeng Zhu,Yuqian Xiang,Xiaohui Yan,Chenglong Shi,Cheng Chen,Hongxing Liu,Bin Wang,Yanshuo Li,Dapeng Wu
Crosslinked and uncrosslinked polyacrylamide stationary phases were prepared on porous silica gel (SiL-PAAm) by atom transfer radical polymerization (ATRP), and their hydrophilic interaction liquid chromatography (HILIC) separation performance and stability were evaluated systematically. After aminosilylation and esterification with 2-bromoisobutyryl bromide on silica gel, surface-initiated ATRP with acrylamide or acrylamide/N,N’-methylenebisacrylamide mixtures at molar ratios of 1:0.1 and 1:0.2 was carried out, and SiL-PAAm-0, SiL-PAAm-10, and SiL-PAAm-20 HILIC materials were obtained. SiL-PAAms were characterized by FT-IR, TGA and nitrogen adsorption–desorption isotherms. It was confirmed that these three SiL-PAAms had very similar specific surface area of 130–143 m 2 g −1 , pore size of 8.67–8.89 nm, and PAAm bonding amount of 177–181 mg g −1 . Their HILIC performances were evaluated and compared by separating nucleosides, vitamins, sugars, and amino acids, respectively. It was found that SiL-PAAms exhibited significantly stronger retention and higher separation selectivity than both bare silica and commercial amide columns. However, an excessive increase in the crosslinking degree also led to a decrease in retention strength. Additionally, the SiL-PAAm-10 and SiL-PAAm-20 exhibited significantly reduced column bleeding and enhanced reproducibility, far surpassing both SiL-PAAm-0 and commercial amide columns. Generally, the suitably crosslinked PAAm by ATRP has been proven as one highly efficient and robust HILIC stationary phase for the chromatographic separation of a wide range of polar compounds.
研究领域:
分析化学
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材料科学
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高影响因子
BMC PLANT BIOLOGY
·
2025
·Vol. 25
·期 1
·1-17
·
IF 4.8
Deng Dehai,Qin Yichao,Lin Xiuying,Chu Meng,Lv Daizhu,Lin Huan
Background The oil palm ( Elaeis guineensis ) is a crucial agricultural commodity, yielding the highest oil output among oil-bearing crops. Despite its significance, productivity challenges persist due to genetic and environmental factors. This study breaks new ground by mapping tRNA modifications in oil palm, exploring their roles during fruit ripening, an area not extensively studied in non-model crops. Results Utilizing advanced RNA mass spectrometry techniques, we identified 48 distinct tRNA modifications across 88 sites, alongside 164 genes associated with tRNA modifying enzymes. This comprehensive mapping reveals the decreasing nature of most tRNA modifications during fruit development, except for adenosine 2’-O methylation (Am). It hints at a gradual weakening of protein translation quality control and highlights a unique role for Am during fruit ripening. Additionally, lipidomic analysis tracked 674 lipids in oil palm fruits, indicating a correlation between tRNA modifications and the accumulation of specific lipids. Conclusions This study mapped tRNA modifications in oil palm for the first time and showed the diversity of dynamic changes in tRNA modifications as the fruits develop.
研究领域:
植物学
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分子生物学
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农业科学
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PubMed
高影响因子
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
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2012
·Vol. 404
·期 5
·1477-1484
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IF 3.778
Zhang Lei,Dai Xiaojun,Xu Fei,Wang Fuqiang,Gong Bolin,Wei Yinmao
A novel imidazole-functionalized stationary phase for hydrophilic interaction chromatography (HILIC) was prepared via surface-initiated atom transfer radical polymerization (SI-ATRP). 1-Vinylimidazole as a monomer was polymerized on the surface of initiator-immobilized silica by SI-ATRP using CuCl and 2,2′-bipyridyl as a catalyst. The graft chain length and polymer grafting density were controlled by varying the ratio of monomer to initiator. The resulting materials were characterized by elemental analysis and thermogravimetric analysis. Then, high-performance liquid chromatography separation of eight nucleobases/nucleosides was performed on the imidazole-functionalized chromatographic column in HILIC mode. The effects of mobile phase composition, buffer pH, and column temperature on the separation of nucleobases/nucleosides were investigated, and the retention mechanisms were studied. Chromatographic parameters were calculated, and the results showed that surface adsorption through hydrogen bonding and electrostatic interaction dominated the retention behavior of the solutes in HILIC mode. Lastly, the stationary phase was successfully used to determine the nucleobases and nucleosides from Cordyceps militaris .
