ANALYTICAL CHEMISTRY
·
2013
·
IF 5.695
Shao-Ting Wang,Wei Huang,Wei Lu,Bi-Feng Yuan,Yu-Qi Feng
A novel TiO2-based SPE strategy was developed for eliminating normal ribonucleosides before mass spectrometry (MS) analysis of 2′-deoxynucleosides and 2′-O-modified ribonucleosides. The chromatographic research for the retention behavior of ribonucleosides and 2′-deoxynucleosides on TiO2 materials was investigated using TiO2 separation column. The results indicated a specific affinity interaction mechanism between TiO2 and cis-diol-containing ribonucleosides, and the interaction was proved effective even under a wide range of pH conditions and salt concentrations. Benefiting from these features, a TiO2-based solid phase extraction (SPE) method was developed for highly efficient elimination of RNA contamination from genomic DNA. Compared with the widely used enzymatic digestion method, the proposed TiO2-based SPE method showed much more efficiency for the removal of RNA as well as provided high recoveries for the 2′-deoxynucleosides. In addition, the sample processing time is dramatically shortened using the TiO2-based SPE method (∼5 min) compared to the traditional enzymatic digestion method (∼12 h). Finally, the purification of 2′-O-methylated ribonucleosides from RNA was successfully achieved in HeLa cells by the TiO2-based SPE method, which provided a proof-of-concept for the purification of relevant modified ribonucleosides from bulky normal ribonucleosides. Taken together, this strategy developed in the current study offers a promising option to purify 2′-deoxynucleosides/2′-O-modified ribonucleosides for their sensitive and accurate determination by eliminating normal ribonucleosides in biological samples.
研究领域:
分析化学
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生物化学
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DOI
PubMed
高影响因子
JOURNAL OF CHROMATOGRAPHY A
·
2013
·
IF 4.612
Sheng Guo,Jin-ao Duan,Dawei Qian,Hanqing Wang,Yuping Tang,Yefei Qian,Dawei Wu,Shulan Su,Erxin Shang
In this study, a rapid and sensitive analytical method was developed for the determination of 20 nucleobases, nucleosides and nucleotides in Ziziphus plants at trace levels by using hydrophilic interaction ultra-high performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (HILIC–UHPLC-TQ-MS/MS) in multiple-reaction monitoring (MRM) mode. Under the optimized chromatographic conditions, good separation for 20 target compounds were obtained on a UHPLC Amide column with sub-2 μm particles within 10 min. The overall LODs and LOQs were between 0.11–3.12 ng mL −1 and 0.29–12.48 ng mL −1 for the 20 analytes, respectively. It is the first report about simultaneous analysis of nucleobases, nucleosides and nucleotides in medicinal plants using HILIC–UHPLC-TQ-MS/MS method, which affords good linearity, precision, repeatability and accuracy. The developed method was successfully applied to Ziziphus plant ( Z. jujuba , Z. jujuba var. spinosa and Z. mauritiana ) samples. The analysis showed that the fruits and leaves of Ziziphus plants are rich in nucleosides and nucleobases as well as nucleotides, and could be selected as the healthy food resources. Our results in present study suggest that HILIC–UHPLC-TQ-MS/MS method could be employed as a useful tool for quality assessment of the samples from the Ziziphus plants as well as other medicinal plants or food samples using nucleotides, nucleosides and nucleobases as markers.
