Synthesis of Isonucleoside-Incorporated Oligonucleotides and Their Binding Abilities with Complementary Sequences

Aim To synthesize isonucleoside-incorporated oligonucleotides and investigatetheir binding abilities with complementary sequences. Methods The synthesis was performed on DNAsynthesizer, and the binding behavior was investigated by thermal denaturation studies. Results Fourkinds of single isonucleoside containing oligonucleotides were synthesized. The results of thermaldenaturation showed that the existence of isonucleoside decreased the stability of duplex, and theeffect was more obvious when the isonucleoside was in the middle of the sequence. No obviousdifference was observed when 6'-OH of isonucleoside was free or was protected by allyl group.Conclusions The existence of isonucleoside in oli-gonucleotide makes chain twist and decreased thestability of duplex.

Nucleotide excision repair gene polymorphisms and hepatoblastoma susceptibility in Eastern Chinese children:A five-center case-control study

Objective:Nucleotide excision repair(NER)plays a vital role in maintaining genome stability,and the effect of NER gene polymorphisms on hepatoblastoma susceptibility is still under investigation.This study aimed to evaluate the relationship between NER gene polymorphisms and the risk of hepatoblastoma in Eastern Chinese Han children.Methods:In this five-center case-control study,we enrolled 966 subjects from East China(193 hepatoblastoma patients and 773 healthy controls).The TaqMan method was used to genotype 19 single nucleotide polymorphisms(SNPs)in NER pathway genes,including ERCC1,XPA,XPC,XPD,XPF,and XPG.Then,multivariate logistic regression analysis was performed,and odds ratios(ORs)and 95%confidence intervals(95%CIs)were utilized to assess the strength of associations.Results:Three SNPs were related to hepatoblastoma risk.XPC rs2229090 and XPD rs3810366 significantly contributed to hepatoblastoma risk according to the dominant model(adjusted OR=1.49,95%CI=1.07−2.08,P=0.019;adjusted OR=1.66,95%CI=1.12−2.45,P=0.012,respectively).However,XPD rs238406 conferred a significantly decreased risk of hepatoblastoma under the dominant model(adjusted OR=0.68,95%CI=0.49−0.95;P=0.024).Stratified analysis demonstrated that these significant associations were more prominent in certain subgroups.Moreover,there was evidence of functional implications of these significant SNPs suggested by online expression quantitative trait loci(eQTLs)and splicing quantitative trait loci(sQTLs)analysis.Conclusions:In summary,NER pathway gene polymorphisms(XPC rs2229090,XPD rs3810366,and XPD rs238406)are significantly associated with hepatoblastoma risk,and further research is required to verify these findings.

Nucleotide Contribution to the Functioning of SERT, Na /K ATPase and GPCR Proteins

Purine nucleotides are crucial for the effective operation of cell membrane proteins maintaining the neurotransmitter responses of 5-HT. Major protein targets in the treatment of depression include SERT, N/K ATPase and GPCR. Each protein target is responsive to a specific complement of drugs: antidepressants (SERT), lithium and cardiogenic steroids (N/K ATPase), 5-HT receptor ligands (GPCR). Computational software is useful for comparing molecular similarity within ligand-ligand and ligand-nucleotide structures. Previous studies demonstrate that GPCR ligands of different pharmacologic classes display relative molecular similarity to nucleotide structures. The current study applies this methodology to compound structures modulating SERT and N/K ATPase receptors. Minimum energy conformers of SERT antagonists demonstrate relative molecular similarity to the structural template of GTP nucleotide. GTP template fits of 5-HT and psilocin are similar, whereas a SERT-like fit is one of several for the ketamine structure. Endogenous and pharmaceutical modulators of Na/K ATPase relate to adenine nucleotide. The fits of cardiogenic steroids to a cGMP template demonstrate similarities and differences between compounds. Relative molecular similarity within the structures of hormones, drugs and nucleotides has implications for neurotransmitter transport and cell signal transduction processes.