研究领域:
分析化学
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色谱技术
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PubMed
高影响因子
JOURNAL OF CHROMATOGRAPHY A
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2016
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IF 3.926
Jialiang Guo,Yuan Xiao,Yuanjing Lin,Jacques Crommen,Zhengjin Jiang
Low column efficiency for enantioseparations in capillary liquid chromatography (CLC) is a major problem commonly encountered with β -cyclodextrin ( β -CD) functionalized polymer-based monoliths. In order to investigate the effect of the crosslinker type on enantioseparation performance, three commonly used crosslinkers, i.e. 1,4-bis(acryloyl)piperazine (PDA), ethylene dimethacrylate (EDMA) and N , N -methylenebisacrylamide (MBA), were copolymerized using the one-pot approach with glycidyl methacrylate-mono-6-amino-6-deoxy- β -CD (GMA-NH 2 - β -CD) as functional monomer. The three monolithic columns, including poly(GMA-NH 2 - β -CD- co -PDA) and poly(GMA-NH 2 - β -CD- co -MBA), as well as the previously reported column poly(GMA-NH 2 - β -CD- co -EDMA) were systematically compared with respect to morphology, permeability, β -CD density, retention mechanism and efficiency. The enantioseparation ability of each column was evaluated using 14 chiral compounds, including mandelic acid derivatives, profens, N -derivatized amino acids, and herbicides, as test substances. The β -CD-functionalized monolith with MBA as crosslinker was found to exhibit higher polarity, higher column efficiency and better enantioseparation performance than those with PDA or EDMA as crosslinker.
研究领域:
分析化学
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色谱技术
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高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
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2021
·
IF 3.935
Zhiwei Lu,Xinyue Liu,Xuejiao Li,Chuanjia Zhai,Yulian Shi,Xiaoyan Gao
Profiling of new modified nucleosides from urine plays an important role in exploring biomarkers for cancer. However, limitations from the nature of the compound, bio-sample, instrumentation, and analytical method pose great challenges to achieving a comprehensive analysis of urinary nucleosides. Herein, a method of BH + /MH + -matching (BH + , protonated nucleobase ion; MH + , protonated precursor ion) was developed to discover novel modified nucleosides from human urine samples based on solid phase extraction targeted toward specific modified nucleosides combined with ultra-performance liquid chromatography coupled with dual-mass spectrometry platforms. Firstly, nucleosides containing 2,3-diol structure on ribose were effectively enriched by PBA (Phenylboronic Acid) cartridges. Secondly, a novel method, “BH + /MH + -matching” was established to achieve rapid screening of modified nucleosides. Based on the in-source fragmentation pattern of nucleosides, a series of putative modified nucleosides were rationally designed and characterized by matching the daughter ion BH + and its parent ion MH + in UPLC-MS E spectra. Finally, as a complement to UPLC Q-TOF/MS, UPLC Q-Trap/MS was employed to validate the structure of putative compounds by MRM-IDA-EPI mode. Using the strategy, 12 new cis -diol-containing nucleoside analogs were successfully characterized, which were formed by modified base (m 1 A, m 6 A, m 2,2,7 G, ac 4 C) and modified ribose containing C5′- O -formylation or C5′- O -methylation. Taken together, the results demonstrated our strategy could efficiently support the rapid discovery of cis -diol-containing nucleosides with modifications on either ribose or base moiety (or both), which exhibited a promising perspective in the future application of biochemical analysis and clinical diagnosis.