研究领域:
分析化学
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植物化学
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药用植物学
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DOI
PubMed
高影响因子
MOLECULES
·
2019
·Vol. 25
·期 1
·100
·
IF 3.06
Gaofei Liu,Tiantong Cheng,Jianlin Chu,Sui Li,Bingfang He
Purine nucleoside phosphorylases (PNPs) are promising biocatalysts for the synthesis of purine nucleoside analogs. Although a number of PNPs have been reported, the development of highly efficient enzymes for industrial applications is still in high demand. Herein, a new trimeric purine nucleoside phosphorylase (AmPNP) fromAneurinibacillus migulanusAM007 was cloned and heterologously expressed inEscherichia coliBL21(DE3). TheAmPNP showed good thermostability and a broad range of pH stability. The enzyme was thermostable below 55 °C for 12 h (retaining nearly 100% of its initial activity), and retained nearly 100% of the initial activity in alkaline buffer systems (pH 7.0–9.0) at 60 °C for 2 h. Then, a one-pot, two-enzyme mode of transglycosylation reaction was successfully constructed by combining pyrimidine nucleoside phosphorylase (BbPyNP) derived fromBrevibacillus borstelensisLK01 andAmPNP for the production of purine nucleoside analogs. Conversions of 2,6-diaminopurine ribonucleoside (1), 2-amino-6-chloropurine ribonucleoside (2), and 6-thioguanine ribonucleoside (3) synthesized still reached >90% on the higher concentrations of substrates (pentofuranosyl donor: purine base; 20:10 mM) with a low enzyme ratio ofBbPyNP:AmPNP (2:20 μg/mL). Thus, the new trimericAmPNP is a promising biocatalyst for industrial production of purine nucleoside analogs.Keywords:trimeric nucleoside phosphorylase;thermostability;purine nucleoside analogs;enzyme ratio
研究领域:
生物化学
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生物技术
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酶学
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产品关联
DOI
PubMed
高影响因子
ChemCatChem
·
2024
·
IF 3.8
Li Zhang,Haiyan Xu,Xiaofan Wu,Yitong Li,Yuan Tao,Zedu Huang,Fener Chen
Graphical Diversification of commercially available 3’-amino-3’-deoxythymidine via nucleoside phosphorylase Ec PPNP- and/or nucleoside 2’-deoxyribosyltransferase Ll NDT-catalyzed transglycosylation has been demonstrated as a generally applicable, straightforward means to access a variety of valuable 3’-amino containing nucleosides in good yields. The synthetic utility was further showcased by the successful synthesis of 3’-amino-2’,3’-dideoxy-5-bromouridine in 29% isolated yield at a preparative scale. A systematic study on the enzymatic transglycosylation of 3′-amino nucleosides has been reported. Using the commercially available 3′-amino-3′-deoxythymidine as the sugar donor, 13 pyrimidine and purine nucleobases were shown as the viable sugar acceptors in the nucleoside phosphorylase Ec PPNP- and/or nucleoside 2′-deoxyribosyltransferase Ll NDT-catalyzed reactions, furnishing the corresponding 3′-amino containing nucleosides in 23%–73% NMR yields at an analytical scale. The synthetic utility of this diversification approach was further showcased by the successful synthesis of 3′-amino-2′,3′-dideoxy-5-bromouridine in 29% isolated yield at a preparative scale. The current work demonstrates the transglycosylation activity of Ec PPNP for the first time, expands the substrate scope of Ll NDT, and provides an efficient, direct access to various 3′-amino nucleosides of high value.
研究领域:
生物化学
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药物化学
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酶学
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DOI
高影响因子
FOOD CHEMISTRY
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2019
·
IF 5.399
Meng Dong,Lei Qin,Li-Xin Ma,Zi-Yuan Zhao,Ming Du,Konno Kunihiko,Bei-Wei Zhu
Nucleotide degradation in fish is an important biochemical change after death, which is closely related to freshness and sensory quality. However, except ATP-relative nucleotides, it remains unclear about changes in other nucleotide metabolites during postmortem stage. In this study, a strategy for the simultaneous quantification of 28 nucleobases, nucleosides, and nucleotides using hydrophilic interaction chromatography coupled with tandem mass spectrometry (HILIC-MS/MS) with positive/negative ion switching was developed. This method showed good linearity, precision, repeatability, and recovery. Furthermore, it was successfully applied to monitor the postmortem nucleotide degradation of turbot mince during chill (4 °C) and partial freezing (−3 °C) storage for 168 h. It was noted that the patterns of the changes in nucleotide metabolites differed considerably depending on the storage temperature. Meanwhile, the different pathway and speed of nucleotide catabolism in turbot mince was summarized based on the quantification data.