Metformin promotes anti-tumor immunity in STK11 mutant NSCLC through AXIN1-dependent upregulation of multiple nucleotide metabolites

Background:Metformin has pleiotropic effects beyond glucose reduction,including tumor inhibition and immune regulation.It enhanced the anti-tumor effects of programmed cell death protein 1(PD-1)inhibitors in serine/threonine kinase 11(STK11)mutant non-small cell lung cancer(NSCLC)through an axis inhibition protein 1(AXIN1)-dependent manner.However,the alterations of tumor metabolism and metabolites upon metformin administration remain unclear.Methods:We performed untargeted metabolomics using liquid chromatography(LC)-mass spectrometry(MS)/MS system and conducted cell experiments to verify the results of bioinformatics analysis.Results:According to the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway database,most metabolites were annotated into metabolism,including nucleotide metabolism.Next,the differentially expressed metabolites in H460(refers to H460 cells),H460_met(refers to metformin-treated H460 cells),and H460_KO_met(refers to metformin-treated Axin1-/-H460 cells)were distributed into six clusters based on expression patterns.The clusters with a reversed expression pattern upon metformin treatment were selected for further analysis.We screened out metabolic pathways through KEGG pathway enrichment analysis and found that multiple nucleotide metabolites enriched in this pathway were upregulated.Furthermore,these metabolites enhanced the cytotoxicity of activated T cells on H460 cells in vitro and can activate the stimulator of the interferon genes(STING)pathway independently of AXIN1.Conclusion:Relying on AXIN1,metformin upregulated multiple nucleotide metabolites which promoted STING signaling and the killing of activated T cells in STK11 mutant NSCLC,indicating a potential immunotherapeutic strategy for STK11 mutant NSCLC.

The Nucleosides Contents and Their Variation in Natural Cordyceps sinensis and Cultured Cordyceps Mycelia

Aim: To compare the contents of nucleosides from natural Cordyceps sinensis and cultured Cordyceps mycelia, and to study the effect of humidity and heat on the content of nucleosides. Methods: The contents of nucleosides were determined by using high performance capillary electrophoresis (HPCE). Beckman P/ACE System 5010 apparatus equipped with a UV detector and a Beckman untreated fused-silica capillary (57 cm 75 mm, 50 cm effective length) was used. Before sample injection, the capillary was rinsed with 1 molL-1 sodium hydroxide solution and running buffer for 5 min, respectively. A voltage of 20 kV was applied for the separation. Pressure injection was 586 kPa for 6 seconds, and the wavelength of detector was 254 nm. The running time was 20 min at 20 oC. The effect of humidity and heat on the contents of nucleosides from natural Cordyceps sinensis and cultured Cordyceps mycelia was observed for 1, 3, 5 and 10 days at temperature 40 oC, and relative humidity 75%. Results: The content of nucleosides from natural Cordyceps sinensis was higher than that from cultured Cordyceps mycelia. But the contents of nucleosides from freshly collected natural Cordyceps sinensis were very low, even below the limit of quantitation. The contents of nucleosides from natural Cordyceps sinensis were significantly increased by humidity and heat, but this phenomenon was not observed in cultured Cordyceps mycelia. Conclusion: There are differences between the nucleosides from natural Cordyceps sinensis and cultured Cordyceps mycelia. The nucleosides in natural Cordyceps sinensis may be derived from the degradation of nucleic acids. This implies that adenosine being used for the quality control of natural Cordyceps sinensis may have to be reconsidered.

Separation of Nucleotides in Swine Tissues Using Capillary Zone Electrophoresis

Capillary zone electrophoresis has been applied to the analysis of nucleotides. The effects of buffer concentration. pH and other operating conditions on the separation were investigated and optimized. By using the method, separation and identification of nuclotides in swine tissues were completed.

Simultaneous determination of five nucleosides and nucleobases in Panax notoginseng using high-performance liquid chromatography

Aim To quantitatively determine five nucleosides and nucleobases, including cytidine, uridine, guanosine, adenosine and uracil in different parts of Panax notoginseng. Methods Separation was performed on a Zorbax SB-Aq column using a gradient elution with mobile phase of 8 mmol^L-1 ammonium acetate aqueous solution （A） and methanol （B）. The assay was carried out at a flow rate of 1 mL·min^-1 at 25 ℃ with the diode-array detection at 260 nm. Results Cytidine, uridine, guanosine, adenosine and uracil had good linearity in the ranges of 1.79 - 57.40 μg·mL^-1 （r^2 = 1.0000）, 3.30 - 105.60 μg·mL^-1 （r^2 = 1.0000）, 3.09 - 98.80 μg·mL^ -1（r^2 = 0.9999）, 2.77 - 88.60 μg·mL^-1 （r^2 = 1.0000） and 0.38 - 12.30 μg·mL ^-1 （r^2 = 1.0000） with average recoveries of 93.9%, 96.5%, 92.7%, 93.2% and 98.8%, respectively. The content of cytidine, uridine, guanosine, adenosine and uracil in different parts of P. notogingeng were significantly different. Conclusion This is the first report on quantitative determination of nucleosides and nucleobases in P notoginseng.