研究领域:
生物化学
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医学诊断
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分析化学
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PubMed
高影响因子
TALANTA
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2023
·
IF 6.1
Gefei Huang,Feng Zhang,Dongying Xie,Yiming Ma,Pengxi Wang,Guodong Cao,Leijian Chen,Siyi Lin,Zhongying Zhao,Zongwei Cai
Although next-generation sequencing technology has been used to delineate RNA modifications in recent years, the paucity of appropriate converting reactions or specific antibodies impedes the accurate characterization and quantification of numerous RNA modifications, especially when these modifications demonstrate wide variations across developmental stages and cell types. In this study, we developed a high-throughput analytical platform coupling ultra-performance liquid chromatograph (UPLC) with complementary mass spectrometry (MS) to identify and quantify RNA modifications in both synthetic and biological samples. Sixty-four types of RNA modifications, including positional isomers and hypermodified ribonucleosides , were successfully monitored within a 16-min single run of UPLC–MS. Two independent methods to cross-validate the purity of RNA extracted from Caenorhabditis elegans ( C. elegans ) were developed using the coexisting C. elegans and Escherichia coli ( E. coli ) as a surveillance system. To test the validity of the method, we investigated the RNA modification landscape of three model organisms, C. elegans , E. coli , and Arabidopsis thaliana ( A. thaliana ). Both the identity and molarity of modified ribonucleosides markedly varied among the species. Moreover, our platform is not only useful for exploring the dynamics of RNA modifications in response to environmental cues (e.g., cold shock) but can also help with the identification of RNA-modifying enzymes in genetic studies. Cumulatively, our method presents a novel platform for the comprehensive analysis of RNA modifications, which will be of benefit to both analytical chemists involved in biomarker discovery and biologists conducting functional studies of RNA modifications.
研究领域:
生物化学
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分析化学
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分子生物学
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高影响因子
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
·
2015
·Vol. 120
·期 1
·1009-1025
·
IF 2.042
Wang Xue-Jie,You Jin-Zong
The thermal decomposition processes for ten pyrimidine nucleoside analogs were measured with thermogravimetry and differential scanning calorimetry. The IR spectra, high-performance liquid chromatography, and liquid chromatography–mass spectrometry of pyrimidine nucleoside analogs and their residues of thermal decomposition at various temperatures were determined. The molecular bond orders of pyrimidines and pyrimidine nucleoside analogs were calculated with an ab initio method from the GAMESS program. We then discuss mechanisms of thermal decomposition in these pyrimidine nucleoside analogs. The results indicate that there are four types of mechanisms. The decomposition mechanism depends on the relative strength of the peptide bond and the amide bond within pyrimidine ring and whether or not accompanied by oxidation reaction. The substituent groups affect the thermal stability and the thermal decomposition mechanism of pyrimidine nucleoside analogs. Increasing the number of electron-donating groups on the pyrimidine ring and furan ring will enhance the peptide bond, and will elevate the temperature of thermal decomposition. There is a positive correlation between the molecular bond orders calculated by quantum chemistry and the thermal decomposition temperature of pyrimidine nucleoside analogs. The stronger the weakest bond order, the higher the decomposition temperature. The molecular bond orders thus can be used as a basis to judge molecular thermal stability for analog compounds with similar molecular structure, size, and energy.
研究领域:
药物化学
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物理化学
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高影响因子
JOURNAL OF CHROMATOGRAPHY A
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2016
·
IF 3.926
Haibin Li,Chusheng Liu,Qiqin Wang,Haibo Zhou,Zhengjin Jiang
In order to investigate the effect of charged groups present in hydrophilic monolithic stationary phases on their chromatographic properties, three charged hydrophilic monomers, i.e. N,N -dimethyl- N -acryloyloxyethyl- N -(3-sulfopropyl)ammonium betaine (SPDA), [2-(acryloyloxy)ethyl]trimethylammonium chloride (AETA), and 3-sulfopropyl acrylate potassium salt (SPA) were co-polymerized with the crosslinker N,N '-methylenebisacrylamide (MBA), respectively. The physicochemical properties of the three resulting charged hydrophilic monolithic columns were evaluated using scanning electron microscopy, ζ-potential analysis and micro-HPLC. High column efficiency was obtained on the three monolithic columns at a linear velocity of 1 mm/s using thiourea as test compound. Comparative characterization of the three charged HILIC phases was then carried out using a set of model compounds, including nucleobases, nucleosides, benzoic acid derivatives, phenols, β-blockers and small peptides. Depending on the combination of stationary phase/mobile phase/solute, both hydrophilic interaction and other potential secondary interactions, including electrostatic interaction, hydrogen-bonding interaction, molecular shape selectivity, could contribute to the over-all retention of the analytes. Because of the strong electrostatic interaction provided by the quaternary ammonium groups in the poly (AETA- co -MBA) monolith, this cationic HILIC monolith exhibited the strongest retention for benzoic acid derivatives and small peptides with distorted peak shapes and the weakest retention for basic β-blockers. The sulfonyl groups on the poly (SPA- co -MBA) hydrophilic monolith could provide strong electrostatic attraction and hydrogen bonding for positively charged analytes and hydrogen-donor/acceptor containing analytes, respectively. Therefore, basic drugs, nucleobases and nucleotides exhibited the strongest retention on this anionic monolith. Because of the weak but distinct cation exchange properties of the zwitterionic poly (SPDA- co -MBA) hydrophilic monolith, it exhibited the best separation for most test analytes (including phenols, β-blockers and small peptides) in terms of selectivity, peak shape and analysis time. The poly (AETA- co -MBA) hydrophilic monolithic column provides the best separation of nucleobases and nucleosides. These results could guide the selection and application of these charged HILIC monoliths in the future.