研究领域:
食品科学
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生物化学
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分析化学
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DOI
PubMed
高影响因子
ADVANCED FUNCTIONAL MATERIALS
·
2015
·Vol. 25
·期 23
·3541-3550
·
IF 11.805
Bang Lin Li,Hao Lin Zou,Lu Lu,Yu Yang,Jing Lei Lei,Hong Qun Luo,Nian Bing Li
Size-dependent optical absorption of semiconductive (2H) layered molybdenum disulfide (MoS 2 ), exhibiting great discrimination abilities to single- and double-stranded DNA (ssDNA) and (dsDNA), is studied. In the presence of high concentration of salt, layered MoS 2 trends to aggregate rapidly, leading to the increases of sizes in both vertical and lateral dimensions of the nanosheets, which results from the interplay between van der Waals attraction and electrical double-layer repulsion. Meanwhile, the aggregation behavior of layered MoS 2 is remarkably inhibited by the synergistic effects of DNA oligonucleotides. ssDNA can adsorb on the surface of layered MoS 2 , resulting in a great dispersion, even in the presence of high concentration of salt, while the dispersion behavior is weakened when ssDNA is replaced by dsDNA. Whereas compared to graphene with zero bandgap energy, layered MoS 2 , with semiconductive properties, exhibits great characteristic optical absorption in visible wavelength region devoted to exploring the aggregation behavior of layered MoS 2 . Therefore, DNA oligonucleotides induced size control of layered MoS 2 , contributing to the regular change of its characteristic absorption in visible region, is considered a label-free bioassay for the detection of single-nucleotide polymorphism. Due to its easy operation and high specificity, it is expected that the proposed assay holds great promise for further applications.
研究领域:
材料科学
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生物化学
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纳米技术
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DOI
高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
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2017
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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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产品关联
DOI
PubMed
高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
·
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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产品关联
DOI
PubMed
高影响因子
JACS Au
·
2024
·
IF 8.5
Gaofei Liu,Jialing Wang,Jianlin Chu,Tianyue Jiang,Song Qin,Zhen Gao,Bingfang He
Nucleoside phosphorylases (NPs) are the key enzymes in the nucleoside metabolism pathway and are widely employed for the synthesis of nucleoside analogs, which are difficult to access via conventional synthetic methods. NPs are generally classified as purine nucleoside phosphorylase (PNP) and pyrimidine or uridine nucleoside phosphorylase (PyNP/UP), based on their substrate preference. Here, based on the evolutionary information on the NP-I family, we adopted an insertions–deletions (InDels) strategy to engineer the substrate promiscuity of nucleoside phosphorylase AmPNPΔS2V102 K, which exhibits both PNP and UP activities from a trimeric PNP (AmPNP) of Aneurinibacillus migulanus. Furthermore, the AmPNPΔS2V102 K exerted phosphorylation activities toward arabinose nucleoside, fluorosyl nucleoside, and dideoxyribose, thereby broadening the unnatural-ribose nucleoside substrate spectrum of AmPNP. Finally, six purine nucleoside analogues were successfully synthesized, using the engineered AmPNPΔS2V102 K instead of the traditional “two-enzymes PNP/UP” approach. These results provide deep insights into the catalytic mechanisms of the PNP and demonstrate the benefits of using the InDels strategy to achieve substrate promiscuity in an enzyme, as well as broadening the substrate spectrum of the enzyme.