Nucleoside diphosphate-linked moiety X-type motif 15 R139C genotypes impact 6-thioguanine nucleotide cut-off levels to predict thiopurine-induced leukopenia in Crohn’s disease patients

BACKGROUND Thiopurine-induced leukopenia(TIL)is a life-threatening toxicity and occurs with a high frequency in the Asian population.Although nucleoside diphosphate-linked moiety X-type motif 15(NUDT15)variants significantly improve the predictive sensitivity of TIL,more than 50%of cases of this toxicity cannot be predicted by this mutation.The potential use of the 6-thioguanine nucleotide(6TGN)level to predict TIL has been explored,but no decisive conclusion has been reached.Can we increase the predictive sensitivity based on 6TGN by subgrouping patients according to their NUDT15 R139C genotypes?AIM To determine the 6TGN cut-off levels after dividing patients into subgroups according to their NUDT15 R139C genotypes.METHODS Patients’clinical and epidemiological characteristics were collected from medical records from July 2014 to February 2017.NUDT15 R139C,thiopurine S methyltransferase,and 6TGN concentrations were measured.RESULTS A total of 411 Crohn’s disease patients were included.TIL was observed in 72 individuals with a median 6TGN level of 323.4 pmol/8×10^8 red blood cells(RBC),which was not different from that of patients without TIL(P=0.071).Then,we compared the 6TGN levels based on NUDT15 R139C.For CC(n=342)and CT(n=65)genotypes,the median 6TGN level in patients with TIL was significantly higher than that in patients without(474.8 vs 306.0 pmol/8×10^8 RBC,P=9.4×10-^5;291.7 vs 217.6 pmol/8×10^8 RBC,P=0.039,respectively).The four TT carriers developed TIL,with a median 6TGN concentration of 135.8 pmol/8×10^8 RBC.The 6TGN cut-off levels were 411.5 and 319.2 pmol/8×108 RBC for the CC and CT groups,respectively.CONCLUSION The predictive sensitivity of TIL based on 6TGN is dramatically increased after subgrouping according to NUDT15 R139C genotypes.Applying 6TGN cut-off levels to adjust thiopurine therapies based on NUDT15 is strongly recommended.

Purine nucleotides and their metabolites in patients with type 1 and 2 diabetes mellitus

We measured the erythrocyte levels of principal nucleotides (ATP, ADP, AMP, GTP, GDP, GMP, IMP), nucleosides (Ado, Guo, Ino) and Hyp with HPLC. Purine concentrations were determined in the erythrocytes of 36 type 1 and 40 type 2 diabetic patients. The increased dephosphorylation of adenine and guanine nucleotides, indicated by increased Ado, Ino, Guo and Hyp concentrations as the products of purine nucleotide degradation, suggests serious energy metabolism disruptions in diabetes. An increase in AMP, GMP, IMP concentrations, as well as a decrease in AEC and GEC values, points to significant alterations in erythrocyte purine nucleotide concentration.

Response to an Escherichia coli K88 oral challenge and productivity of weanling pigs receiving a dietary nucleotides supplement

Background： Dietary nucleotides, considered as antibiotics alternative, were shown to have positive effects on intestinal hyperaemia, systemic immunity, small-intestinal growth, and hepatic composition in pigs. However, there is no previous research on nucleotide supplementation in weanling pigs under an oral challenged E. coil K88. Therefore, 2 experiments were conducted to investigate the effects of dietary nucleotides on weanling pig growth performance, nutrient digestibility, fecal score, and blood profile after being orally challenged with E. coli K88. Methods： In Exp. 1, a total of 140 weanling pigs [8.33 ± 0.33 kg of body weight （BW）, 28-d old] were used in this 42-d feeding trial. Pigs were distributed into 1 of 4 treatments, 5 pigs/pen （3 barrows and 2 gilts） and 7 pens/treatment. Treatments were a control basal diet （CON） or the CON supplemented with 150 （R150）, 220 （R220）, or 275 （R275） mg/kg to give the three treatment diets. In Exp. 2, 28 weanling pigs （BW = 8.40 ± 0.22 kg, 28-d old） were distributed into 1 of 4 treatments to give 1 pig/pen and 7 pens/treatment in a 42-d feeding and challenge trial. Dietary treatments were the same as in Exp. 1. 0n d 14, all those pigs （BW= 13.3±0.15 kg, 42-d old） were orally dosed with 1.5 mL suspension containing 10 cfu/mL of E. coli K88. Twenty four hours after challenge, blood and excreta samples were collected from each pigs for analysis. Fecal scores were measured on d 7, 14, 21, and 28 of the study. Results： In Exp. 1, overall BW, average daily gain （ADG）, gain/feed （G/F） ratio, and nutrient digestibilities were lower （P 〈 0.05） in CON group compared with the nucleotides fed pigs. In Exp. 2, after challenge, IgA, IgM, and IGF-I were higher （P〈 0.05） in the nucleotide groups compared with CON. However, the nucleotide groups had lower （P 〈 0.05） cortisol and TNF-o compared with CON. Fecal E. coil counts and fecal score for the nucleotide groups were lower （P 〈 0.05） than for CON. Conclusions： In conclusion, dietary nucleotides supplementation could improve growth performance, nutrient digestibility, immune status, microbial balance, reduce diarrhea, and provide protection against enterotoxigenic E. coli K88 infection in weanling pigs.