研究领域:
分析化学
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色谱技术
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PubMed
高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
·
2017
·
IF 3.255
Yang Huang,Tingting Zhang,Yumei Zhao,Haibo Zhou,Guangyun Tang,Marianne Fillet,Jacques Crommen,Zhengjin Jiang
Nucleobases, nucleosides and ginsenosides, which have a significant impact on the physiological activity of organisms, are reported to be the active components of ginseng, while they are less present in ginseng extracts. Few analytical methods have been developed so far to simultaneously analyze these three classes of compounds with different polarities present in ginseng extracts. In the present study, a simple and efficient analytical method was successfully developed for the simultaneous separation of 17 nucleobases, nucleosides and ginsenosides in ginseng extracts using supercritical fluid chromatography coupled with single quadrupole mass spectrometry (SFC-MS). The effect of various experimental factors on the separation performance, such as the column type, temperature and backpressure, the type of modifier and additive, and the concentration of make-up solvent were systematically investigated. Under the selected conditions, the developed method was successfully applied to the quality evaluation of 14 batches of ginseng extracts from different origins. The results obtained for the different batches indicate that this method could be employed for the quality assessment of ginseng extracts.
研究领域:
分析化学
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植物化学
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药理学
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PubMed
高影响因子
Genes
·
2023
·Vol. 14
·期 6
·1287
·
IF 3.5
Meng Chu,Yichao Qin,Xiuying Lin,Li Ma,Dehai Deng,Daizhu Lv,Pengcheng Fu,Huan Lin
The coconut (Cocos nuciferaL.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living species ofCocoshas only been preliminarily studied at molecular levels. Benefiting from the genomic sequence data published in 2017 and 2021, we investigated the transfer RNA (tRNA) modifications and modifying enzymes of the coconut in this survey. An extraction method for the tRNA pool from coconut flesh was built. In total, 33 species of modified nucleosides and 66 homologous genes of modifying enzymes were confirmed using a nucleoside analysis using high-performance liquid chromatography combined with high-resolution mass spectrometry (HPLC-HRMS) and homologous protein sequence alignment. The positions of tRNA modifications, including pseudouridines, were preliminarily mapped using a oligonucleotide analysis, and the features of their modifying enzymes were summarized. Interestingly, we found that the gene encoding the modifying enzyme of 2′-O-ribosyladenosine at the 64th position of tRNA (Ar(p)64) was uniquely overexpressed under high-salinity stress. In contrast, most other tRNA-modifying enzymes were downregulated with mining transcriptomic sequencing data. According to previous physiological studies of Ar(p)64, the coconut appears to enhance the quality control of the translation process when subjected to high-salinity stress. We hope this survey can help advance research on tRNA modification and scientific studies of the coconut, as well as thinking of the safety and nutritional value of naturally modified nucleosides.Keywords:Cocos nucifera;epitranscriptomics;LC-MS/MS;nucleoside misidentification;RNA modification
研究领域:
植物学
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遗传学
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分子生物学
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PubMed
高影响因子
危险品化学品经营许可证（带存储）