研究领域:
生物化学
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酶工程
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药物化学
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DOI
PubMed
高影响因子
Analytical Methods
·
2012
·Vol. 5
·期 1
·285-290
·
IF 1.547
Xia Liu,Tao Li,Dianjun Liu,Zhenxin Wang
Here, a three-dimensional (3D) oligonucleotide microarray-based fluorescent assay has been developed for single nucleotide polymorphisms (SNPs) and allele frequency determination. The 3D oligonucleotide microarray is fabricated on a home-made polyacrylamide hydrogel microarray which is generated by UV light photopolymerization of tiny acrylamide monomer droplets on a PEG terminated glass slide. After activation by glutaraldehyde (GA), the polyacrylamide hydrogel is able to react with NH2-modified oligonucleotides with high efficiency to generate a high signal-to-background ratio without the conventional blocking step. We demonstrate that the assay is able to detect complimentary 25 mer oligonucleotide target (fragment of a tumor suppressor gene P53) down to 100 pM and SNP with true-to-false ratios (the ratio of fluorescence signal from perfect matched DNA strands to that from the one-base mismatched DNA strands) above 20. Taking advantage of the high specificity of the assay, allele frequency as low as 2% can be accurately determined.
研究领域:
生物化学
·
分子生物学
·
基因组学
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产品关联
DOI
高影响因子
PHARMACOLOGICAL RESEARCH
·
2023
·
IF 9.3
Depeng Li,Meihong Zhang,A.La Teng Zhu La,Zhengtian Lyu,Xin Li,Yuqing Feng,Dan Liu,Yuming Guo,Yongfei Hu
The development of hyperuricemia (HUA) and gout is associated with dysbiosis of the gut microbiota. Quercetin can reduce serum uric acid levels and thus alleviate HUA by modulating the gut microbiota. However, the detailed mechanisms involved in this process are not fully understood. Here, we showed that quercetin significantly reduced the serum uric acid level in a chicken HUA model by altering the chicken cecal microbiota structure and function and increasing the abundance of Lactobacillus aviarius . An L. aviarius strain, CML180, was isolated from the quercetin-treated chicken gut microbiota. Strain characterization indicated that quercetin promoted the growth of L. aviarius CML180 and increased its adhesion, hydrophobicity, and co-aggregation abilities. Gavage of live L. aviarius CML180 to a mouse model of HUA—established by adenosine and potassium oxonate—reduced the serum uric acid level and alleviated HUA. The ability of L. aviarius CML180 to decrease the level of uric acid was due to its degradation of purine nucleosides, which are the precursors for uric acid production. A nucleoside hydrolase gene, nhy69 , was identified from the genome of L. aviarius CML180, and the resulting protein, Nhy69, exhibited strong purine nucleoside-hydrolyzing activity at mesophilic temperature and neutral pH conditions. These findings provide mechanistic insights into the potential of quercetin to treat HUA or gout diseases via a specific gut microbe.
研究领域:
微生物学
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药理学
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分子生物学
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营养学
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产品关联
DOI
PubMed
高影响因子
TALANTA
·
2020
·
IF 5.339
Jinhua Liu,Changpeng Zou,Can Chen,Haixiao Fang,Qiong Wu,Haidong Yu,Jixin Zhu,Lin Li,Sheng Yang,Wei Huang
Topochemical assembly carbon materials with unique structure rarely investigated and reported. Herein, we demonstrate the feasibility of using topochemical assembly levodopa nanoparticles with dendritic structure (LNDS) network as a new high-performance biosensing platform based on noncovalent functionalization of LNDS with a fluorescent oligonucleotide . The proposed platform is dependent on the competition of π-π stacking and electrostatic repulsion interactions between LNDS and fluorescent oligonucleotide. The obtained LNDS with 96.1% quenching efficiency is synthesized by using levodopa as the single precursor by natural oxidation or microwave irradiation . The constructed platform can be used for simple and efficient probing single-nucleotide polymorphisms (SNPs) and cDNA by fluorescence restoration with a highly sensitivity and selectivity , remarkably superior to those based on graphenes. Additionally, an aptasensor is further constructed for small molecule ATP detention in serum with a low detection limit of 4 μM. To the best of our knowledge, this is the first attempt to use LNDS to design a biosensing platform, and therefore opens possibilities for new types of nanoparticle-based molecule approaches, and sequencing technologies.
研究领域:
生物传感
·
材料科学
·
分子生物学
✓ 已验证
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）