Individual and Combined Effects of Nucleotides and Human Milk Oligosaccharides on Proliferation, Apoptosis and Necrosis in a Human Fetal Intestinal Cell Line

Nucleotides (NT) and human milk oligosaccharides (HMO) individually affect epithelial cell growth, but their combined effects had not been studied. Herein, the impact of NT and HMO on cell proliferation, apoptosis, necrosis and cell cycle in the fetal epithelial cell line (FHs-74 Int) was determined. Cells were incubated with media containing 2.5% FBS and no epidermal growth factor (Control);fucosyllactose (FL) mix [85% 2’FL/15% 3’FL], sialyllactose (SL) mix [40% 6’SL/10% 3’SL/50% sialic acid (SA)] or LNnT at 125, 250, 500 or 1000 μg/mL with and without 250 μg/mL NT (43% CMP, 18.5% UMP, 16.4% AMP, and 22.0% GMP) for 24 or 72 h. NT alone significantly increased proliferation, but did not affect cell cycle or apoptosis/necrosis. All HMO treatments at 1000 μg/mL significantly decreased proliferation and some were also inhibitory at 250 or 500 μg/mL. When NT and HMO were simultaneously added, NT ameliorated the anti-proliferative effect of HMO. FL significantly increased cells in S phase and SL and LNnT treatments significantly increased cells in G2/M and S phases, which concomitantly decreased cells in G0/G1. HMO with NT significantly decreased the percent of cells in the G2/M phase compared to HMO alone. Higher HMO doses significantly increased the percentage of apoptotic and necrotic cells compared to control. In conclusion, HMO reduced cell proliferation and this effect is partially ameliorated by NT. It appears that HMO initially induced apoptosis/necrosis, which was later evidenced by G2/M cell cycle arrest and decreased proliferation.

An efficient and green preparation of 5-aminophosphonate substituted pyrimidine nucleosides under solvent-free conditions

An environmentally benign and highly efficient one-pot preparation of α-aminophosphonates under solvent-free conditions was developed. By employing this method, 5-aminophosphonate substituted pyrimidine nucleosides were synthesized in good to excellent yields starting from 5-forrnyl-2＇-deoxyuridine, aniline and dimethylphosphite.

Synthesis and X-Ray Structure of New Anticancer Nucleosides Based on 1-((2-Hydroxyethoxy)methyl)-5-(phenylthio)-1H-1,2,4-triazole-3-carboxamide

A pair of new anticancer nucleosides based on 1,2,4-triazole nucleosides and 1-((2-hydroxyethoxy) methyl)-5-(phenylthio)-1H-1,2,4-triazole-3-carboxamide have been synthesized, and have given the corresponding products in excellent yields. Its structures and conformations were confirmed by single crystal X-ray diffraction.

Induction of Recombinant Uridine Phosphorylase and Its Application in Biosynthesis of Pyrimidine Nucleosides

Recombinant Escherichia coli pUDP,which overexpressed uridine phosphorylase（UPase）,was constructed.0.5 mmol·L 1lactose had a similar induction effect as the commonly used inducer IPTG during 2.5-5.5 h of cell growth.The lactose-induced UPase was stable at 50°C.Wet cells of pUDP was used as catalyst to biosynthesize 5-fluorouridine from 30 mmol·L 1uridine and 5-fluorouracil in phosphate buffer（pH 7.0）catalyzed at 50°C for 1.5 h and the yield of 5-fluorouridine was higher than 68%.Under the optimum reaction conditions for production of 5-fluorouridine,5-methyluridine and azauridine were synthesized from uridine by pUDP,the yield was 61.7%and 47.2%respectively.Deoxynucleosides were also synthesized by pUDP,but the yield was only about 20%.

Simultaneous determination of ten nucleosides and bases in Ganoderma by micellar electrokinetic chromatography

Ganoderma(lingzhi)is a famous herbal medicine and edible supplement in oriental countries for a long history.In this study,a simple micellar electrokinetic chromatography(MEKC)method was established for the analysis of nucleosides and bases,the major bioactive components in Ganoderma for the first time.By optimizing the borate concentration,the sodium dodecyl sulfate(SDS)concentration and the pH value of running buffer,10 nucleosides and bases achieved an ideal separation.In real sample analysis,the developed method was successfully used to determine the 10 target analytes in 23 batches of Ganoderma samples from different regions.Results indicated that contents of 10 investigated analytes in each sample showed obvious variation.The principal components analysis(PCA)and hierarchical cluster analysis(HCA)analysis classified the samples into three groups,and the HCA tree visualized the relationships which was mainly contributed by geographical partition.The results indicated geographical origin to be an important factor that affect the accumulation of nucleosides and bases in Ganoderma.In summary,this study provides a simple and practical strategy for quality assessment and cultivation reference of Ganoderma.

Frequency and Correlation of Nearest Neighboring Nucleotides in Human Genome

Zipf＇s approach in linguistics is utilized to analyze the statistical features of frequency and correlation of 16 nearest neighboring nucleotides （AA, AC, AG, …, TT） in 12 human chro- mosomes （Y, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, and 12）. It is found that these statistical features of nearest neighboring nucleotides in human genome： （i） the frequency distribution is a linear function, and （ii） the correlation distribution is an inverse function. The coefficients of the linear function and inverse function depend on the GC content. It proposes the correlation distribution of nearest neighboring nucleotides for the first time and extends the descriptor about nearest neighboring nueleotides.

Quick and Simple Spectrophotometric Method of Identification of the Thermal State of Meat on the Basis of Composition and Content of Free Nucleotides

At present, there is no method for identifying meat frozen in a thermal state acceptable for production control. The role of free nucleotides in the processes of refrigeration and storage of meat, affecting the structural and mechanical properties of muscle tissue, the formation of taste and its biological value is known. In this article we compared methods for identifying the thermal state of meat based on the determination of the composition and content of free nucleotides by high-performance liquid chromatography (HPLC) and spectrophotometry [SF]. High-purity reference substances were used: free nucleotides—ATP, ADP, AMP, IMP and nucleosides-inosine and hypoxanthine. It has been experimentally established that the characteristic peaks of the absorption spectra for extracts of free nucleotides of meat frozen depended from thermal state of meat. The content of ATP is 21.8 times higher in meat frozen in a fresh state, and the amount of IMF is 12.3 times lower than in meat frozen after cooling. The results of studies of meat frozen using the HPLC method and the developed SF method show the adequacy of the data obtained by both methods. SF-method based on the determination of the optical density of the extracts of free nucleotides is recommended to justify the choice of technological process meat defrost modes.

Design and Synthesis of Lipids Bearing Nucleosides as Gene Vectors

Some novel lipids bearing nucleosides were designed and synthesized as gene vectors, and the structures of these compounds were characterized by UV, IR, 1HNMR, 13CNMR and elemental analysis.

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 Me3SiCl, KCN and a catalytic mount of NaI in DMF/CH3CN.

Interaction between N-phosphoryl-α-,β-and γ-amino acids and nucleosides

The reactions of four different N-（O,O＇-diisopropyl） phosphoamino acids （DIPP-aa）, such as N-phosphoryl-L-α-alanine （DIPP- L-α-Ala）, N-phosphoryl-D-α-alanine （DIPP-D-α-A1a）, N-phosphoryl-β-alanine （DIPP-β-A1a） and N-phosphoryl-γ-amino butyric acid （DIPP-γ-Aba）, and four nucleosides, adenosine （A）, guanosine （G）, cytidine （C） and uridine （U）, were studied by electrospray ionization tandem mass spectrometry （ESI-MS/MS） and HPLC/ESI-MS. DIPP-L-α-A1a and DIPP-D-α-A1a produced the same phosphorylated nucleosides, dinucleotides and phosphoroligopeptide. However, DIPP-β-A1a and DIPP-γ-Aba gave no relevant products.